Gintautas Tamulaitis

Type III CRISPR-Cas systems in prokaryotes provide immunity against invading nucleic acids through the coordinated degradation of transcriptionally active DNA and its transcripts by the Csm effector complex. The Cas10 subunit of the complex contains an HD nuclease domain that is responsible for DNA degradation and two Palm domains with elusive functions. In addition, Csm6, a ribonuclease that is not part of the complex, is also required to provide full immunity. We show here that target RNA binding by the Csm effector complex of Streptococcus thermophilus triggers Cas10 to synthesize cyclic oligoadenylates (cA n ; n = 2 to 6) by means of the Palm domains. Acting as signaling molecules, cyclic oligoadenylates bind Csm6 to activate its nonspecific RNA degradation. This cyclic oligoadenylate-based signaling pathway coordinates different components of CRISPR-Cas to prevent phage infection and propagation.

Immunity against viruses and plasmids provided by CRISPR-Cas systems relies on a ribonucleoprotein effector complex that triggers the degradation of invasive nucleic acids (NA). Effector complexes of type I (Cascade) and II (Cas9-dual RNA) target foreign DNA. Intriguingly, the genetic evidence suggests that the type III-A Csm complex targets DNA, whereas biochemical data show that the type III-B Cmr complex cleaves RNA. Here we aimed to investigate NA specificity and mechanism of CRISPR interference for the Streptococcus thermophilus Csm (III-A) complex (StCsm). When expressed in Escherichia coli, two complexes of different stoichiometry copurified with 40 and 72 nt crRNA species, respectively. Both complexes targeted RNA and generated multiple cuts at 6 nt intervals. The Csm3 protein, present in multiple copies in both Csm complexes, acts as endoribonuclease. In the heterologous E. coli host, StCsm restricts MS2 RNA phage in a Csm3 nuclease-dependent manner. Thus, our results demonstrate that the type III-A StCsm complex guided by crRNA targets RNA and not DNA.

Streptococcus thermophilus (St) type III-A CRISPR-Cas system restricts MS2 RNA phage and cuts RNA in vitro. However, the CRISPR array spacers match DNA phages, raising the question: does the St CRISPR-Cas system provide immunity by erasing phage mRNA or/and by eliminating invading DNA? We show that it does both. We find that (1) base-pairing between crRNA and target RNA activates single-stranded DNA (ssDNA) degradation by StCsm; (2) ssDNase activity is confined to the HD-domain of Cas10; (3) target RNA cleavage by the Csm3 RNase suppresses Cas10 DNase activity, ensuring temporal control of DNA degradation; and (4) base-pairing between crRNA 5'-handle and target RNA 3'-flanking sequence inhibits Cas10 ssDNase to prevent self-targeting. We propose that upon phage infection, crRNA-guided StCsm binding to the emerging transcript recruits Cas10 DNase to the actively transcribed phage DNA, resulting in degradation of both the transcript and phage DNA, but not the host DNA.

Based on perspectives of the development of semiconductor materials systems for high-power light-emitting diodes (LEDs), an illumination facility for greenhouse plant cultivation was designed with the dominating 640 nm photosynthetically active component delivered by AlGaInP LEDs and supplementary components from AlGaN (photothropic action, 455 nm) and AlGaAs (photosynthetic 660 nm and photomorphogenetic 735 nm) LEDs. Photosynthesis intensity, photosynthetic productivity and growth morphology as well as chlorophyll and phytohormone concentrations were investigated in radish and lettuce grown in phytotron chambers under the LED-based illuminators and under high-pressure sodium (HPS) lamps with an equivalent photon flux density. Advantages of the high-power LED-based illuminators over conventional HPS lamps, applicability of AlGaInP LEDs for photosynthesis and control of plant growth by circadian manipulation of a relatively weak far-red component were demonstrated.

For a long time the mechanism of immunity provided by the Type III CRISPR-Cas systems appeared to be inconsistent: the Type III-A Csm complex of Staphylococcus epidermidis was first reported to target DNA while Type III-B Cmr complexes were shown to target RNA. This long-standing conundrum has now been resolved by finding that the Type III CRISPR-Cas systems are both RNases and target RNA-activated DNA nucleases. The immunity is achieved by coupling binding and cleavage of RNA transcripts to the degradation of invading DNA. The base-pairing potential between the target RNA and the CRISPR RNA (crRNA) 5'-handle seems to play an important role in discriminating self and non-self nucleic acids; however, the detailed mechanism remains to be uncovered.

We report on structural, optical, and electrical properties of AlxInyGa1−x−yNGaN heterostructures grown on sapphire and 6H–SiC substrates. Our results demonstrate that incorporation of In reduces the lattice mismatch, Δa, between AlInGaN and GaN, and that an In to Al ratio of close to 1:5 results in nearly strain-free heterostructures. The observed reduction in band gap, ΔEg, determined from photoluminescence measurements, is more than 1.5 times higher than estimated from the linear dependencies of Δa and ΔEg on the In molar fraction. The incorporation of In and resulting changes in the built-in strain in AlInGaN/GaN heterostructures strongly affect the transport properties of the two-dimensional electron gas at the heterointerface. The obtained results demonstrate the potential of strain energy band engineering for GaN-based electronic applications.

Abstract Effects of illumination spectrum on the morphogenesis of chrysanthemum plantlets (Chrysanthemum morifolium Ramat. ‘Ellen’) grown in vitro were studied using an illumination system consisting of four groups of light-emitting diodes (LEDs) in the following spectral regions: blue (450nm), red (640nm), red (660nm), and far-red (735nm). Taking into account all differences in shoot height, root length, and fresh and dry weight (FW and DW, respectively), observed while changing the total photon flux density (PFD), the optimal total PFD for growth of chrysanthemum plantlets in vitro was estimated. For 16 h photoperiod and typical fractions of the spectral components (14%, 50%, 28%, and 8%, respectively), the optimal total PFD was found to be 40 µmol m−2 s−1. Our study shows that the blue component in the illumination spectrum inhibits the plantlet extension and formation of roots and simultaneously increases the DW to FW ratio and content of photosynthetic pigments. We demonstrate photomorphogenetic effects in the blue region and its interaction with the fractional PFD of the far-red spectral component. Under constant fractional PFD of the blue component, the root number, length of roots and stems, and fresh weight of the plantlets have a correlated nonmonotonous dependence on the fractional PFD of the far-red component.

A single crystal scintillation material (Gd_0.5–Y_0.5)₃Al₂Ga₃O₁₂ (GYAGG) doped with Ce and codoped with Mg at a small concentration was grown by the Czochralski technique and studied for its scintillation properties for the first time.

Cerium-doped mixed garnet-type single crystals (GdxY1-x)3Al2Ga3O12 with different yttrium content have been fabricated and studied as a prospective scintillating material enabling improvement of scintillation properties by tuning the composition of the matrix-building crystal. The influence of the matrix composition on the emitting Ce ion is studied using linear and time-resolved nonlinear optical absorption and time-resolved photoluminescence spectroscopy. The study of photoluminescence at resonant excitation revealed a composite origin of Ce3+ emission band. This behavior is interpreted by the contribution of Ce3+ ions located in inequivalent positions expected due to the disorder caused in the garnet-type lattice of a mixed crystal by compositional fluctuations. The substitution of gadolinium by yttrium in the lattice results not only in an emission blue shift and in decreased splitting of the lowest doublet 5d state of Ce3+ but also in an increased separation between the lowest doublet level 5d1 and the lowest triplet 5d3 level, as well as in changing the rates of intracenter and extracenter energy relaxation.

The temperature dependences of the peak position and width of the photoluminescence band in Al0.1In0.01Ga0.89N layers were explained by Monte Carlo simulation of exciton localization and hopping. The introduction of a doubled-scaled potential profile due to inhomogeneous distribution of indium allowed obtaining a good quantitative fit of the experimental data. Hopping of excitons was assumed to occur through localized states distributed on a 16 meV energy scale within the In-rich clusters with the average energy in these clusters dispersed on a larger (42 meV) scale.

The dynamics of photoexcited excitons in thin $\mathrm{In}\mathrm{Ga}\mathrm{N}∕\mathrm{Ga}\mathrm{N}$ multiple quantum wells (QW's) with different In contents was studied by comparing the experimental data obtained by photoluminescence (PL), PL excitation, and photoreflectance spectroscopy techniques with the results of Monte Carlo simulations of exciton hopping. The temperature dependence of the PL linewidth was demonstrated to be in a fair agreement with the model of phonon-assisted exciton in-plane hopping within In-rich regions with inhomogeneous broadening taken into account. The band potential fluctuations, which scale the dispersion of localized states the excitons are hopping over, were attributed to compositional disorder inside the In-rich regions. Meanwhile, the inhomogeneous broadening was explained by variation in mean exciton energy among the individual In-rich regions. For typical $2.5\text{\ensuremath{-}}\mathrm{nm}$-thick ${\mathrm{In}}_{x}{\mathrm{Ga}}_{1\ensuremath{-}x}\mathrm{N}$ $(x\ensuremath{\approx}0.22)$ QW's, the simulation revealed fluctuations of the band potential $(31\phantom{\rule{0.3em}{0ex}}\mathrm{meV})$ with additional inhomogeneous broadening $(29\phantom{\rule{0.3em}{0ex}}\mathrm{meV})$ and a crossover from a nonthermalized to thermalized exciton energy distribution at about $150\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. Both the fluctuations and inhomogeneous broadening showed an enhancement with increasing of In content. Simultaneously, a Bose-Einstein-like temperature dependence of the exciton energy in the wells was extracted using data on the PL peak position. The dependence exhibited a fair conformity with the photoreflectance data. Moreover, the density of localized states used in the simulation was found to be consistent with the PL excitation spectrum.

The spectra of luminescence and photoexcitation as well as emission decay kinetics in various parts of spectra are investigated in ZnWO4 and CdWO4 crystals in a wide temperature range (4.2 to 300 K). The bands of red afterglow and of rapidly decaying violet luminescence are observed for the first time. The likeness of the emission properties of ZnWO4 and CdWO4 allows the explanation of the luminescence in these tungstenite type crystals in terms of configurational coordinate diagrams of self-activated radiation centre and of self-trapped exciton. [Russian Text Ignored].

The study of interactions of protein with DNA is important for gaining a fundamental understanding of how numerous biological processes occur, including recombination, transcription, repair, etc. In this study, we use the EcoRII restriction enzyme, which employs a three-site binding mechanism to catalyze cleavage of a single recognition site. Using high-speed atomic force microscopy (HS-AFM) to image single-molecule interactions in real time, we were able to observe binding, translocation, and dissociation mechanisms of the EcoRII protein. The results show that the protein can translocate along DNA to search for the specific binding site. Also, once specifically bound at a single site, the protein is capable of translocating along the DNA to locate the second specific binding site. Furthermore, two alternative modes of dissociation of the EcoRII protein from the loop structure were observed, which result in the protein stably bound as monomers to two sites or bound to a single site as a dimer. From these observations, we propose a model in which this pathway is involved in the formation and dynamics of a catalytically active three-site complex.

High quality multiple quantum well Al0.35Ga0.65N active layers with narrow wells designed for ultraviolet (UV) light-emitting diodes using the phonon engineering approach are characterized using quasi-steady-state and time-resolved photoluminescence spectroscopy. The photoluminescence intensity decrease with temperature increasing from 10to300K was very small, and the upper limit of the internal quantum efficiency (IQE) of up to 70% was estimated based on this temperature dependence. Carrier lifetime measurements yielded the lower bound of the IQE to be ∼35% under optical pumping, whereas IQE of ∼25% was estimated from the measured external quantum efficiency and the light extraction efficiency calculated by ray tracing. The observed photoluminescence features and the high IQE are interpreted as a consequence of strong carrier (exciton) localization.

Y3−xMg2AlSi2O12:Cex3+ (YMASG:Ce) phosphors were synthesized by sol–gel combustion technique at different temperatures from 1400 to 1550 °C. Samples with x = 0.015, 0.03, 0.045, and 0.06 were fabricated and characterized using powder X-ray diffraction (XRD), photoluminescence spectroscopy, and fluorescence lifetime measurements in frequency domain. XRD patterns confirmed single-phase garnet crystal structure for all the samples independently of their substitutional level and annealing temperature. In respect to Y3Al5O12:Ce3+ (YAG:Ce) phosphor, which was synthesized for comparison by a different sol–gel procedure, the photoluminescence band of these garnets is red shifted, indicating a prospective for application of this novel phosphor in warm-white light emitting diodes (LEDs). The luminescence decays bi-exponentially. The main component has a characteristic decay time decreasing from 72 to of 50 ns with increasing sintering temperature and cerium content, while ∼2% of the excitation decays with a characteristic decay time of ∼8 ns.

DNA cytosine methylation is a widespread epigenetic mark. Biological effects of DNA methylation are mediated by the proteins that preferentially bind to 5-methylcytosine (5mC) in different sequence contexts. Until now two different structural mechanisms have been established for 5mC recognition in eukaryotes; however, it is still unknown how discrimination of the 5mC modification is achieved in prokaryotes. Here we report the crystal structure of the N-terminal DNA-binding domain (McrB-N) of the methyl-specific endonuclease McrBC from Escherichia coli. The McrB-N protein shows a novel DNA-binding fold adapted for 5mC-recognition. In the McrB-N structure in complex with methylated DNA, the 5mC base is flipped out from the DNA duplex and positioned within a binding pocket. Base flipping elegantly explains why McrBC system restricts only T4-even phages impaired in glycosylation [Luria, S.E. and Human, M.L. (1952) A nonhereditary, host-induced variation of bacterial viruses. J. Bacteriol., 64, 557–569]: flipped out 5-hydroxymethylcytosine is accommodated in the binding pocket but there is no room for the glycosylated base. The mechanism for 5mC recognition employed by McrB-N is highly reminiscent of that for eukaryotic SRA domains, despite the differences in their protein folds.

The emission efficiency droop and internal quantum efficiency (IQE) in AlGaN epilayers and heterostructures were investigated by studying photoluminescence intensity dependence on excitation power density at different temperatures in the range from 8 to 300 K in three AlGaN samples with similar Al content (33%-35%) and different strength of carrier localization: an epilayer and multiple quantum wells with well widths of 5.0 and 2.5 nm. It is shown that the phenomena leading to the efficiency droop strongly influence the photoluminescence intensity dependence on temperature and, therefore, affect the estimation of IQE based on this dependence. A procedure to optimize the determination of IQE is proposed.

Time‐resolved spectroscopic study of the photoluminescence response to femtosecond pulse excitation and free carrier absorption at different wavelengths, thermally stimulated luminescence measurements and investigation of differential absorption are applied to amend the available data on excitation transfer in GAGG:Ce scintillators, and an electronic energy‐level diagram in this single crystal is suggested to explain the influence of codoping with divalent Mg on luminescence kinetics and light yield. The conclusions are generalized by comparison of the influence of aliovalent doping in garnets (GAGG:Ce) and oxyorthosilicates (LSO:Ce and YSO:Ce). In both cases, the codoping facilitates the energy transfer to radiative Ce 3+ centers, while the light yield is increased in the LYSO:Ce system but reduced in GAGG:Ce.

Coincidence time resolution (CTR) of scintillation detectors based on Ce- and Mg-codoped Gd <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sub> (GAGG) scintillation crystals and high-density silicon photomultipliers (SiPMs) is shown to be 165 ps (full width at half maximum) for 511-keV <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\gamma $ </tex-math></inline-formula> -quanta, approaching that achieved by using LSO scintillators. To study the prospective for further improvement of the time resolution, the population of the emitting Ce centers was investigated by optical pump and probe technique using selective photoexcitation and probing by a white light continuum with subpicosecond time resolution. The importance of free electron trapping for excitation transfer to emitting Ce ions was revealed. The influence of transfer delay on the scintillation response time is described, and the dynamics of electron relaxation to the lowest excited level of Ce ion is studied experimentally and analyzed by taking into account intracenter relaxation and relaxation via conduction band. The influence of electron diffusivity on the rise time of the population of the emitting level is described. It is shown that codoping of GAGG:Ce by magnesium even at the level as low as 10 ppm efficiently decreases the scintillator response time by enhancing the electron diffusivity.

This book gives a good review of the state of art of the modern spectroscopy of scintillators and provides timing properties of the scintillation materials under wide debates. Study of the transient phenomena is a powerful tool which is applied in chemistry, biology and semiconductor physics.

Abstract The type III CRISPR–Cas systems provide immunity against invading nucleic acids through the coordinated transcription-dependent DNA targeting and cyclic adenylate (cAn)-activated RNA degradation. Here, we show that both these pathways contribute to the Streptococcus thermophilus (St) type III-A CRISPR–Cas immunity. HPLC-MS analysis revealed that in the heterologous Escherichia coli host the StCsm effector complex predominantly produces cA5 and cA6. cA6 acts as a signaling molecule that binds to the CARF domain of StCsm6 to activate non-specific RNA degradation by the HEPN domain. By dissecting StCsm6 domains we demonstrate that both CARF and HEPN domains act as ring nucleases that degrade cAns to switch signaling off. CARF ring nuclease converts cA6 to linear A6&amp;gt;p and to the final A3&amp;gt;p product. HEPN domain, which typically degrades RNA, also shows ring nuclease activity and indiscriminately degrades cA6 or other cAns down to A&amp;gt;p. We propose that concerted action of both ring nucleases enables self-regulation of the RNase activity in the HEPN domain and eliminates all cAn secondary messengers in the cell when viral infection is combated by a coordinated action of Csm effector and the cA6-activated Csm6 ribonuclease.

We report on an indium–silicon co-doping approach for high-Al-content AlGaN layers. Using this approach, very smooth crack-free n-type AlGaN films as thick as 0.5 μm with Al mole fraction up to 40% were grown over sapphire substrates. The maximum electron concentration in the layers, as determined by Hall measurements, was as high as 8×1017 cm−3 and the Hall mobility was up to 40 cm2/Vs. We used this doping technique to demonstrate solar-blind transparent Schottky barrier photodetectors with the cut-off wavelength of 278 nm.

An approach for growing high-quality AlGaN/AlN multiple quantum wells (MQW) emitting in deep UV region is proposed. The structures are deposited on bulk AlN substrates. Structural analysis by using x-ray diffraction confirms high crystalline quality of these structures. Photoluminescence dependences on excitation intensity and temperature under band-to-band excitation of AlN barrier layers and under selective excitation of the quantum wells are presented. Al0.5Ga0.5N/AlN MQW grown on bulk AlN demonstrate emission at 260 nm with high emission intensity. Stimulated emission of these structures at 258 nm was observed. The results prove great potential of growing structures with high-aluminum-content layers on bulk AlN substrates.

We report on AlGaN single-quantum-well light-emitting diodes (LEDs) on sapphire with peak emission at 285 nm. A study is presented to identify the key material parameters controlling the device quantum efficiency. At room temperature, for a 200 μm×200 μm square geometry mesa type device, we obtain a power as high as 0.25 mW for 650 mA pulsed pumping. The LEDs show significantly higher output powers at temperatures below 100 K.

Cerium-doped yttrium aluminium garnet (Y3Al5O12, YAG) microcrystals were grown using sol–gel technique. The samples were characterized by application of X-ray diffraction (XRD), photoluminescence (PL) spectroscopy and frequency-domain fluorescence lifetime measurements. The PL output, which is important for wavelength conversion in white light emitting diodes (LEDs), was studied as a function of Ce content and annealing temperature. XRD analysis evidenced that sintering of polycrystalline Y3Al5O12:Ce powders at 1000 °C results in the formation of monophasic garnet materials up to 10 mol% of Ce doping; however, concentration quenching is observed in samples with the Ce content exceeding ∼4% probably due to optical losses in the tail states of the imperfect lattice. PL output increased and the concentration quenching disappeared when a higher sintering temperature of 1300 °C was used. However, in high Ce content (>4%) samples, the increase in sintering temperature was found to result in the formation of CeO2 phase accompanied by an uncontrolled bouncing of PL intensity in powders with similar Ce content.

Photoluminescence studies of carrier dynamics in AlGaN epilayers with different degrees of carrier localization and densities of nonradiative recombination centers show that the prevailing droop mechanism in AlGaN epilayers with strong carrier localization and comparatively high density of nonradiative recombination centers is enhanced nonradiative recombination due to the carrier delocalization at elevated carrier density. The photoluminescence was investigated under quasi-steady-state excitation in the temperature range from 8 to 300 K. The results proved that the onset of this droop effect is below the threshold for the droop due to high-density effects in the epilayers, such as carrier heating, phase space filling, nonradiative Auger recombination, and stimulated emission.

The time resolution of scintillation detectors of ionizing radiation is one of the key parameters sought for in the current and future high-energy physics experiments. This study is encouraged by the necessity to find novel detection methods enabling a sub-10-ps time resolution in scintillation detectors and is focused on the exploitation of fast luminescence rise front. Time-resolved photoluminescence (PL) spectroscopy and thermally stimulated luminescence techniques have been used to study two promising scintillators: self-activated lead tungstate (PWO, PbWO4) and Ce-doped gadolinium aluminum gallium garnet (GAGG, Gd3Al2Ga3O12). A sub-picosecond PL rise time is observed in PWO, while longer processes in the PL response in GAGG:Ce are detected and studied. The mechanisms responsible for the PL rise time in self-activated and doped scintillators are under discussion.

The influence of co-doping of Gd3Al2GA3O12:Ce (GAGG:Ce) scintillator with magnesium on the rise time of luminescence response was studied in two GAGG:Ce crystals grown in nominally identical conditions except of Mg co-doping in one of them. Time-resolved photoluminescence spectroscopy and free carrier absorption techniques were exploited. It is evidenced that the Mg co-doping decreases the rise time down to sub-picosecond domain. Meanwhile, the light yield decreases by ∼20%. Thus, the feasibility of exploitation of the fast rise edge in luminescence response for ultrafast timing in scintillation detectors is demonstrated. The role of Mg impurities in facilitating the excitation transfer to radiative recombination centers is discussed.

The type III-A Csm complex of Streptococcus thermophilus (StCsm) provides immunity against invading nucleic acids through the coordinated action of three catalytic domains: RNase (Csm3), ssDNase (Cas10-HD), and cyclic oligoadenylates synthase (Cas10-Palm). The matured StCsm complex is composed of Cas10:Csm2:Csm3:Csm4:Csm5 subunits and 40-nt CRISPR RNA (crRNA). We have carried out gene disruptions for each subunit and isolated deletion complexes to reveal the role of individual subunits in complex assembly and function. We show that the Cas10-Csm4 subcomplex binds the 5'-handle of crRNA and triggers Csm3 oligomerization to form a padlock for crRNA binding. We demonstrate that Csm5 plays a key role in target RNA binding while Csm2 ensures RNA cleavage at multiple sites by Csm3. Finally, guided by deletion analysis, we engineered a minimal Csm complex containing only the Csm3, Csm4, and Cas10 subunits and crRNA and demonstrated that it retains all three catalytic activities, thus paving the way for practical applications.

A Czochralski-grown single crystal of GAGG:Ce,Mg allows for a high Ce dopant and Mg codopant concentration in the crystal, resulting in acceleration of scintillation decay down to several nanoseconds at the expense of light yield.

Heavy Mg-codoping substantially increases the emission decay rate of Ce-doped garnet-type scintillators by introducing Mg–Ce centers with a lower barrier for thermal quenching and a channel for temperature-independent nonradiative recombination.

Article20 April 2006free access Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease Matthias Bochtler Corresponding Author Matthias Bochtler International Institute of Molecular and Cell Biology, Warsaw, Poland Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany Search for more papers by this author Roman H Szczepanowski Roman H Szczepanowski International Institute of Molecular and Cell Biology, Warsaw, Poland Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany Search for more papers by this author Gintautas Tamulaitis Gintautas Tamulaitis Institute of Biotechnology, Vilnius, Lithuania Search for more papers by this author Saulius Grazulis Saulius Grazulis Institute of Biotechnology, Vilnius, Lithuania Search for more papers by this author Honorata Czapinska Honorata Czapinska International Institute of Molecular and Cell Biology, Warsaw, Poland Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany Search for more papers by this author Elena Manakova Elena Manakova Institute of Biotechnology, Vilnius, Lithuania Search for more papers by this author Virginijus Siksnys Corresponding Author Virginijus Siksnys Institute of Biotechnology, Vilnius, Lithuania Search for more papers by this author Matthias Bochtler Corresponding Author Matthias Bochtler International Institute of Molecular and Cell Biology, Warsaw, Poland Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany Search for more papers by this author Roman H Szczepanowski Roman H Szczepanowski International Institute of Molecular and Cell Biology, Warsaw, Poland Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany Search for more papers by this author Gintautas Tamulaitis Gintautas Tamulaitis Institute of Biotechnology, Vilnius, Lithuania Search for more papers by this author Saulius Grazulis Saulius Grazulis Institute of Biotechnology, Vilnius, Lithuania Search for more papers by this author Honorata Czapinska Honorata Czapinska International Institute of Molecular and Cell Biology, Warsaw, Poland Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany Search for more papers by this author Elena Manakova Elena Manakova Institute of Biotechnology, Vilnius, Lithuania Search for more papers by this author Virginijus Siksnys Corresponding Author Virginijus Siksnys Institute of Biotechnology, Vilnius, Lithuania Search for more papers by this author Author Information Matthias Bochtler 1,2, Roman H Szczepanowski1,2, Gintautas Tamulaitis3, Saulius Grazulis3, Honorata Czapinska1,2, Elena Manakova3 and Virginijus Siksnys 3 1International Institute of Molecular and Cell Biology, Warsaw, Poland 2Max-Planck-Institute for Molecular Cell Biology and Genetics, Dresden, Germany 3Institute of Biotechnology, Vilnius, Lithuania *Corresponding authors: International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland. Tel.: +48 22 5970732; Fax: +48 22 5970715; E-mail: [email protected] of Biotechnology, Graiciuno 8, Vilnius LT-02241, Lithuania. Tel.: +370 5 2602108; Fax: +370 5 2602116; E-mail: [email protected] The EMBO Journal (2006)25:2219-2229https://doi.org/10.1038/sj.emboj.7601096 PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Restricion endonuclease Ecl18kI is specific for the sequence /CCNGG and cleaves it before the outer C to generate 5 nt 5′-overhangs. It has been suggested that Ecl18kI is evolutionarily related to NgoMIV, a 6-bp cutter that cleaves the sequence G/CCGGC and leaves 4 nt 5′-overhangs. Here, we report the crystal structure of the Ecl18kI–DNA complex at 1.7 Å resolution and compare it with the known structure of the NgoMIV–DNA complex. We find that Ecl18kI flips both central nucleotides within the CCNGG sequence and buries the extruded bases in pockets within the protein. Nucleotide flipping disrupts Watson–Crick base pairing, induces a kink in the DNA and shifts the DNA register by 1 bp, making the distances between scissile phosphates in the Ecl18kI and NgoMIV cocrystal structures nearly identical. Therefore, the two enzymes can use a conserved DNA recognition module, yet recognize different sequences, and form superimposable dimers, yet generate different cleavage patterns. Hence, Ecl18kI is the first example of a restriction endonuclease that flips nucleotides to achieve specificity for its recognition site. Introduction Type II restriction endonucleases recognize short nucleotide sequences usually 4–8 bp in length and cleave DNA leaving blunt ends or 5′- or 3′-overhangs. Most Type IIP enzymes are active as dimers and many recognize target sequences in DNA that match the two-fold symmetry of the enzymes (Pingoud et al, 2005a). Strict matches require palindromic DNA sequences with an even number of base pairs, which are cleaved to generate either blunt ends or overhangs with an even number of nucleotides. Target sequences with an odd number of base pairs in the recognition sequence are necessarily pseudopalindromic, break the two-fold symmetry at the central base pair, and yield overhangs with an odd number of nucleotides upon cleavage (Figure 1). Figure 1.Oligonucleotides used for cocrystallization of Ecl18kI (this work) and NgoMIV (Deibert et al, 2000). The recognition sequence is shown in bold letters, boxes indicate the cleavage patterns with 5 nt and 4 nt 5′ overhangs, respectively. Download figure Download PowerPoint Most Type IIP enzymes cut within the boundaries of the recognition sequence. Among those, palindrome cutters predominate over pseudopalindrome cutters, and 4 nt 5′-overhangs or blunt ends are the most common cleavage products (Roberts et al, 2005). Not surprisingly, a vast majority of mechanistic and structural studies of restriction endonucleases have focused on such enzymes (Pingoud et al, 2005a). Comparative structural analysis reveals that Type IIP restriction enzymes share a conserved core that harbors active site residues (Venclovas et al, 1994; Aggarwal, 1995; Kovall and Matthews, 1998). Different DNA cleavage patterns result from changes in the dimerization mode that alter the distance between active sites and hence the number of base pairs interspaced between scissile phosphates, as shown by a comparison of the EcoRI (G/AATTC) and EcoRV (GAT/ATC) crystal structures (Venclovas et al, 1994). Much less is known about pseudopalindrome sequence cutters, in part because very few enzymes in this group have been structurally characterized. Structures are available for apo-EcoRII(/CCWGG, W=A or T) (Zhou et al, 2004) and for EcoO109I (RG/GNCCY, R=A or G; Y=T or C) (Hashimoto et al, 2005), BglI (GCCNNNN/NGGC) and SfiI (GGCCNNNN/NGGCC) complexes with DNA (Newman et al, 1998; Vanamee et al, 2005). BglI and SfiI are very similar to the blunt end-cutter EcoRV in terms of monomer structure, but generate 3 nt 3′-overhangs rather than blunt ends, because the enzymes dimerize in very different ways (Newman et al, 1998; Vanamee et al, 2005). In contrast, EcoO109I (RG/GNCCY) and BsoBI (C/YCGRG) (van der Woerd et al, 2001) generate different cleavage patterns despite strikingly similar dimerization modes. In fact, EcoO109I partially unstacks the DNA within its recognition sequence due to the interaction between an indole ring of a tryptophan residue and cytosine, resulting in DNA stretching and a register shift in the cleavage pattern with respect to BsoBI (Hashimoto et al, 2005). Thus, local changes of DNA structure and not alterations of the dimerization mode explain the different cleavage patterns of EcoO109I and BsoBI. It is unlikely that the DNA ‘stretching mechanism’ employed by EcoO109I can account for the cleavage patterns of Ecl18kI (/CCNGG) (Den'mukhametov et al, 1997), EcoRII(/CCWGG) (Bigger et al, 1973; Boyer et al, 1973) and PspGI (/CCWGG) (Morgan et al, 1998), because it would require 6 nt 5′-overhang cutters as ‘precursors’, which are currently unknown. Instead, amino-acid sequence similarities and extensive mutagenesis data (Pingoud et al, 2002, 2005b; Tamulaitis et al, 2002) argue for a close evolutionary link between Ecl18kI (/CCNGG) and the crystallographically characterized palindrome cutters NgoMIV (G/CCGGC) (Deibert et al, 2000), Cfr10I (R/CCGGY) (Bozic et al, 1996) and Bse634I (R/CCGGY) (Grazulis et al, 2002), which all generate 4 nt 5′-overhangs. How Ecl18kI, EcoRII and PspGI accommodate the extra base pair within their recognition sites and generate 5 nt overhangs is unclear. To address these questions, we have determined the crystal structure of Ecl18kI restriction endonuclease from Enterobacter cloaceae in complex with a 9 bp oligonucleotide duplex containing the recognition site. The amino-acid sequence of Ecl18kI is over 99% identical to the isoschizomeric restriction endonucleases SsoII (Karyagina et al, 1993), SenPI (Ibanez et al, 1997) and StyD4I (Miyahara et al, 1997). Results Ecl18kI crystals Ecl18kI was crystallized in complex with two different 9-mer oligodeoxynucleotide duplexes (Figure 1, oligos 1/2a and oligos 1/2b, respectively) in space group P212121. The best crystal was grown in a drop with Ecl18kI and the 5-iodo-deoxyuridine containing oligonucleotide duplex 1/2b more than a year prior to data collection and diffracted to 1.7 Å resolution. Surprisingly, we did not find a strong electron density peak for the iodine atom, and also no significant anomalous peak for iodine, although anomalous signal equivalent to about three electrons should have been present at the data collection wavelength 1.05 Å (see Materials and methods). Owing to this uncertainty, we crystallized Ecl18kI with the unmodified oligonucleotide duplex 1/2a, but the best diffraction data extended only to 2.0 Å resolution and suffered from high mosaicity and weak ice rings. The structure was solved by the multiple anomalous diffraction (MAD) technique using the selenomethionine variant of the protein and a potassium bromide soak (Supplementary Table SI). The refined structures of the Ecl18kI–DNA complexes with modified and unmodified DNA duplexes were almost identical. Protomer structure The Ecl18kI protomer is built around the typical folding motif of Type II restriction endonucleases, which consists of a mixed β-sheet and connecting helices (Venclovas et al, 1994; Aggarwal, 1995; Kovall and Matthews, 1998). In Ecl18kI, the core motif comprises residues 140–247, if region boundaries are chosen to coincide with the ends of secondary structure elements, and includes strands β1–β6, and the connecting helices (Figure 2A and B; Supplementary Figure S1). As expected, the core motif anchors almost all residues that were previously implicated either in catalysis or in sequence recognition (Tamulaitis et al, 2002) (Figure 2B and Supplementary Figure S2). On the N-terminal side, the core region is flanked by an almost entirely helical region (residues 1–139). On the C-terminal side, the nuclease core is followed by three extra helices. Figure 2.Ecl18kI protomer structure. (A) Stereoview of a Cα-trace of an Ecl18kI protomer. Every 10th residue is marked with a closed circle and labeled where possible to avoid undue crowding. β-Strands are shown as black thick lines, α-helices as gray lines. The dashed line represents the regions (residues 145–155) in the crystal structure that are poorly ordered in all four protomers in the asymmetric unit. (B) Schematic diagram of the protomer fold, shown in the same orientation as in (A). Secondary structure elements are numbered. Residues that are involved in DNA-backbone contacts are shown in white boxes, residues that form hydrogen bonds with the bases of the recognition sequence are shown in light gray boxes, residues that are involved in catalysis are in dark gray boxes, and residues that sandwich the flipped bases are shown on black background. Download figure Download PowerPoint The core region of Ecl18kI (Figure 3A) is structurally similar to the equivalent regions of EcoRII (Figure 3B) and NgoMIV (Figure 3C); however, the so-called dimerization and tetramerization loops of NgoMIV have no equivalents in Ecl18kI. On the other hand, NgoMIV lacks most of the N-terminal α-helical region of Ecl18kI (Figure 3A and C). Interestingly, a structurally similar region is present in the EcoRII restriction endonuclease between the effector and core domains (Figure 3A and B). Figure 3.Structural comparisons of Ecl18kI. (A–C) Comparison of the protomer folds of Ecl18kI (A), EcoRII (B) and NgoMIV (C). The polypeptide chains have been colour-ramped from dark to light green from the N- to the C-terminus, except for the catalytic cores in red and the effector domain of EcoRII in grey (A). The equivalent regions in EcoRII and NgoMIV are colored analogously. In (B), the effector domain, which is unique to EcoRII (Zhou et al, 2004), is shown in gray. (D, E) Overall view of the Ecl18kI–DNA and NgoMIV–DNA (Deibert et al, 2000) complexes in the asymmetric units of the crystals. The protein is shown in ribbon- and DNA in wireframe-representation. Protein chains A, B, C, D of Ecl18kI are shown in red, magenta, blue and cyan, respectively. In the structure shown in (D), the DNA chains E and F are at the top and chains G and H are at the bottom. In NgoMIV (E), the so-called tetramerization loops are shown by bold lines and are labeled by the letter ‘T’. Download figure Download PowerPoint Oligomer structure The asymmetric unit of the Ecl18kI crystals contains four protein monomers and two DNA duplexes. Protein subunits AB and CD (Figure 3D) form primary dimers, which completely encircle double-stranded DNA molecules. Using the program SURFACE (Collaborative Computational Project Number 4 (CCP4), 1994), we calculated that the formation of the dimer buries ∼3400 Å2 of solvent accessible surface. The interface is bipartite with contributions from the N-terminal region and from the nuclease core. The latter contacts are mediated by helices and are similar to the contacts in NgoMIV and in many EcoRI-like orthodox restriction enzymes (Pingoud and Jeltsch, 2001). Therefore, the primary dimers AB and CD are likely to represent the minimal functional units of Ecl18kI. In the asymmetric unit of the Ecl18kI crystals, two Ecl18kI dimers (subunits AB and CD) associate to form tetramers of 222 point symmetry, which differ significantly from the tetramers of the NgoMIV restriction enzyme (Figure 3E). First, the angle between the long axes of two bound DNA molecules is only ∼30° in the Ecl18kI–DNA complex, but ∼60° in the NgoMIV–DNA complex. Second, the dimer–dimer interface of Ecl18kI in the crystals is far less extensive than the equivalent dimer–dimer interface of NgoMIV (buried surface area 3400 Å2 in Ecl18kI versus 12 800 Å2 in NgoMIV). Moreover, the tetramerization loops of NgoMIV (Figure 3E) are missing in Ecl18kI. It remains to be determined if Ecl18kI tetramers are functionally relevant or a crystal packing artifact. DNA binding and sequence recognition As anticipated, the pseudo-two-fold axis of the DNA coincides with the two-fold axis of Ecl18kI. Therefore, there are two ways for the DNA duplex to bind to the enzyme, which are equivalent in solution, but not in the crystal. Crystallographic quality parameters indicate that both binding modes are possible, and therefore both DNA duplexes were modeled in two conformations. The electron density for the sugar-phosphate backbone and for the specifically recognized G:C bases, which obey the two-fold symmetry, is unaffected by this ambiguity, but the electron density for the bases of the central nucleotides and the flanking sequences is an average and therefore more difficult to interpret. The specifically bound DNA is almost entirely wrapped by Ecl18kI. Positively charged residues cluster around the DNA backbone (Supplementary Figure S2). The crystallographic results are in excellent agreement with prior biochemical data, which have implicated R-box arginines Arg116, Arg117 and Arg119 in DNA backbone contacts (Pingoud et al, 2002). Due to the symmetry of the Ecl18kI dimer, all specific protein–DNA contacts occur in duplicate, and therefore only one half-site of Ecl18kI needs to be described. Ecl18kI contacts the bases of the recognition sequence primarily from the major groove side (Figure 4A). Major groove contacts are exclusively mediated by Arg186, Glu187 and Arg188. The three consecutive residues are localized at the N-terminal end of the 3/10 helix-3, which is known as the ‘recognition helix’ in related Type II enzymes (Figure 2B). Arginines 186 and 188 donate bidentate hydrogen bonds to the outer (±2 according to Figure 1) and inner (±1 according to Figure 1) guanines, respectively. The side chain oxygen atoms of Glu187 accept one hydrogen bond each from the two neighboring cytosines of the recognition sequence. Sequence-specific minor groove contacts are mediated exclusively by glutamine 114. The main chain oxygen atom of this residue accepts a hydrogen bond from the outer guanine (±2), and the side chain forms two hydrogen bonds with the inner guanine (±1). There are no direct specific contacts between the protein and the cytosines in the minor groove, but the guanidino groups of Arg117 form water-mediated hydrogen bonds with the O2 atoms of the inner cytosines. The recognition pattern of the CC:GG nucleotides in Ecl18kI is strikingly similar to that of NgoMIV (Figure 4B), confirming an earlier prediction that was based on a mutational and biochemical analysis (Tamulaitis et al, 2002). Figure 4.Sequence recognition by Ecl18kI and NgoMIV (Deibert et al, 2000). (A) Stereoview of Ecl18kI interactions with one half-site of the CCNGG sequence. Only direct interactions with base pairs +1 and +2 according to Figure 1 are shown. The electron density in (A) was calculated from the MAD phases after solvent-flattening and four-fold averaging and contoured at 1.3σ. Except for the model-dependent averaging masks, no information from the final model was used. (B) Stereoview of NgoMIV interactions with one half-site of GCCGGC sequence. Only interactions with the central base pairs (+1, +2 according to Figure 1) are shown. Download figure Download PowerPoint Active site Based on very weak sequence similarity between Ecl18kI and NgoMIV and mutational studies, Tamulaitis et al (2002) suggested that the sequence motif 159-VDX21KX12E represents an active site of Ecl18kI. Structural comparison between Ecl18kI and NgoMIV reveals that the predicted residues indeed correspond to the active site residues of NgoMIV (Figure 5A). In NgoMIV, Asp140 bridges two Mg2+ ions in the active site, and we presume that Asp160 in the Ecl18kI has the same role. However, Mg2+ ions are absent from the Ecl18kI crystals, which could only be grown in the presence of the metal-chelator ethylenediaminetetraacetic acid (EDTA). Attempts to diffuse divalent metal ions into the crystals resulted in a loss of crystal diffraction. Other catalytic/metal chelating residues of NgoMIV are also conserved in Ecl18kI (Figure 5A). The Cα atom of Glu201 in NgoMIV coincides with the Cα atom of Glu195 in Ecl18kI, but the side chain is in a different rotamer conformation. It is possible that the conformation of Glu195 may change in the presence of metal ions. Mutational data of Ecl18kI residues Glu125, Asp160, Lys182 and Glu195 are consistent with their active site function (Tamulaitis et al, 2002). Hence, Ecl18kI possesses an NgoMIV-like active site as predicted. Figure 5.Comparison between Ecl18kI and NgoMIV. (A) Stereoview of the superimposed active sites of Ecl18kI and NgoMIV (shown in orange and green colors, respectively). Active site residues of NgoMIV Glu70, Asp140, Lys187 and Glu201 superimpose with Ecl18kI residues Glu125, Asp160, Lys182 and Glu195 demonstrated to be important in catalysis (Tamulaitis et al, 2002). Two Mg2+-ions present in NgoMIV–DNA complex are shown as gray spheres, water molecules are not shown. (B) Stereoview of the conserved dimer interface between Ecl18kI and NgoMIV. The Ecl18kI dimer (orange) was superimposed with an equivalent pair of NgoMIV protomers (green). Large spheres indicate Cα-atoms of residues implicated in catalysis. Small spheres indicate Cα-atoms of residues that form hydrogen bonds with bases of the target sequence. The yellow labels on the left side indicate residues in Ecl18kI, the green labels on the right side mark the corresponding residues in NgoMIV. Download figure Download PowerPoint Conserved Ecl18kI dimer arrangement Ecl18kI and NgoMIV (Tamulaitis et al, 2002) share the fold, catalytic mechanism and recognize common bases in their target sequences similarly, yet have different specificities and generate overhangs of different length, prompting the question how the different cleavage patterns are generated. An obvious possibility could be that protomers in Ecl18kI dimerize in a different way, matching the distance between catalytic sites to the distance between the scissile phosphates. To check this possibility, we superimposed the Ecl18kI dimer with an equivalent pair of NgoMIV protomers. The superposition was based on an identification of structurally equivalent regions with STRUPRO (Kleywegt and Jones, 1998), and a subsequent optimal alignment of these regions with LSQKAB (CCP4, 1994). No special weight was attached to residues that are involved in catalysis or sequence recognition, but after the superposition was calculated, the Cα-atoms of these residues were found to almost coincide (Figure 5B). Therefore, the different cleavage patterns generated by Ecl18kI and NgoMIV are not due to differences of the dimerization modes. Instead, the Ecl18kI structure reveals a novel mechanism that provides an elegant explanation of the different specificities and cleavage patterns of Ecl18kI and NgoMIV. DNA conformation: the central nucleotides of the CCNGG recognition sequence are flipped out The DNA-duplex in complex with Ecl18kI is dramatically deformed. The hydrogen bonds of the central base pair are broken, and the nucleotides are flipped out, which places their bases outside the sugar-phosphate backbone (Figure 6A and C). Each extruded base is accommodated into a ‘pocket’ of Ecl18kI made by the side chain atoms of Arg57 on one face and the indole ring of Trp61 on the other face (Figure 7A, B and E). Nucleotide flips seen in the crystal structure are in excellent agreement with the photocrosslinking results for SsoII in solution, which indicated that 5-iodo-deoxyuridine in the central position of the recognition sequence forms a covalent bond with Trp61 of the enzyme upon irradiation (Kubareva et al, 2000). Figure 6.DNA conformation. DNA in complexes with Ecl18kI (A, C) and NgoMIV (B, D) is shown in stick representation. Views in (C) and (D) differ from (A) and (B) by a 90° rotation around the vertical axis. The central nucleotide pair is flipped out of the DNA helix in Ecl18kI–DNA complex (A, C). The electron density for the central bases is averaged due to the two possible binding modes. The flipped out nucleotide is shown in one of the possible conformations, since there is still an uncertainty whether the flipped nucleotides have syn- or anti-conformation. Phosphorous atoms at scissile phosphates are shown as green spheres. The distance between these phosphorous atoms is 17.2 Å in both Ecl18kI–DNA and NgoMIV–DNA complexes. Download figure Download PowerPoint Figure 7.Close-up view of the central nucleotides in the Ecl18kI–DNA and NgoMIV–DNA complexes. (A, B) Three central nucleotides (−1, 0, +1 according to Figure 1) of one strand in the recognition sequence of Ecl18kI are shown in stick representation and CPK colors. Note that there is still uncertainty whether the extruded bases have syn- or anti-conformation. Arg57 and Trp61 residues of Ecl18kI that sandwich the extruded base are shown in stick representation. (C, D) Two central nucleotides (−1, +1 according to Figure 1) in one strand of the NgoMIV recognition sequence are shown in stick representation and CPK colors. (B) and (D) differ from (A) and (C) by 90°-rotations about the horizontal axis. (E) Structural conservation of the binding pocket for the flipped nucleotide in Ecl18kI and EcoRII (shown in red and green colors, respectively). Superposition between the Ecl18kI and EcoRII protomers reveals that Arg57 and Trp61 residues sandwiching the extruded base spatially coincide with Arg222 and Tyr226 of EcoRII. A flipped out base in the Ecl18kI–DNA complex is shown in gray, for one of the two possible binding modes of the DNA. Download figure Download PowerPoint The nucleotide flips shift the DNA register Due to the backbone rearrangements that accompany the base extrusions, the values for the rise between the inner G:C base pairs within the recognition site are intermediate between the values characteristic for canonical single and two base pair steps (compare Figure 7B and D). The DNA is strongly kinked at the side of the nucleotide flips (Figure 6C). This deformation opens the minor groove and bends the DNA towards the major groove. Together, the register shift and the kink reduce the distance between scissile DNA phosphates to 17.2 Å, which is within 0.1 Å identical to the distance between scissile phosphates in the complex of NgoMIV with cleaved DNA. Thus, Ecl18kI generates longer overhangs than NgoMIV simply because the enzyme makes the central 5 bp duplex in its recognition sequence mimic a 4 bp duplex (Figure 6). Discussion In the crystal structure, there are four Ecl18kI protomers in the asymmetric unit, which form primary dimers AB and CD, respectively, which in turn interact to assemble tetramers (Figure 3D). Analytical ultracentrifugation indicates that Ecl18kI is a dimer in solution in the absence of DNA (Tamulaitis et al, 2002), but Denjmukhametov et al (1998) reported that Ecl18kI migrates as a tetramer in sizing chromatography experiments. The isoschizomeric SsoII enzyme (sharing >99% of identical amino acids with Ecl18kI) is a homodimer in solution both in the absence and presence of DNA, according to the analytical ultracentrifugation and gel filtration experiments (Pingoud et al, 2002), but may bind two copies of its recognition sequence according to electron microscopy, which again suggests the possibility of tetramer formation (Pingoud et al, 2003). At present, one cannot exclude that Ecl18kI exists in solution in the apo-form as a dimer and tetramerizes in the presence of DNA similarly to the restriction enzyme SgrAI (Wood et al, 2005). Is nucleotide flipping relevant in solution? The flipped nucleotides are a hallmark of the Ecl18kI–DNA structure. In the case of the Ecl18kI crystals with the modified oligonucleotide duplex (oligo 1/2b), we cannot exclude that the flips could be due to the chemical reactivity of the iodine atom or the minor base-pair mismatch. These explanations for base-flipping, however, can be ruled out, because the crystal structure of Ecl18kI in complex with unmodified DNA shows essentially identical nucleotide flips, albeit at somewhat lower resolution. The strongest argument for the relevance of the nucleotide flips comes from photocrosslinking studies in solution. Kubareva et al (2000) used a modified oligodeoxynucleotide duplex with 5-iodo-uracil in the central position of the SsoII recognition sequence and identified a specific crosslink between Trp61 and the central modified base, suggesting close proximity between the indole ring of Trp61 and the base. The formation of such a zero-length crosslink product is difficult to explain in the case of regular B-DNA, but it makes perfect sense if nucleotide flipping is occurring in solution because the central bases become extruded and buried in the pockets made by the Trp61 and Arg57 residues (Figure 7A, B and E). The promiscuity of SsoII with respect to the nucleotide or its analogues in the central position of the target sequence is also consistent with the crystallographic data for Ecl18kI. Experimentally, SsoII was found to accept all four naturally occurring nucleotides and various analogues, including 1,2-dideoxy-D-ribofuranose (an analogue without base), 9-[1′-hydroxy-2′-(hydroxymethyl)ethoxy]methylguanine (an analogue with a substitute for the sugar) and 1,3-propanediol (a simple spacer). In some cases, the incorporation of the nonstandard building blocks led to cleavages at noncanonical sites (Kubareva et al, 1992). 2-Aminopurine (2-AP) is often used as a fluorescence probe to detect base flipping in solution (Holz et al, 1998). Preliminary studies indicate ∼3-fold increase of the 2-AP fluorescence upon Ecl18kI binding to a 25 bp oligonucleotide duplex containing 2-AP at the central position of the Ecl18kI recognition sequence (unpublished data). The observed increase of the 2-AP fluorescence may reflect the extrusion of bases occurring in solution upon Ecl18kI binding, but could also result from base unstacking due to DNA distortion without nucleotide flipping. To unambiguously demonstrate nucleotide flipping in solution, 2-AP fluorescence lifetime experiments should be performed (Neely et al, 2005). Do other Type II restriction endonucleases flip nucleotides? Nucleotides are flipped in the Ecl18kI–DNA complex (Figure 7A and B), but not in the NgoMIV–DNA complex (Figure 7C and D). The structure explains the difference. The pocket for the extruded base, which is formed by Arg57 and Trp61, has no counterpart in NgoMIV, where the spatially equivalent region is occluded by Ile21 and Leu22 (data not

RNA interference is a powerful experimental tool for RNA knockdown, but not all organisms are amenable. Here, we provide a proof of principle demonstration that a type III Csm effector complex can be used for programmable mRNA transcript degradation in eukaryotes. In zebrafish, Streptococcus thermophilus Csm complex (StCsm) proved effective for knockdown of maternally expressed EGFP in germ cells of Tg(ddx4:ddx4-EGFP) fish. It also led to significant, albeit less drastic, fluorescence reduction at one day postfertilization in Tg(myl7:GFP) and Tg(fli1:EGFP) fish that express EGFP zygotically. StCsm targeted against the endogenous tdgf1 elicited the characteristic one-eyed phenotype with greater than 50% penetrance, and hence with similar efficiency to morpholino-mediated knockdown. We conclude that Csm-mediated knockdown is very efficient for maternal transcripts and can also be used for mixed maternal/early zygotic and early zygotic transcripts, in some cases reaching comparable efficiency to morpholino-based knockdown without significant off-target effects.

A new inorganic scintillation material based on Ba-Gd silica glass doped with cerium (BGS) is fabricated and studied. With the highest light yield among heavy glasses at the level of 2500 ph/MeV and fast scintillation response, the new scintillator ensures a good coincidence time resolution of < 230 ps FWHM for 511 keV γ-quanta from a 22Na source and SiPM readout. In addition to good performance in γ-quanta detection, the material demonstrates capability for efficient detection of low-energetic​ neutrons. The scintillator is produced by exploiting the standard industrial glass technology, which allows for an unlimited scaling up the conversion of raw material into a high-quality scintillator at a high rate. The glass can be casted in application-specific molds, so minimizing the material losses. The presented glass scintillator has potential for further improvement of its light output and scintillation response time.

We present a photoluminescence excitation study of CdSe nanocrystals embedded in a silicate glass matrix. The band edge emission was found to be strongly dependent on the excitation photon energy (hvL) when hvL is much higher than the fundamental absorption peak. Using the theoretical energies of electronic states in CdSe nanocrystal calculated by Ekimov et al. [J. Opt. Soc. Am. B 10, 100 (1993)] we showed our results can be understood as a size-selective effect. We also show that it is possible to use such excitation spectroscopy to determine the excited state energies and also the size distribution in nanocrystal samples.

We present a study on the time evolution of the electroluminescence (EL) spectra of AlGaN-based deep ultraviolet light-emitting diodes (LEDs) under pulsed current pumping. The EL spectra peaks at 285 nm and 330 nm are found to result from recombination involving band-to-band and free carriers to deep acceptor level transitions. The 330 nm long-wavelength transitions to deep acceptor levels in the p-AlGaN layer as well as the nonradiative processes significantly influence the LED internal quantum efficiency.

The electromagnetic calorimeter of PANDA at the FAIR facility will rely on the operation of lead tungstate (PbWO4, PWO) scintillating crystals at temperatures near -25∘C to provide sufficient resolution for photons in the energy range from 8 GeV down to 10 MeV. The radiation hardness of PWO crystals was studied at the IHEP (Protvino) irradiation facility in the temperature range from +20∘C (room temperature) down to -23∘C. These studies have indicated significantly different behavior in the time evolution of the damaging processes well below room temperature. Different signal loss levels at the same dose rate but at different temperatures were observed. The effect of a deep suppression of the crystal recovery process at temperatures below 0∘C has been seen.

Interactions between distantly separated DNA regions mediated by specialized proteins lead to the formation of synaptic protein−DNA complexes. This is a ubiquitous phenomenon which is critical in various genetic processes. Although such interactions typically occur between two sites, interactions among three specific DNA regions have been identified, and a corresponding model has been proposed. Atomic force microscopy was used to test this model for the EcoRII restriction enzyme and provide direct visualization and characterization of synaptic protein−DNA complexes involving three DNA binding sites. The complex appeared in the images as a two-loop structure, and the length measurements proved the site specificity of the protein in the complex. The protein volume measurements showed that an EcoRII dimer is the core of the three-site synaptosome. Other complexes were identified and analyzed. The protein volume data showed that the dimeric form of the protein is responsible for the formation of other types of synaptic complexes as well. The applications of these results to the mechanisms of the protein−DNA interactions are discussed.

Restriction endonuclease MvaI recognizes the sequence CC/WGG (W stands for A or T, '/' designates the cleavage site) and generates products with single nucleotide 5'-overhangs. The enzyme has been noted for its tolerance towards DNA modifications. Here, we report a biochemical characterization and crystal structures of MvaI in an apo-form and in a complex with target DNA at 1.5 A resolution. Our results show that MvaI is a monomer and recognizes its pseudosymmetric target sequence asymmetrically. The enzyme consists of two lobes. The catalytic lobe anchors the active site residues Glu36, Asp50, Glu55 and Lys57 and contacts the bases from the minor grove side. The recognition lobe mediates all major grove interactions with the bases. The enzyme in the crystal is bound to the strand with T at the center of the recognition sequence. The crystal structure with calcium ions and DNA mimics the prereactive state. MvaI shows structural similarities to BcnI, which cleaves the related sequence CC/SGG and to MutH enzyme, which is a component of the DNA repair machinery, and nicks one DNA strand instead of making a double-strand break.

Efficiency of sol–gel derived Y3−xAl5O12:Cex3+ (YAG:Ce) and Y3−xMg2AlSi2O12:Cex3+ (YMASG:Ce) phosphors, which are prospective for application in white light emitting diodes (LED), is studied. Sets of samples containing different cerium amount x from 0.015 to 0.06 and sintered at different temperatures (1400–1550 °C) were investigated. Importance of absorption peculiarities in agglomerates of phosphor nanocrystals is demonstrated by studying the excitation wavelength dependence of quantum efficiency and by applying PL measurements in confocal mode. Emission saturation is demonstrated to occur at higher excitation intensities than those typical for operating white LEDs.

The trench defects in InGaN/GaN multiple quantum well structures are studied using confocal photoluminescence (PL) spectroscopy and atomic force microscopy. A strong blueshift (up to ∼280 meV) and an intensity increase (by up to a factor of 700) of the emission are demonstrated for regions enclosed by trench loops. The influence of the difference in the well width inside and outside the trench loops observed by transmission electron microscopy, the compositional pulling effect, the strain relaxation inside the loop, and corresponding reduction in the built-in field on the PL band peak position and intensity were estimated. The competition of these effects is mainly governed by the width of the quantum wells in the structure. It is shown that the PL band blueshift observed within the trench defect loops in the InGaN structures with wide quantum wells is mainly caused by the reduction in efficiency of the quantum-confined Stark effect due to strain relaxation.

Capabilities of repeated deposition of ultrathin layers by pulsed metalorganic chemical vapor deposition (MOCVD) for improvement of structural and luminescence properties of InN thin films on GaN/sapphire templates were studied by varying the growth temperature and the durations of pulse and pause in the delivery of In precursor. X-ray diffraction, atomic force microscopy, and spatially-resolved photoluminescence (PL) spectroscopy were exploited to characterize the structural quality, surface morphology and luminescence properties. Better structural quality is achieved by using longer trimethylindium pulses. However, it is shown that the luminescence properties of InN epilayers correlate with the pause and pulse ratio rather than with their absolute lengths, and the deposition of 1.5–2 monolayers of InN during one growth cycle is optimal to achieve the highest PL intensity. Moreover, the use of temperature ramping enabled achieving the highest PL intensity and the smallest blue shift of the PL band. The luminescence parameters are linked with the structural properties, and domain-like patterns of InN layers are revealed.

Growth of BGaN epitaxial layers by metalorganic chemical vapor deposition (MOCVD) using triethylboron (TEB) as a boron source was studied on 6H-SiC substrate and on GaN and AlN templates on sapphire. X-ray diffraction, atomic force microscopy and photoluminescence spectroscopy were exploited to characterize the structural quality, surface morphology, luminescence efficiency, and boron content. Silicon carbide was shown to be slightly superior to AlN/sapphire and considerably better than GaN/sapphire as the most favorable substrate to incorporate a possibly higher boron content. Increasing TEB flow rate at correspondingly optimized growth temperature and V/III ratio enabled us to achieve the boron content of up to 5.5%, though at the expense of structural quality. We showed that the band gap bowing parameter is similar for the epilayers deposited on all the three templates/substrates under study and is approximately equal to 4 eV, substantially lower than reported before.

Non-linear absorption spectroscopy in pump and probe configuration has been used to test the population of non-equilibrium carriers in Ce-doped Y3Al5O12 (YAG), Lu3Al5O12 (LuAG), and Gd3AlxGa(5-x)O12 (GAGG) crystals with and without codoping by Mg2+ ions. A faster rise time of the induced optical density has been observed in all crystals codoped with Mg with respect to that in Mg-free samples. A significant difference in the time evolution of the differential optical density in GAGG with respect to YAG and LuAG crystals has also been measured. In both GAGG:Ce and GAGG:Ce,Mg an absorption band with maximum in the blue-green range and a decay time of 1.4 ps is present. This band is due to the absorption by free electrons before they are trapped or re-captured by Ce3+ ions. A broad absorption band in the yellow-red region with very short rise time and a decay time longer than 150 ps has been observed in all the Ce-doped garnets under study and can be attributed to the absorption from the Ce3+ excited states.

The aim of this work has been to improve the time resolution of radiation detectors for future high-energy physics experiments and medical imaging applications. Ce-doped oxyorthosilicate Lu2SiO5:Ce (LSO) and mixed oxyorthosilicate Lu1.6Y0.4SiO5:Ce (LYSO) have been investigated as prospective scintillators for such high-time-resolution applications. A differential optical absorption technique with sub-picosecond time resolution upon selective excitation of Ce3+ ions to different excited states has been adopted to study carrier dynamics in these scintillators, and coincidence time resolution measured using 511 keV γ-quanta has been exploited to test their timing properties. A delay in population of the emitting level of Ce3+ has been observed, and is interpreted in terms of electron trapping, which is more pronounced in mixed yttrium-containing LYSO crystals due to composition fluctuations. It is shown that the delay, which affects the luminescence response time, can be eliminated by co-doping of LYSO:Ce with calcium at concentrations as low as 5 ppm. The faster kinetics of electron transfer correlates with a better coincidence time resolution. Thermalization and spatial distribution of non-equilibrium carriers has been studied theoretically to link the results obtained by the time-resolved differential optical absorption technique with the behavior of the non-equilibrium carriers generated by irradiation.

We report on the spectral dynamics of the reflectivity, site-selectively excited photoluminescence, photoluminescence excitation, and time-resolved luminescence in quaternary AlInGaN epitaxial layers grown on GaN templates. The incorporation of a few percents of In into AlGaN causes significant smoothening of the band-bottom potential profile in AlInGaN layers owing to improved crystal quality. An abrupt optical bandgap indicates that a nearly lattice-matched AlInGaN/GaN heterostructure with large energy band offsets can be grown for high-efficiency light-emitting devices.

A catalytic sequence motif PDX10-30(E/D)XK is found in many restriction enzymes. On the basis of sequence similarities and mapping of the conserved residues to the crystal structure of NgoMIV we suggest that residues D160, K182, R186, R188 and E195 contribute to the catalytic/DNA binding site of the Ecl18kI restriction endonuclease. Mutational analysis confirms the functional significance of the conserved residues of Ecl18kI. Therefore, we conclude that the active site motif 159VDX21KX12E of Ecl18kI differs from the canonical PDX10-30(E/D)XK motif characteristic for most of the restriction enzymes. Moreover, we propose that two subfamilies of endonucleases Ecl18kI/PspGI/EcoRII and Cfr10I/Bse634I/NgoMIV, specific, respectively, for CCNGG/CCWGG and RCCGGY/GCCGGC sites, share conserved active site architecture and DNA binding elements.

Excitation-power dynamics of near-band-edge photoluminescence (PL) peak position in InxGa1−xN∕GaN multiple quantum wells (x∼0.15) was analyzed as a function of well width. The analysis was based on energy reference provided by photoreflectance (PR) spectra. The difference in spectral position of the PR feature and low-excitation PL band (the Stokes Shift) revealed carrier localization energy, which exhibited a remarkable sensitivity to the well width, increasing from 75meV in 2nm wells to about 250meV in 4nm wells. Meanwhile collating of the PR data with the flat-band model for the optical transition energy in quantum wells rendered a relatively weak (0.5MV∕cm) built-in piezoelectric field. The blueshift of the PL peak position with increasing photoexcitation power density was shown to be in qualitative agreement with the model of filling of the band-tail states with some contribution from screening of built-in field in the thickest (4nm) wells. Increased incident photon energy resulted in an additional blueshift of the PL peak, which was explained by a nonthermalized distribution of localized carriers and/or carrier localization in the interface region. Our results are consistent with a concept of emission from partially relaxed large In-rich regions with internal band potential fluctuations, which are enhanced with increasing the growth time.

PspGI is a representative of a group of restriction endonucleases that recognize a pentameric sequence related to CCNGG. Unlike the previously investigated Ecl18kI, which does not have any specificity for the central base pair, PspGI prefers A/T over G/C in its target site. Here, we present a structure of PspGI with target DNA at 1.7 Å resolution. In this structure, the bases at the center of the recognition sequence are extruded from the DNA and flipped into pockets of PspGI. The flipped thymine is in the usual anti conformation, but the flipped adenine takes the normally unfavorable syn conformation. The results of this and the accompanying manuscript attribute the preference for A/T pairs over G/C pairs in the flipping position to the intrinsically lower penalty for flipping A/T pairs and to selection of the PspGI pockets against guanine and cytosine. Our data show that flipping can contribute to the discrimination between normal bases. This adds a new role to base flipping in addition to its well-known function in base modification and DNA damage repair.

A set of Al0.35Ga0.65N∕Al0.49Ga0.51N multiple quantum wells (MQWs) with fixed barrier width and well widths varying from 1.65to5.0nm has been grown by metal-organic chemical vapor deposition. Carrier dynamics in the MQWs were studied using time-resolved photoluminescence (PL) spectroscopy and light-induced transient grating (four wave mixing) technique. The authors observed that the lifetime of nonequilibrium carriers (excitons) increases with decreasing well width and interpreted the effect by stronger localization preventing their migration to nonradiative recombination centers. Meanwhile the radiative decay time is also influenced by screening of the built-in electric field, which spatially separates the electrons and holes. It is shown that this effect affects the initial part of PL intensity decay after pulsed excitation. It becomes more pronounced with increase in the initial carrier density but saturates when the carrier density is high enough to completely screen the built-in electric field. The screening effect on PL decay is stronger in wider quantum wells.

Restriction endonuclease BcnI cleaves duplex DNA containing the sequence CC/SGG (S stands for C or G, / designates a cleavage position) to generate staggered products with single nucleotide 5′-overhangs. Here, we show that BcnI functions as a monomer that interacts with its target DNA in 1:1 molar ratio and report crystal structures of BcnI in the absence and in the presence of DNA. In the complex with DNA, BcnI makes specific contacts with all five bases of the target sequence and not just with a half-site, as the protomer of a typical dimeric restriction endonuclease. Our data are inconsistent with BcnI dimerization and suggest that the enzyme introduces double-strand breaks by sequentially nicking individual DNA strands, although this remains to be confirmed by kinetic experiments. BcnI is remotely similar to the DNA repair protein MutH and shares approximately 20% sequence identity with the restriction endonuclease MvaI, which is specific for the related sequence CC/WGG (W stands for A or T). As expected, BcnI is structurally similar to MvaI and recognizes conserved bases in the target sequence similarly but not identically. BcnI has a unique machinery for the recognition of the central base-pair.

To cut DNA at their target sites, restriction enzymes assemble into different oligomeric structures. The Ecl18kI endonuclease in the crystal is arranged as a tetramer made of two dimers each bound to a DNA copy. However, free in solution Ecl18kI is a dimer. To find out whether the Ecl18kI dimer or tetramer represents the functionally important assembly, we generated mutants aimed at disrupting the putative dimer–dimer interface and analysed the functional properties of Ecl18kI and mutant variants. We show by atomic force microscopy that on two-site DNA, Ecl18kI loops out an intervening DNA fragment and forms a tetramer. Using the tethered particle motion technique, we demonstrate that in solution DNA looping is highly dynamic and involves a transient interaction between the two DNA-bound dimers. Furthermore, we show that Ecl18kI cleaves DNA in the synaptic complex much faster than when acting on a single recognition site. Contrary to Ecl18kI, the tetramerization interface mutant R174A binds DNA as a dimer, shows no DNA looping and is virtually inactive. We conclude that Ecl18kI follows the association model for the synaptic complex assembly in which it binds to the target site as a dimer and then associates into a transient tetrameric form to accomplish the cleavage reaction.

Stimulated emission (SE) is studied in AlGaN/AlGaN multiple quantum wells (MQWs) with different Al content grown on sapphire substrate. The spectra of spontaneous and stimulated emission and their transformations with increasing temperature as well as stimulated emission thresholds were measured in the temperature range from 8 to 300 K. Phonon-assisted band broadening in low-Al-content MQWs and double-scaled potential profile in high-Al-content MQWs were observed in the samples and linked with carrier localization conditions. The temperature dependence of the stimulated emission threshold was similar in the samples where the stimulated transitions occur between extended states and in the samples where the transitions occur in localized states. The stimulated emission threshold depends predominantly on the density of nonradiative recombination centers.

The influence of carrier localization on photoluminescence efficiency droop and stimulated emission is studied in AlGaN multiple quantum wells with different strength of carrier localization. We observe that carrier delocalization at low temperatures predominantly enhances the nonradiative recombination and causes the droop, while the main effect of the delocalization at elevated temperatures is enhancement of PL efficiency due to increasing contribution of bimolecular recombination of free carriers. When the carrier thermal energy exceeds the dispersion of the potential fluctuations causing the carrier localization, the droop is caused by stimulated carrier recombination.

This report presents results on the significant improvement of GAGG:Ce based scintillation detector performance with temperature decrease. When temperature of a PMT based detector is lowered to −45 °C, its amplitude response at registration of γ-quanta is improved by 30%; FHHM was found to be better up to factor of 0.85, whereas scintillation kinetics become even faster in crystals co-doped with magnesium and magnesium and titanium. All this opens an opportunity for a wide application of GAGG scintillation detectors, particularly in a combination with SiPM photo-sensors, which signal-to-noise ratio would also improve with temperature decrease.

We provide evidences that multicomponent garnet-type Ce-doped crystal GAGG (Gd3Al2Ga3O12) is a promising scintillator to be applied in harsh irradiation environments, particularly, in high-energy physics experiments and reactor research facilities, where long-term operation is mandatory. Applicability of this scintillator for the upgrade of the detectors at future accelerators with high luminosity like High luminosity LHC is considered and GAGG:Ce with different codopings is compared with Ce-doped oxyorthosilicate crystals, which are currently also strong candidates for such applications. It is shown that the irradiation with 24 GeV protons at a fluence of 5x1014 p/cm2 has no significant effect on optical absorption in the spectral range of the scintillator emission. The contribution of radioisotopes formed in the material by irradiation with protons to the noise pedestal and the noise energy equivalent due to harmful radio-luminescence excited by the radionuclides remains negligible at short gates in collider experiments. Moreover, we show that the irradiation-generated color centers absorb outside the spectral range of Ce luminescence. These centers do not significantly affect the dynamics of nonequilibrium carriers, which is responsible for the timing properties of the scintillator. The density of free carriers decays with a characteristic time of 2 ps, while the decay constant for trapped carriers is ∼50 ns both before and after irradiation.

Nonlinear absorption of glass doped with PbS nanocrystals is studied and application of this composite material as a saturable absorber for mode locking in lasers is discussed. By using time resolved absorption pump-probe investigation, bleaching due to filling of discrete states caused by quantum confinement in the nanocrystals as well as induced absorption are revealed and characterized. The origin of the induced absorption is discussed. Kinetics of the transient absorption is studied. Two components observed in the decay of the nonlinearities are observed and interpreted in terms of the carrier trapping.

Time-resolved photoluminescence and light-induced transient grating measurements of GaN epilayers show that the photoluminescence decay can be described by two coupled exponential terms and that carrier mobility and lifetime in GaN epilayers are correlated within the model which accounts for nonradiative carrier recombination predominantly at dislocations. The obtained results demonstrate that migration-enhanced metalorganic chemical vapor deposition (MEMOCVD™) allows for growth of high-quality GaN epilayers on sapphire substrates with the dislocation density close to 108cm−2, carrier lifetime as long as 2 ns, and ambipolar diffusion coefficient of 2.1cm2s−1 corresponding to the hole mobility of approximately 40cm2V−1s−1.

Impact of controlled illumination spectrum on photosynthetic system and productivity of lettuce (Lactuca sativa L. cv. Grand Rapids) grown in phytotron was investigated. The variable-spectrum lighting modules were designed using four types of high-power light-emitting diodes (LEDs) with emission peaked in red at the wavelengths of 660 nm and 640 nm, in blue at 455 nm, and in far-red at 735 nm. Biometric characteristics, pigments content and photosynthesis intensity in lettuce grown under eight different light irradiance were measured and compared. A corresponding experiment under a conventional high-pressure sodium lamp was also performed for reference. The treatments were carried out under photoperiod of 14 hand 21115·C (day/night) temperature. Lettuce was grown for 29 days after sowing in a phytotron chamber. Stomata size of lettuce grown under LED was larger than that of the plants growing under high-pressure sodium lamp. The lowest number and largest size of stomata were observed under light without the red component, peaked at 660 nm. Elimination of the blue component (455 nm) resulted in an enhancement of fresh mass production and increased leaf area, but the photosynthetic productivity did not sbow similar effect. Tbe cblorophylls content in lettuce leaves was high during tbe entire growtb period, but strongly decreased at the end of tbe treatment without blue ligbt. Tbe photosynthesis in lettuce leaves was most intensive under irradiance without the far-red component (735 nm). We conclude that productivity of lettuce can be optimized by adjusting the light spectrum and flux density. INTRODUCTION Spectral quality affects various physiological processes in plants. Red light is important for the development of the photosynthetic apparatus (Saebo et aI., 1995). Blue light has' effect on the formation of chlorophyll, stomata opening and photomorphogenesis (Senger, 1982; Dougher and Bugbee, 1998; Schuerger et aI., 1997; Heo et aI., 2002). Lighting with a fixed spectrum is neither spectrally optimal nor . energetically effective and remains probably the most conservative technological factor in plant cultivation. Recently developed high-brightness light emitting diodes (LEOs) ground the future lighting technology (solid-state lighting). These optoelectronic devices feature high radiant efficiency; longevity, relatively narrow emission spectra and small . switching time and contain no mercury as most conventional light sources do. Using the new-generation light sources offers tremendous untapped reserves in increasing of the efficiency of photophysiological processes in plants, accelerating of the selection cycles, improving of quality of vegetable food. saving of energy resources, and elimination of the , impact of mercury on the environment (Bula et aI., 1991; Zukauskas et aI., 2002). Lettuce is an important greenhouse vegetable, intensively grown during the i seasons of low solar irradiation. The supplementation by artificial light is relatively . expensive. Therefore the search for alternative lighting sources is highly important. LEDProc. v,n IS on Artificial Lighting Ed. R. Moe Acta Hort. 711, ISHS 2006 183 based lighting presented herein might result in accelerated growth and increased quality oflettuce and other similar vegetables. The aim of the present study is to determine the spectrum of light that is optimal for growth, photosynthetic system and productivity of lettuce. MA TERIALS AND METHODS Lettuce was grown in growth chambers in Reat substrate (pH 6.0-6.5) prepared with fertilizes PG MIX (NPK 14-16-18; I.3 kg/m ). All experiments were carried out under 14 h photoperiod and 21/l5°C (day/night) temperature. LED-based lighting facility for plant cultivation under different spectral composition was designed using high-power LEOs with the useful light emitting area of 0.22 m• Four types of LEOs were used: 6 LEOs LuxeonTM type LXHL-LR3C (peak wavelength A = 455 nm) and 100 LEOs LuxeonTM type LXHL-MOID (A = 640 nm) of LUMILEDS LiGHTfNG, USA, and 9 LEOs L660-66-60 (A. = 660 nm) and 22 LEOs L73505-AU of EPITEX, Japan (A = 735 nm). The spectral and circadian characteristics for all experiments are presented in Table I. For comparison, the plants were growing under of high-pressure sodium lamps SON-T-Agro (PHILIPS). Leaf area of lettuce was measured by a CI-202 Leaf Area Meter (CID Inc., USA). Photosynthesis intensity was measured using a CI-3IO Portable Photosynthesis System (CID Inc., USA). The content of chlorophylls was determined in 100% acetone extract using a spectrophotometer Genesys 6 (ThermoSpectronic, USA). Samples were taken from the 2 or 3'd fully expanded shoot leaves. The dry weight of lettuce leaves was estimated after drying at the temperature of I05°C. For stomata measurements, the epidermal layer was removed and examined by means of optical microscopy. Stomata were counted on the lower leaf side in 10 visual fields of 0.17 mm; the average length was determined from 30 stomata. All measurements were performed at the end of experiments, except the chlorophyll content that was determined 4 times during each experiment. RESULTS Elimination of the blue component (455 nm) resulted in an enhancement of the fresh mass production and in an increase ofleafarea (Fig. 1), while elimination offar-red component (735 run) decreased both the indices. In general, irradiation by the 735 nm component at night had a tendency to decrease the fresh mass production compared to treatments without nocturnal break. The highest photosynthetic productivity was observed in EXP 2, where 735 nm component was applied for I h at night. In contrast, the lowest values were observed in EXP 8 (without 735 nm component) as well as under high-pressure sodium lamps (Fig. 2). The stomata length in lettuce leaves varied in the range of 51-59 !lm. This index was higher in plants that were grown under LEOs as compared to SON-T -Agro treatment (Fig. 3). The number of stomata in visuaJ field of 0.17 mm ranged from 4 to 10. The treatment without blue (445 run) component resulted in the most elongated stomata and in the least number of those per visual field (4-5 units). The chlorophylls content in lettuce leaves was high during the entire growth period, but strongly decreased at the end of the treatment without blue light (Fig. 4). The chlorophyll content in other treatments was development-dependent, although no significant tendencies were observed. The photosynthesis in lettuce leaves was most intense under illumination without the far-red 735 nm component (Fig. 5). DISCUSSION A number of investigators indicated that the blue component in small quantities is essential for plant growth and development, although an overexposure may reduce the photosynthesis intensity and yield (Yanagi et aJ., 1996; Goins et aI., 1997; Yorio et at,

According to the current paradigm type IIE restriction endonucleases are homodimeric proteins that simultaneously bind to two recognition sites but cleave DNA at only one site per turnover: the other site acts as an allosteric locus, activating the enzyme to cleave DNA at the first. Structural and biochemical analysis of the archetypal type IIE restriction enzyme EcoRII suggests that it has three possible DNA binding interfaces enabling simultaneous binding of three recognition sites. To test if putative synapsis of three binding sites has any functional significance, we have studied EcoRII cleavage of plasmids containing a single, two and three recognition sites under both single turnover and steady state conditions. EcoRII displays distinct reaction patterns on different substrates: (i) it shows virtually no activity on a single site plasmid; (ii) it yields open-circular DNA form nicked at one strand as an obligatory intermediate acting on a two-site plasmid; (iii) it cleaves concertedly both DNA strands at a single site during a single turnover on a three site plasmid to yield linear DNA. Cognate oligonucleotide added in trans increases the reaction velocity and changes the reaction pattern for the EcoRII cleavage of one and two-site plasmids but has little effect on the three-site plasmid. Taken together the data indicate that EcoRII requires simultaneous binding of three rather than two recognition sites in cis to achieve concerted DNA cleavage at a single site. We show that the orthodox type IIP enzyme PspGI which is an isoschisomer of EcoRII, cleaves different plasmid substrates with equal rates. Data provided here indicate that type IIE restriction enzymes EcoRII and NaeI follow different mechanisms. We propose that other type IIE restriction enzymes may employ the mechanism suggested here for EcoRII.

Monte Carlo simulation of phonon-assisted localized exciton hopping has been employed to describe the photoluminescence linewidth variation with temperature and to reveal band potential profile of ternary AlGaN epilayers with different carrier lifetimes. The lifetimes of 30 and 190 ps were experimentally determined in the layers with AlN buffers grown by conventional metal-organic chemical vapor deposition (MOCVD) and by migration-enhanced MOCVD (MEMOCVD™), respectively. The potential profile in AlGaN is shown to consist of double-scaled fluctuations. Exciton hopping in Al0.26Ga0.74N occurs within the random potential fluctuations (on the scale σ≈19meV) in isolated low-potential regions with the average localization energy dispersed on the scale Γ≈19meV. Such a pattern of band potential profile was found to be independent on the growth technique used for the deposition of their AlN buffer layers. This implies that the large difference in carrier lifetimes estimated in the AlGaN epilayers with the same Al content is caused by different densities of nonradiative recombination centers rather than by carrier localization in the potential fluctuations.

Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the observation of extrahelical nucleotides in a co-crystal of REase Ecl18kI with the cognate sequence, CCNGG, was unexpected. It turned out that Ecl18kI reads directly only the CCGG sequence and skips the unspecified N nucleotides, flipping them out from the helix. Sequence and structure conservation predict nucleotide flipping also for the complexes of PspGI and EcoRII with their target DNAs (/CCWGG), but data in solution are limited and indirect. Here, we demonstrate that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI enhance the fluorescence of 2-aminopurines (2-AP) placed at the centers of their recognition sequences. The fluorescence increase is largest for PspGI, intermediate for EcoRII-C and smallest for Ecl18kI, probably reflecting the differences in the hydrophobicity of the binding pockets within the protein. Omitting divalent metal cations and mutation of the binding pocket tryptophan to alanine strongly increase the 2-AP signal in the Ecl18kI-DNA complex. Together, our data provide the first direct evidence that Ecl18kI, EcoRII-C and PspGI flip nucleotides in solution.

Shift of the transition energy after pulsed optical excitation in Al0.35Ga0.65N∕Al0.49Ga0.51N quantum well (QW) structures with varying well width has been studied by time-resolved photoluminescence. The shift dynamics, which is due to descreening of the intrinsic electric field, has characteristic times similar to carrier lifetimes revealing negligible influence of trapped carriers on screening. Comparison of the experimental spectral shifts with the calculations has shown that the intrinsic field in our AlGaN QWs is about 0.4–0.5MV∕cm, which is about a factor of two smaller than the value calculated using the theoretical polarization constants.

The photoluminescence droop effect, i.e., the decrease in emission efficiency with increasing excitation intensity, is observed and studied in GaN epilayers with different carrier lifetimes. Spontaneous and stimulated emissions have been studied in the front-face and edge emission configurations. The onset of stimulated recombination occurs simultaneously with the droop onset in the front-face configuration and might be considered as an origin of the droop effect in GaN epilayers.

Endonucleases that generate double-strand breaks in DNA often possess two identical subunits related by rotational symmetry, arranged so that the active sites from each subunit act on opposite DNA strands. In contrast to many endonucleases, Type IIP restriction enzyme BcnI, which recognizes the pseudopalindromic sequence 5'-CCSGG-3' (where S stands for C or G) and cuts both DNA strands after the second C, is a monomer and possesses a single catalytic center. We show here that to generate a double-strand break BcnI nicks one DNA strand, switches its orientation on DNA to match the polarity of the second strand and then cuts the phosphodiester bond on the second DNA strand. Surprisingly, we find that an enzyme flip required for the second DNA strand cleavage occurs without an excursion into bulk solution, as the same BcnI molecule acts processively on both DNA strands. We provide evidence that after cleavage of the first DNA strand, BcnI remains associated with the nicked intermediate and relocates to the opposite strand by a short range diffusive hopping on DNA.

The paper presents a review of the recent development of III-nitride based deep UV light emitting diodes (LEDs).Main applications of the deep UV LEDs are introduced.Review of material issues is focused on the lattice mismatch between the substrate and the active layer and at heterojunctions in multiple quantum well structures forming the active layer, the localization of nonequilibrium carriers, the material properties limiting the internal quantum efficiency, and the effect of efficiency droop at high density of nonequilibrium carriers.AlGaN is currently the semiconductor of choice for development of deep UV LEDs, so this material is the most discussed one in this review, though some information on AlInGaN is also provided.

Dynamics of radiative and nonradiative recombination of non-equilibrium carriers is investigated in thick AlGaN epitaxial layers with Al content ranging from 0.11 to 0.71. The internal quantum efficiency (IQE) in the epilayers was obtained using two approaches: either estimated from PL measurements or calculated using the recombination coefficients of a simple ABC model, retrieved by fitting the kinetics of light induced transient gratings (LITG). At photoexcited carrier densities below ~1019 cm−3, both approaches provided similar IQE values indicating that the simple ABC model is applicable to analyze carrier recombination at such carrier densities. The increase in IQE at higher carrier densities slowed down for the values extracted from PL considerably faster than for those obtained from LITG transients. This discrepancy is explained in terms of the mixed nature of the rate coefficient B caused by the onset of the density-activated nonradiative recombination at high carrier densities.

Substantially faster scintillators for radiation detectors are currently in demand for future high-luminosity high energy physics experiments and medical imaging devices. To meet this demand, the excitation transfer through Gd-sublattice in Ce-activated garnet-type scintillators is studied by time-resolved cathodoluminescence (CL) and photoluminescence (PL) techniques. The transfer is evidenced in the different decay rate in CL experiments and after resonant photoexcitation of Ce ions and is confirmed by the simulation of excitation transport through gadolinium subsystem and from Gd3+ to Ce3+ ions using the Monte Carlo technique. Energy levels of Gd3+ involved in the transfer are identified. The comparison of the results of time-resolved PL and CL measurements and the simulations of carrier dynamics revealed that the emission decay in Ce-doped Gd-containing garnets is accelerated by aliovalent codoping due to blocking the excitation transfer via gadolinium subsystem.

ZnSeTe single crystals with 2 wt% of Te fabricated for application as scintillating material in radiation detectors are studied by means of photoluminescence spectroscopy. Time evolution of the luminescence spectra, which is found to be strongly dependent on thermal treatment in different environments, reveals competition between nonradiative recombination and channels of radiative recombination resulting in two strongly overlapping emission bands. The origin of the bands is interpreted by recombination involving defect complexes containing Zn vacancies. Stabilization of the complexes by doping ZnSe with isoelectronic Te is discussed. Influence of annealing in Zn on reduction of concentration of nonradiative recombination centers and stabilization of the defect complexes, which are employed in ZnSe scintillation detectors, is demonstrated.

Conductive undoped and semi-insulating vanadium-doped 6H-SiC substrates were studied using the light-induced transient grating technique and photoluminescence (PL) spectroscopy. Carrier lifetime of 400±10 ps and diffusion coefficient of 2.7±0.2 cm2 s−1 were obtained for the nominally undoped wafer, while the corresponding parameters for the V-doped wafer were estimated to be 130±5 ps and 0.9±0.5 cm2 s−1, respectively. The peak PL intensity in the vanadium-doped wafers is more than three orders of magnitude lower than that in nominally undoped wafers. Low-temperature cw PL spectra revealed a band peaked at 507 nm, which is caused by V doping.

The archetypal Type IIE restriction endonuclease EcoRII is a dimer that has a modular structure. DNA binding studies indicate that the isolated C-terminal domain dimer has an interface that binds a single cognate DNA molecule whereas the N-terminal domain is a monomer that also binds a single copy of cognate DNA. Hence, the full-length EcoRII contains three putative DNA binding interfaces: one at the C-terminal domain dimer and two at each of the N-terminal domains. Mutational analysis indicates that the C-terminal domain shares conserved active site architecture and DNA binding elements with the tetrameric restriction enzyme NgoMIV. Data provided here suggest possible evolutionary relationships between different subfamilies of restriction enzymes.

The GIY-YIG nuclease domain was originally identified in homing endonucleases and enzymes involved in DNA repair and recombination. Many of the GIY-YIG family enzymes are functional as monomers. We show here that the Cfr42I restriction endonuclease which belongs to the GIY-YIG family and recognizes the symmetric sequence 5'-CCGC/GG-3' ('/' indicates the cleavage site) is a tetramer in solution. Moreover, biochemical and kinetic studies provided here demonstrate that the Cfr42I tetramer is catalytically active only upon simultaneous binding of two copies of its recognition sequence. In that respect Cfr42I resembles the homotetrameric Type IIF restriction enzymes that belong to the distinct PD-(E/D)XK nuclease superfamily. Unlike the PD-(E/D)XK enzymes, the GIY-YIG nuclease Cfr42I accommodates an extremely wide selection of metal-ion cofactors, including Mg2+, Mn2+, Co2+, Zn2+, Ni2+, Cu2+ and Ca2+. To our knowledge, Cfr42I is the first tetrameric GIY-YIG family enzyme. Similar structural arrangement and phenotypes displayed by restriction enzymes of the PD-(E/D)XK and GIY-YIG nuclease families point to the functional significance of tetramerization.

Restriction enzymes Ecl18kI, PspGI and EcoRII-C, specific for interrupted 5-bp target sequences, flip the central base pair of these sequences into their protein pockets to facilitate sequence recognition and adjust the DNA cleavage pattern. We have used time-resolved fluorescence spectroscopy of 2-aminopurine-labelled DNA in complex with each of these enzymes in solution to explore the nucleotide flipping mechanism and to obtain a detailed picture of the molecular environment of the extrahelical bases. We also report the first study of the 7-bp cutter, PfoI, whose recognition sequence (T/CCNGGA) overlaps with that of the Ecl18kI-type enzymes, and for which the crystal structure is unknown. The time-resolved fluorescence experiments reveal that PfoI also uses base flipping as part of its DNA recognition mechanism and that the extrahelical bases are captured by PfoI in binding pockets whose structures are quite different to those of the structurally characterized enzymes Ecl18kI, PspGI and EcoRII-C. The fluorescence decay parameters of all the enzyme-DNA complexes are interpreted to provide insight into the mechanisms used by these four restriction enzymes to flip and recognize bases and the relationship between nucleotide flipping and DNA cleavage.

The effect of carrier localization on stimulated emission (SE) in Al0.35Ga0.65N/Al0.49Ga0.51N quantum wells (QWs) on sapphire substrate was studied under photoexcitation in the edge emission configuration in the temperature range from 8 K to 300 K. The band potential profile responsible for carrier localization was modulated by the variation of QW width and monitored using fitting the experimental temperature dependence of the spontaneous luminescence band width to that obtained by the Monte Carlo simulation of exciton hopping. A faster increase of SE threshold with increasing temperature was observed in narrow QWs and was attributed to deeper carrier localization due to the modulation of quantum confinement energy by well width fluctuations. Meanwhile, delocalized carriers were shown to contribute to the filling of states at the mobility edge, where SE occurs. These results imply that the deep ultraviolet AlGaN/AlGaN laser structures can be optimized in terms of carrier localization effect through the selection of appropriate QW width.

BGaN epilayers were grown on GaN/sapphire templates in hydrogen atmosphere by metal organic chemical vapor deposition (MOCVD). The growth was attempted at different temperatures and flow rates of triethylboron, which was used as boron precursor. According to XRD measurements, up to 2.9% of boron was incorporated in 500 nm-thick BGaN layers deposited at 870 °C. Comparison of XRD results with the red shift observed in the photoluminescence band with increasing boron content confirms an extremely large value of ∼10 eV for the bowing parameter in BGaN.

Novel glasses and glass ceramics with compositions corresponding to stoichiometric lithium and barium disilicates and doped with different combinations of Ce3+, Eu2+,3+, Tb3+, and Dy3+ have been fabricated and studied as prospective light converters for white high-power light emitting diodes and laser diodes. Spatially resolved photoluminescence spectroscopy and structural analysis have been employed. The emission spectra and CIE color coordinates of these materials evidence their good prospective as phosphors for white light sources. Structural analysis proves a high level of crystallization of the ceramics fabricated by annealing the glasses, while spectroscopic study revealed the influence of crystallization on the emission properties of this system. The results show a high potential of these materials be exploited as temperature-resistant phosphors in high-power white light emitting diodes.

Nonequilibrium carrier dynamics in the scintillators prospective for fast timing in high energy physics and medical imaging applications was studied. The time-resolved free carrier absorption investigation was carried out to study the dynamics of nonequilibrium carriers in wide-band-gap scintillation materials: self-activated led tungstate (PbWO4, PWO) ant two garnet crystals, GAGG:Ce and YAGG:Ce. It was shown that free electrons appear in the conduction band of PWO and YAGG:Ce crystals within a sub-picosecond time scale, while the free holes in GAGG:Ce appear due to delocalization from Gd3+ ground states to the valence band within a few picoseconds after short-pulse excitation. The influence of Gd ions on the nonequilibrium carrier dynamics is discussed on the base of comparison the results of the free carrier absorption in GAGG:Ce containing gadolinium and in YAGG without Gd in the host lattice.

The timing performance of radiation detectors based on Ce-doped perovskites YAlO3 (YAP) and (Lu1−x-Yx)AlO3 (LuYAP) coupled with near-UV sensitive silicon photomultipliers (NUV-HD SiPMs) have been compared in coincidence time resolution (CTR) experiments. The single-detector time resolution full width at half maximum (FWHM) of YAP was found to be 169 ps, i.e., by a factor of two better than that observed earlier with photomultiplier readout. Introduction of lutetium into YAP structure deteriorates the time resolution to 286 ps and 309 ps for a Lu/Y atomic ratio of 1:1 and 0.7:0.3, respectively. The study of the dynamics of Ce3+excited state population after selective optical excitation with short (200 fs) pulses by using the differential absorption technique in pump and probe configuration evidenced the importance of electron trapping, which is enhanced by antisite LuAl defects having favorable conditions to occur in LuAP.

ввCeramic scintillators are promising due to their potentially low cost. Here, we report on our study of Ce-doped ceramics. Typical garnet-type ceramics Gd2.97Ce0.03Al2Ga3O12 was fabricated for the study from co-precipitated powders by high-temperature sintering in air. Its structure and composition are characterized using Scanning Electron Microscope (SEM) imaging, Transmission Electron Microscopy (TEM), Electron Energy Loss Spectroscopy (EELS), Electron Backscattered Diffraction (EBSD) mapping, X-Ray Diffraction (XRD) and X-ray Absorption Near Edge Structure (XANES) measurements. The spatial distribution of luminescence properties at the micro-level is studied using scanning confocal microscopy. Cerium segregation at the grain boundaries was revealed by compositional characterization and is in line with enhanced Ce3+ photoluminescence observed at the boundaries. Meanwhile, no excess partitioning of Ce4+ ions at the grain boundaries is observed. It is found that most of Ce ions in the ceramics are stabilized in the state Ce3+, what is encouraging in view of the further development of GAGG:Ce ceramics as a promising luminescence material for lighting and scintillator application.

Temperature and excitation power dependences of the photoluminescence Stokes shift and bandwidth were studied in quaternary AlInGaN epilayers as a function of indium content. At low excitation power, gradual incorporation of indium into AlGaN is shown to result in S- and W-shaped temperature dependences of the band peak position and bandwidth, respectively. At high excitation power, the S- and W-behavior disappears; however, increased indium molar fraction boosts the redshift of the luminescence band at high temperatures. Our results indicate that the incorporation of indium into AlGaN has a noticeable impact on the alloy transport properties. At low temperatures and low excitation power, the indium incorporation facilitates hopping of localized excitons, whereas at high temperatures and high excitation power, it sustains free motion of delocalized carriers that results in the band-gap renormalization via screening.

We report on using Migration Enhanced Metal Organic Chemical Vapor Deposition (MEMOCVDTM) buffers for increasing lifetime of non-equilibrium carriers in GaN and AlGaN players grown on sapphire and SiC substrates. Photoluminescence (PL) and the light-induced grating technique (LITG) were used for the comparative study of the GaN and AlGaN epilayers with the MEMOCVDTM multilayered buffers and with conventional buffers. Measurements on GaN layers grown on sapphire and SiC show carrier lifetime more than 300 ps respectively with MEMOCVD buffer layers which is more than 4 times higher compared to the layers on conventional MOCVD buffers. In the AlGaN layers, PL intensity increases for MEMOCVD buffer layer compared to conventional MOCVD layers possibly due to reduction in defect density. The LITG results also show higher carrier lifetime for Al0.23Ga0.77N (more than 190ps) with MEMOCVD AlN buffers compared to layers with conventional buffer layers. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

For the first time, full size lead tungstate crystals of different suppliers, quality and dopant concentration have been irradiated with gamma-rays at low temperatures down to -25degC at IHEP Protvino. In contrast to the behavior at room temperature, increased damage and extremely slow recovery processes have been observed. These first results are discussed in the light of several very different interpretations. Further more sensitive measurements are under preparation. The outcome will have a strong impact on the presently assembled ALICE-PHOS detector and the design of the EM calorimeter of PANDA at the future FAIR facility.

physica status solidi (a)Volume 157, Issue 1 p. 187-198 Original Paper Photoluminescence of PbWO4 single crystals G. Tamulaitis, G. Tamulaitis Institute of Materials Science and Applied Research, Vilnius University Search for more papers by this authorS. Buraĉas, S. Buraĉas Institute of Single Crystals, Kharkov Search for more papers by this authorV. P. Martinov, V. P. Martinov Institute of Single Crystals, Kharkov Search for more papers by this authorV. D. Ryzhikov, V. D. Ryzhikov Institute of Single Crystals, Kharkov Search for more papers by this authorH. H. Gutbrod, H. H. Gutbrod Gesellschaft für Schwerionenforschung, Darmstadt Search for more papers by this authorV. I. Manko, V. I. Manko Kurchatov National Center, Moscow Search for more papers by this author G. Tamulaitis, G. Tamulaitis Institute of Materials Science and Applied Research, Vilnius University Search for more papers by this authorS. Buraĉas, S. Buraĉas Institute of Single Crystals, Kharkov Search for more papers by this authorV. P. Martinov, V. P. Martinov Institute of Single Crystals, Kharkov Search for more papers by this authorV. D. Ryzhikov, V. D. Ryzhikov Institute of Single Crystals, Kharkov Search for more papers by this authorH. H. Gutbrod, H. H. Gutbrod Gesellschaft für Schwerionenforschung, Darmstadt Search for more papers by this authorV. I. Manko, V. I. Manko Kurchatov National Center, Moscow Search for more papers by this author First published: 16 September 1996 https://doi.org/10.1002/pssa.2211570124Citations: 24 Naugarduko 24, 2006 Vilnius, Lithuania. Prospekt Lenina 60, 310007 Kharkov, Ukraine. D-6100 Darmstadt, Germany. 123182 Moscow, Russia. AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Abstracten Photoluminescence of lead tungstate and its time evolution at different temperatures and excitation conditions were investigated to identify the mechanisms of radiative and nonradiative recombination in this scintillation crystal. Two centers responsible for short-wavelength emission were revealed and characterized. The results indicated the energy transfer between different centers to be of great importance. Red luminescence was shown to be useful for quality control of comparatively perfect crystals. Abstractru [Russian Text Ignored]. Citing Literature Volume157, Issue116 September 1996Pages 187-198 RelatedInformation

Ce-doped Lu2xGd2−2xSiO5 (LGSO:Ce) fiber-shaped crystals (x = 0.5) were grown by the micro-pulling down (µ-PD) technique. To optimize the activator concentration for achieving the best scintillation parameters, the cerium concentration in the melt was varied in the range from 0.01 to 1.5 at.%. Distributions of Gd3+ and Ce3+ in LGSO:Ce crystals grown by the µ-PD and Czochralski (Cz) techniques were compared. The spatial distribution of cations across the LGSO:Ce scintillation crystals grown by the µ-PD technique is studied using wide-field microscopy under simultaneous excitation of two types of Ce-related centers and confocal microscopy under the selective excitation of Ce3+ in CeO6 crystallographic sites. It is revealed that the fiber-shaped crystals contain a single crystal core surrounded by crystalline material with a higher density of inclusions and cracks that are predominantly directed along the crystal axis. The formation of inclusions and cracks is interpreted by a nonuniform radial distribution of LGSO:CE cations.

Luminescence efficiency droop has been studied in AlGaN epitaxial layers and multiple quantum wells (MQWs) with different strength of carrier localization in a wide range of temperatures. It is shown that the dominant mechanism leading to droop, i.e., the efficiency reduction at high carrier densities, is determined by the carrier thermalization conditions and the ratio between carrier thermal energy and localization depth. The droop mechanisms, such as the occupation-enhanced redistribution of nonthermalized carriers, the enhancement of nonradiative recombination due to carrier delocalization, and excitation-enhanced carrier transport to extended defects or stimulated emission, are discussed.

The present study was aimed at revealing the influence of oxygen on formation of alloy ZnSe–ZnTe as well as on development of luminescence centers under thermal treatment of scintillators based on isovalently doped ZnSe crystals. The presence of oxygen in ZnSe(Te) crystals as ZnO phase has been shown to hinder formation of (V′ZnTexSe)′ type luminescence centers responsible for luminescence band peaked at 635–640 nm, which is the principal emission band of this scintillator. In ZnSe(Te) crystals doped by mechanically stimulated ion implantation with active forms of oxygen (O′, Ox, O′2, etc.), luminescence quenching effects are not observed. However, the luminescence band in these crystals is blueshifted towards 600–610 nm. Strong luminescence band peaked at λmax=590–610 nm is observed in Te-free ZnSe crystals doped with oxygen in active forms. The experimental results are interpreted by formation of centers (Zni⋅Oxi)⋅ or (Zni⋅OxSe)⋅. Having larger charge carrier capture cross-section than (Zn⋅iV′ZnTexSe)x, the oxygen-containing centers determine kinetics of luminescence in ZnSe1−xTex crystals (x<0.001) treated by active forms of oxygen during mechanical activation of the initial raw material for crystal growth.

Abstract AlGaN epilayers with different aluminum molar fractions have been comparatively studied by photoluminescence (PL) and light‐induced transient grating (LITG) techniques. The carrier diffusion length determined by LITG is shown to be close to the average distance between two first‐neighbor dislocations, which was roughly estimated by using the dislocation density obtained by etch pit technique. For epilayers containing the same amount of Al, the carrier lifetime and PL intensity are inversely proportional to the density of the dislocations, which limit the carrier lifetime by serving as nonradiative recombination centers. For AlGaN epilayers with similar lifetimes but with different Al contents, the PL intensity decreases with increasing Al fraction, which is explained by the Al content dependence of the radiative recombination rate. It is demonstrated that introduction of AlN/AlGaN superlattices on sapphire substrates by using Migration Enhanced Metal Organic Chemical Vapor Deposition (MEMOCVD TM ) enables growth of AlGaN with an increased nonequilibrium carrier lifetime and enhanced photoluminescence intensity. (© 2005 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Stimulated emission under quasi-resonant photoexcitation was studied in high-quality homoepitaxial GaN layers. Emission escaping perpendicular to the excited surface as well as propagating along the surface was analyzed as a function of the excitation power density in the temperature range from 8 to $600\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. Contributions of stimulated emission due to inelastic exciton--exciton/carrier interaction and recombination in electron-hole plasma (EHP) were revealed and simultaneously observed from the sample edge. The concurrent action of two mechanisms of stimulated emission was interpreted to be caused mainly by spatially inhomogeneous Mott transition due to separation of EHP located at the very surface of the layer and dense exciton gas located deeper in the layer. The separation is facilitated by high carrier diffusion length in homoepitaxial GaN. Stimulated emission due to inelastic exciton--exciton/carrier interaction was unambiguously traced up to the temperature of $440\phantom{\rule{0.3em}{0ex}}\mathrm{K}$.

The photoluminescence (PL) of AlGaN quantum wells with AlN barrier layers deposited on substrates fabricated of AlN single crystals is studied in the temperature range from 11to300K under pulsed band-to-band excitation of the well material. The abnormal temperature dependence of the PL peak position and differences in the character of the peak shift with increasing excitation power density observed at low and elevated temperatures are interpreted in terms of carrier/exciton localization and screening of the built-in electric field. The formation of these localized states with narrow energy distribution and high density is favorable for efficient light emission.

Photoluminescence of Si nanocrystals passivated by different alkanes (hexane, octane, and tridecane) was studied at room temperature. It is shown that the emission band shape is not affected by the length of the carbon chain in the alkanes used for passivation. A pronounced fine structure of the photoluminescence band consisting of peaks separated by 150–160 meV was observed under resonant excitation. The structure is interpreted by predominant contribution from Si nanocrystal groups with particular stable size/shape existing in addition to the previously reported nanocrystals with “magic” numbers of Si atoms. The contribution of these stable nanocrystals is revealed using selective resonant photoexcitation to the higher energy states in the discrete energy spectrum of such nanocrystals.

Restriction endonucleases Ecl18kI and PspGI/catalytic domain of EcoRII recognize CCNGG and CCWGG sequences (W stands for A or T), respectively. The enzymes are structurally similar, interact identically with the palindromic CC:GG parts of their recognition sequences and flip the nucleotides at their centers. Specificity for the central nucleotides could be influenced by the strength/stability of the base pair to be disrupted and/or by direct interactions of the enzymes with the flipped bases. Here, we address the importance of these contributions. We demonstrate that wt Ecl18kI cleaves oligoduplexes containing canonical, mismatched and abasic sites in the central position of its target sequence CCNGG with equal efficiencies. In contrast, substitutions in the binding pocket for the extrahelical base alter the Ecl18kI preference for the target site: the W61Y mutant prefers only certain mismatched substrates, and the W61A variant cuts exclusively at abasic sites, suggesting that pocket interactions play a major role in base discrimination. PspGI and catalytic domain of EcoRII probe the stability of the central base pair and the identity of the flipped bases in the pockets. This 'double check' mechanism explains their extraordinary specificity for an A/T pair in the flipping position.

Abstract Cu 2 S–CdS junctions between polycrystalline layers formed by substitution technique have been examined by combining the standard current–voltage and capacitance–voltage methods together with the barrier evaluation by linearly increasing pulsed voltage technique. Measurements of the capacitance characteristics enabled us to reveal three types of heterojunctions differing in density of dopants and carrier capture centers. Different species of Cu x S precipitates were detected in these three types of structures by using X-ray diffraction analysis. It is shown that the layer deposition temperature and duration have to be optimized to prevent the copper diffusion into CdS layer, to increase the free carrier density, and to diminish the density of deep recombination centers.

Photoluminescence of InGaN structures for green light-emitting diodes (LEDs) with multiple quantum wells as an active medium was studied with spatial and spectral resolution using confocal microscopy. Bright spots of ∼200 nm diameter were observed. Emission from these bright areas was up to 8 times more intense than from the rest of the sample surface and the band peak position in these areas was blueshifted with respect to the band position in the background surface of lower photoluminescence intensity. The data on emission properties in bright and dark areas and the dependence of these properties on the excitation power density were interpreted by assuming inhomogeneous distribution of defects acting as nonradiative recombination centres.

The carrier dynamics in AlGaN epilayers with different degrees of carrier localization were studied using low-temperature photoluminescence spectroscopy at different excitations. We observed a nonmonotonous band peak energy shift with increasing excitation, which is attributed to carrier-density-dependent carrier redistribution within localized states. The carrier redistribution enhances the carrier mobility and increases the nonradiative recombination rate resulting in efficiency droop. These results indicate the significant role of nonradiative recombination even at low temperatures and low carrier densities, despite strong carrier localization. The obtained results are consistent with the excitonic-type nonradiative recombination.

To shift the emission band to long wavelength side, InGaN/GaN multiple quantum wells were grown by metalorganic chemical vapor deposition (MOCVD) using pulsed delivery of the metalorganic precursors at fixed parameters of the pulses but variable growth temperatures and by introducing short-period superlattices (SPSL) as buffer layers. By decreasing the growth temperatures for both SPSL and quantum wells down to 800 °C, a considerable shift of the photoluminescence (PL) band peak down to ~2 eV is achieved at reasonably acceptable decrease in PL intensity at low carrier density. However, increase in the carrier density resulted in considerable blue shift of the band, and the efficiency droop onset occurred at rather low carrier densities. The comparison of the data on PL and differential optical transmittance, which were supported by structural analysis, revealed that the large red shift in the PL band position is predominantly caused by an increasing tail of localized states. Meanwhile, the efficiency droop effect in the samples under study is caused predominantly by the enhancement of nonradiative carrier recombination.

In the last forty years, application of crystalline materials in homogeneous Electromagnetic Calorimeters has played a crucial role in the discovery of matter properties and promoted a continuous progress in the detecting technique. The detection systems progressed from small detectors based on NaI(Tl), CsI(Na), BaF2, PbF2, and Bi4Ge3O12 to giant Electromagnetic Calorimeters of CMS, ALICE Collaborations at LHC and PANDA Collaboration at FAIR, where the systems consisted of thousands lead tungstate PbWO4 scintillation crystals. Lead tungstate (PWO) became the most extensively used scintillation material in high energy physics experiments. PWO possesses a unique combination of scintillation properties including high energy and time resolutions in the detection of high energy particles. Here, we report on the results of the two photon absorption in PWO crystals obtained by pump-probe technique using ultra short laser pulses. The results demonstrate that the relaxation processes in PWO offer capability of this material to be used in detection systems to make a time stamp with precision close to 10-12 s or even better.

Photoluminescence spectroscopy of AlGaN/AlGaN multiple quantum wells under quasi-steady-state conditions in the temperature range from 8 to 300 K revealed a strong dependence of droop onset threshold on temperature that was explained by the influence of carrier delocalization. The delocalization at room temperature results predominantly in enhancement of bimolecular radiative recombination, while being favorable for enhancement of nonradiative recombination at low temperatures. Studies of stimulated emission confirmed the strong influence of carrier localization on droop.

High-boron-content epitaxial layers of BGaN intended for lattice-matching with AlGaN in UV light emitters were grown on SiC substrate and GaN and AlN templates on sapphire. Photoluminescence (PL) of these layers was studied under quasi-steady-state conditions by varying temperature and excitation intensity. The PL spectra in the samples with different boron content and their dynamics evidence formation of boron-rich regions occupying a small fraction of the total layer volume and acting as the emission killers. The room-temperature PL efficiency of the BGaN epilayers was estimated and shown to drastically decrease at increasing boron content with no significant correlation with either the type of substrate/template or technological conditions of the layer deposition.

Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within or close to their DNA target sites, they form different oligomeric assemblies ranging from monomers, dimers, tetramers to higher order oligomers to generate a double strand break in DNA. Type IIP restriction endonuclease AgeI recognizes a palindromic sequence 5΄-A/CCGGT-3΄ and cuts it ('/' denotes the cleavage site) producing staggered DNA ends. Here, we present crystal structures of AgeI in apo and DNA-bound forms. The structure of AgeI is similar to the restriction enzymes that share in their target sites a conserved CCGG tetranucleotide and a cleavage pattern. Structure analysis and biochemical data indicate, that AgeI is a monomer in the apo-form both in the crystal and in solution, however, it binds and cleaves the palindromic target site as a dimer. DNA cleavage mechanism of AgeI is novel among Type IIP restriction endonucleases.