Structural basis for the recognition of diastereomeric 5',8-cyclo-2'-deoxypurine lesions by the human nucleotide excision repair system.

abstract：:We have analysed DNA modification in a HapII site (CCGG) present in the major intron of the discontinuous rabbit beta-globin gene. In most somatic tissues, including erythroid and non-erythroid tissues, about 50% of the DNA is resistant to cleavage at this site by HapII, though 100% cleavage is found with the isoschiz...

journal_title：Nucleic acids research

authors： Waalwijk C,Flavell RA

更新日期：1978-12-01 00:00:00

abstract：:Endonuclease III from Escherichia coli, yeast (yNtg1p and yNtg2p) and human and E.coli endonuclease VIII have a wide substrate specificity, and recognize oxidation products of both thymine and cytosine. DNA containing single dihydrouracil (DHU) and tandem DHU lesions were used as substrates for these repair enzymes. I...

journal_title：Nucleic acids research

authors： Venkhataraman R,Donald CD,Roy R,You HJ,Doetsch PW,Kow YW

更新日期：2001-01-15 00:00:00

abstract：:Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across tax...

journal_title：Nucleic acids research

authors： Zhu C,Mahlich Y,Miller M,Bromberg Y

更新日期：2018-01-04 00:00:00

abstract：:Mouse DNA contains two equally abundant, homologous subfamilies of MspI 3.6 and 5 kb repeated fragments. The first subfamily corresponds to the previously described (1) Bam 4 kb repeats, the second one to Bam repeated fragments of higher molecular weight. These subfamilies account for the vast majority of long Bam rep...

journal_title：Nucleic acids research

authors： Meunier-Rotival M,Bernardi G

更新日期：1984-02-10 00:00:00

abstract：:Modification of cytosine plays an important role in epigenetic regulation of gene expression and genome stability. Cytosine is converted to 5-methylcytosine (5mC) by DNA methyltransferase; in turn, 5mC may be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation enzyme. The structural flexibility of D...

journal_title：Nucleic acids research

authors： Furukawa A,Walinda E,Arita K,Sugase K

更新日期：2021-01-25 00:00:00

abstract：:A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oli...

journal_title：Nucleic acids research

authors： Chartrand P,Harvey SC,Ferbeyre G,Usman N,Cedergren R

更新日期：1995-10-25 00:00:00

abstract：:Recognition of DNA by proteins depends on DNA sequence and structure. Often unanswered is whether the structure of naked DNA persists in a protein-DNA complex, or whether protein binding changes DNA shape. While X-ray structures of protein-DNA complexes are numerous, the structure of naked cognate DNA is seldom availa...

journal_title：Nucleic acids research

authors： Azad RN,Zafiropoulos D,Ober D,Jiang Y,Chiu TP,Sagendorf JM,Rohs R,Tullius TD

更新日期：2018-03-16 00:00:00

abstract：:Two new endonuclease activities, endonuclease B and endonuclease C, obtained from yeast nuclear preparations have been separated and partially characterized. Endonuclease B has a primary requirement for Mn2+ which cannot be replaced by Mg2+ or Ca2+, and makes single-strand scissions in double-stranded DNA. Endonculeas...

journal_title：Nucleic acids research

authors： Pinon R,Leney E

更新日期：1975-07-01 00:00:00

abstract：:The synthesis of stable RNA in Mycoplasma capricolum was studied by [32P] labeling of cellular RNA of cells grown in a partially-defined medium in the presence or absence of an amino acid mixture supplement. The results indicate that M. capricolum employs the same stringent control mechanism used by E. coli cells, as ...

journal_title：Nucleic acids research

authors： Glaser G,Razin A,Razin S

更新日期：1981-08-11 00:00:00

abstract：:A gene encoding a putative DNA helicase from Staphylococcus aureus USA300 was cloned and expressed in Escherichia coli. The protein was purified to over 90% purity by chromatography. The purified enzyme, SauUSI, predominantly cleaves modified DNA containing 5mC and 5-hydroxymethylcytosine. Cleavage of 5mC-modified pla...

journal_title：Nucleic acids research

authors： Xu SY,Corvaglia AR,Chan SH,Zheng Y,Linder P

更新日期：2011-07-01 00:00:00

abstract：:Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better perfo...

journal_title：Nucleic acids research

authors： Burns PD,Li Y,Ma J,Borodovsky M

更新日期：2014-02-01 00:00:00

abstract：:The R-Coffee web server produces highly accurate multiple alignments of noncoding RNA (ncRNA) sequences, taking into account predicted secondary structures. R-Coffee uses a novel algorithm recently incorporated in the T-Coffee package. R-Coffee works along the same lines as T-Coffee: it uses pairwise or multiple seque...

journal_title：Nucleic acids research

authors： Moretti S,Wilm A,Higgins DG,Xenarios I,Notredame C

更新日期：2008-07-01 00:00:00

abstract：:We have characterized triple-helix-mediated inhibition of an artificial bacteriophage promoter with respect to relief of inhibition by incoming RNA polymerases that initiate upstream or downstream from the operator sequence. Whereas oligonucleotide-directed triple-helix formation inhibits the test promoter, promoter a...

journal_title：Nucleic acids research

authors： Skoog JU,Maher LJ 3rd

更新日期：1993-08-25 00:00:00

abstract：:DXZ4 is an X-linked macrosatellite composed of 12-100 tandemly arranged 3-kb repeat units. In females, it adopts opposite chromatin arrangements at the two alleles in response to X-chromosome inactivation. In males and on the active X chromosome, it is packaged into heterochromatin, but on the inactive X chromosome (X...

journal_title：Nucleic acids research

authors： Moseley SC,Rizkallah R,Tremblay DC,Anderson BR,Hurt MM,Chadwick BP

更新日期：2012-02-01 00:00:00

abstract：:Light-inducible systems allow spatiotemporal control of a variety of biological activities. Here, we report newly optimized optogenetic tools to induce transcription with light in mammalian cells, using the Arabidopsis photoreceptor Flavin Kelch-repeat F-box 1 (FKF1) and its binding partner GIGANTEA (GI) as well as CR...

journal_title：Nucleic acids research

authors： Quejada JR,Park SE,Awari DW,Shi F,Yamamoto HE,Kawano F,Jung JC,Yazawa M

更新日期：2017-11-16 00:00:00

abstract：:A new method for evaluating some complex characteristics of the primary structure of E.coli promoters is proposed. The method, of nonparametric statistical significance, selects important conserved single-base positions in combination with 2-base coupling relations of identity and complementarity. The extended consens...

journal_title：Nucleic acids research

authors： Rozkot F,Sázelová P,Pivec L

更新日期：1989-06-26 00:00:00

abstract：:An algorithm is presented which compares two restriction maps, yielding a measure of distance between the maps and relating the maps by an alignment. This new algorithm finds the minimum weighted sum of genetic events required to convert one map into the other, where the genetic events are the appearance/disappearance...

journal_title：Nucleic acids research

authors： Waterman MS,Smith TF,Katcher HL

更新日期：1984-01-11 00:00:00

abstract：:The sequence GCGCGCGCGC contains three overlapping, mutually exclusive, BssHII restriction sites, each corresponding to one of the three different reading frames. When inserted into a plasmid and digested with BssHII, the three sites in this sequence are cleaved at an approximate ratio of 2:1:2. Consequently, this sys...

journal_title：Nucleic acids research

authors： Orum H,Poulsen LK

更新日期：1989-04-25 00:00:00

abstract：:8-Oxo-7,8,-dihydro-2'-deoxyguanosine triphosphate (8-oxo-dGTP) is a major product of oxidative damage in the nucleotide pool. It is capable of mispairing with adenosine (dA), resulting in futile, mutagenic cycles of base excision repair. Therefore, it is critical that DNA polymerases discriminate against 8-oxo-dGTP at...

journal_title：Nucleic acids research

authors： Burak MJ,Guja KE,Garcia-Diaz M

更新日期：2015-09-18 00:00:00

abstract：:An improved algorithm was elaborated to analyse tRNA interaction with aminoacyl-tRNA synthetase based on analysis of tRNA sequences. The fundamental element defining the interaction between the tRNA and the synthetase is not a single nucleotide but a nucleotide combination named a tile which comprises of a given nucle...

journal_title：Nucleic acids research

authors： Steinberg SV,Kisselev LL

更新日期：1993-04-25 00:00:00

abstract：:Giant chromatin-modifying complexes regulate gene transcription in eukaryotes by acting on chromatin substrates and 'setting' the histone code. The histone deacetylase (HDAC)-associated mammalian Sin3 corepressor complex regulates a wide variety of genes involved in all aspects of cellular physiology. The recruitment ...

journal_title：Nucleic acids research

authors： He Y,Imhoff R,Sahu A,Radhakrishnan I

更新日期：2009-04-01 00:00:00

abstract：:The HIRA histone chaperone complex deposits histone H3.3 into nucleosomes in a DNA replication- and sequence-independent manner. As herpesvirus genomes enter the nucleus as naked DNA, we asked whether the HIRA chaperone complex affects herpesvirus infection. After infection of primary cells with HSV or CMV, or transie...

journal_title：Nucleic acids research

authors： Rai TS,Glass M,Cole JJ,Rather MI,Marsden M,Neilson M,Brock C,Humphreys IR,Everett RD,Adams PD

更新日期：2017-11-16 00:00:00

abstract：:Bacillus subtilis OhrR is a dimeric repressor that senses organic peroxides and regulates the expression of the OhrA peroxiredoxin. Derepression results from oxidation of an active site cysteine which ultimately results in formation of a mixed disulfide with a low molecular weight thiol, a cyclic sulfenamide, or overo...

journal_title：Nucleic acids research

authors： Eiamphungporn W,Soonsanga S,Lee JW,Helmann JD

更新日期：2009-03-01 00:00:00

abstract：:We have determined the nucleotide sequence at the 3' end of the vesicular stomatitis virus (VSV) polymerase or L gene and compared it to that obtained from a defective interfering particle (DI) RNA generated by this virus. The latter (DI 0.50) contains a large internal deletion within this gene. The deletion begins ex...

journal_title：Nucleic acids research

authors： De BK,Perrault J

更新日期：1982-11-11 00:00:00

abstract：:Treatment of responsive cells by interferons (IFNs) induces within a few hours a rise in the concentration of several proteins and mRNAs. In order to characterize these IFN-induced mRNA species, we have cloned in E. coli the cDNA made from a 17-18S poly(A)+ RNA of human fibroblastoid cells (SV80) treated with IFN-beta...

journal_title：Nucleic acids research

authors： Chebath J,Merlin G,Metz R,Benech P,Revel M

更新日期：1983-03-11 00:00:00

abstract：:We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions...

journal_title：Nucleic acids research

authors： Ahmad S,Sarai A

更新日期：2004-07-01 00:00:00

abstract：:NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA po...

journal_title：Nucleic acids research

authors： Liu B,Steitz TA

更新日期：2017-01-25 00:00:00

abstract：:The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal ...

journal_title：Nucleic acids research

authors： Arnold EA,Wahn U,Young KE

更新日期：1975-05-01 00:00:00

abstract：:The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial p...

journal_title：Nucleic acids research

authors： Al-Behadili A,Uhler JP,Berglund AK,Peter B,Doimo M,Reyes A,Wanrooij S,Zeviani M,Falkenberg M

更新日期：2018-10-12 00:00:00

abstract：:We have implemented a genome annotation system for prokaryotes called AGMIAL. Our approach embodies a number of key principles. First, expert manual annotators are seen as a critical component of the overall system; user interfaces were cyclically refined to satisfy their needs. Second, the overall process should be o...

journal_title：Nucleic acids research

authors： Bryson K,Loux V,Bossy R,Nicolas P,Chaillou S,van de Guchte M,Penaud S,Maguin E,Hoebeke M,Bessières P,Gibrat JF

更新日期：2006-07-19 00:00:00