A family of DNA sequences is reproducibly rearranged in the somatic nucleus of Tetrahymena.

abstract：:Ionizing radiation induces clustered DNA damage, which presents a challenge to the cellular repair machinery. The repair efficiency of a single-strand break (SSB) is approximately 4x less than that for repair of an abasic (AP) site when in a bistranded cluster containing 8-oxoG. To explore whether this difference in r...

journal_title：Nucleic acids research

authors： Mourgues S,Lomax ME,O'Neill P

更新日期：2007-01-01 00:00:00

abstract：:Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when experimental, restricted to small datasets; particularly poor attention has been given to genes with low CUB. In this work, co...

journal_title：Nucleic acids research

authors： dos Reis M,Wernisch L,Savva R

更新日期：2003-12-01 00:00:00

abstract：:Evidence is presented that the editing mechanisms of aminoacyl-tRNA synthetase operate by two alternative pathways: pre-transfer, by hydrolysis of the non-cognate aminoacyl adenylate; post-transfer, by hydrolysis of the mischarged tRNA. The methionyl-tRNA synthetases from Escherichia coli and Bacillus stearothermophil...

journal_title：Nucleic acids research

authors： Jakubowski H,Fersht AR

更新日期：1981-07-10 00:00:00

abstract：:The laminin (LM)-database, hosted at http://www.lm.lncc.br, was published in the NAR database 2011 edition. It was the first database that provided comprehensive information concerning a non-collagenous family of extracellular matrix proteins, the LMs. In its first version, this database contained a large amount of in...

journal_title：Nucleic acids research

authors： Golbert DC,Santana-van-Vliet E,Mundstein AS,Calfo V,Savino W,de Vasconcelos AT

更新日期：2014-01-01 00:00:00

abstract：:Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the api...

journal_title：Nucleic acids research

authors： Flodell S,Petersen M,Girard F,Zdunek J,Kidd-Ljunggren K,Schleucher J,Wijmenga S

更新日期：2006-01-01 00:00:00

abstract：:The finding in animal species of complexes homologous to the products of six Saccharomyces cerevisiae genes, origin of replication recognition complex (ORC), has suggested that ORC-related mechanisms have been conserved in all eukaryotes. In plants, however, the only cloned putative homologs of ORC subunits are the Ar...

journal_title：Nucleic acids research

authors： Witmer X,Alvarez-Venegas R,San-Miguel P,Danilevskaya O,Avramova Z

更新日期：2003-01-15 00:00:00

abstract：:The solid phase synthesis of oligoribonucleotides using the H-phosphonate approach and the 1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (Ctmp) and dimethoxytrityl (DMTr) groups, respectively, for the protection of the 2'- and 5'-hydroxy functions is described. The use of a new reagent, tris-(1,1,1,3,3,3-hexaf...

journal_title：Nucleic acids research

authors： Sakatsume O,Ohtsuki M,Takaku H,Reese CB

更新日期：1989-05-25 00:00:00

abstract：:The FALC-Loop web server provides an online interface for protein loop modeling by employing an ab initio loop modeling method called FALC (fragment assembly and analytical loop closure). The server may be used to construct loop regions in homology modeling, to refine unreliable loop regions in experimental structures...

journal_title：Nucleic acids research

authors： Ko J,Lee D,Park H,Coutsias EA,Lee J,Seok C

更新日期：2011-07-01 00:00:00

abstract：:DNA restriction fragments located 5' to the human c-myc gene display anomalous electrophoretic mobility on polyacrylamide gels. Computer modeling of the c-myc flanking DNA suggests that the slow-moving DNA fragments spanning nucleotides -1690 to -1054 (relative to c-myc promoter P1) and -718 to -452 form large left ha...

journal_title：Nucleic acids research

authors： Kumar S,Leffak M

更新日期：1989-04-11 00:00:00

abstract：:In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-β-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 Å and 2.80 Å reso...

journal_title：Nucleic acids research

authors： Pei XY,Bralley P,Jones GH,Luisi BF

更新日期：2015-09-18 00:00:00

abstract：:We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein s...

journal_title：Nucleic acids research

authors： Huang HD,Horng JT,Lin FM,Chang YC,Huang CC

更新日期：2005-01-01 00:00:00

abstract：:A class II site-specific endodeoxyribonuclease (SalPI) was identified in cell-free extracts of Streptomyces albus CMI 52766 after high speed centrifugation and fractionation through Bio Gel AO.5M. SalPI cleaves lambda DNA into at least 18 fragments. Five cleavage sites were located in the linear lambda map by the use ...

journal_title：Nucleic acids research

authors： Chater KF

更新日期：1977-06-01 00:00:00

abstract：:EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial...

journal_title：Nucleic acids research

authors： Karp PD,Riley M,Saier M,Paulsen IT,Paley SM,Pellegrini-Toole A

更新日期：2000-01-01 00:00:00

abstract：:3'-O-(5'-phosphoryldeoxycytidyl) phosphorothioate and fluorescent 3'-O-(5'-phosphoryldeoxycytidyl) S-bimane phosphorothioate can be ligated to tRNA by T4 RNA ligase. They are also efficient donors for the enzymatic ligation to oligodeoxynucleotides bearing a 3'-cytidine terminus. Cytidine 3',5'-bisphosphate is also a ...

journal_title：Nucleic acids research

authors： Cosstick R,McLaughlin LW,Eckstein F

更新日期：1984-02-24 00:00:00

abstract：:Present results provide direct evidence of the nature of a conformational change in DNA when nucleosomes are formed from core histones and poly [d(A-T)]. First, we have found some features which have characteristic aspects of the A like conformation of DNA. Thus, an increased contribution due to a sugar conformation c...

journal_title：Nucleic acids research

authors： Brahms S,Brahmachari SK,Angelier N,Brahms JG

更新日期：1981-10-10 00:00:00

abstract：:Bacteriophage Mu has one of the best studied, most efficient and largest transposition machineries of the prokaryotic world. To harness this attractive integration machinery for use in mammalian cells, we cloned the coding sequences of the phage factors MuA and MuB in a eukaryotic expression cassette and fused them to...

journal_title：Nucleic acids research

authors： Schagen FH,Rademaker HJ,Cramer SJ,van Ormondt H,van der Eb AJ,van de Putte P,Hoeben RC

更新日期：2000-12-01 00:00:00

abstract：:More than one-third of the RAG1 protein can be truncated from the N-terminus with only subtle effects on the products of V(D)J recombination in vitro or in a mouse. What, then, is the function of the N-terminal domain? We believe it to be regulatory. We determined, several years ago, that an included RING motif could ...

journal_title：Nucleic acids research

authors： Maitra R,Sadofsky MJ

更新日期：2009-06-01 00:00:00

abstract：:MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression. They are characterized by specific maturation processes defined by canonical and non-canonical biogenic pathways. Analysis of ∼0.5 billion sequences from mouse data sets derived from different tissues, developmental stages and cell types, partly...

journal_title：Nucleic acids research

authors： Castellano L,Stebbing J

更新日期：2013-03-01 00:00:00

abstract：:Benzo[c]phenanthrene dihydrodiol epoxide (B[c] PhDE) is well known as an important environmental chemical carcinogen that preferentially modifies DNA in adenine residues. However, the molecular mechanism by which B[c]PhDE induces tumorigenesis is not fully understood. In this report, we demonstrate that DNA mismatch r...

journal_title：Nucleic acids research

authors： Wu J,Zhu BB,Yu J,Zhu H,Qiu L,Kindy MS,Gu L,Seidel A,Li GM

更新日期：2003-11-15 00:00:00

abstract：:alpha2-Macroglobulin covalently linked to poly(L)-lysine can be used as a vehicle for receptor-mediated gene transfer. This modified alpha2-macroglobulin maintains its ability to bind to the alpha2-macroglobulin receptor, and was shown to introduce a luciferase reporter gene plasmid into HepG2 human hepatoma cells in ...

journal_title：Nucleic acids research

authors： Schneider H,Huse K,Birkenmeier G,Otto A,Scholz GH

更新日期：1996-10-01 00:00:00

abstract：:The chemical shifts of the well-resolved ring nitrogen protons of uracil and a series of substituted uracils, including pseudouridine (5-ribosyl-uracil) and uridine (1-ribosyl-uracil) were determined using nuclear magnetic resonance (NMR). The observed chemical shifts suggest the existence of an atypical syn conformat...

journal_title：Nucleic acids research

authors： Hurd RE,Reid BR

更新日期：1977-08-01 00:00:00

abstract：:The three chromosomal DNAs of S. pombe have been fractionated by pulsed field gel electrophoresis. The resulting molecular karyotype will greatly speed gene mapping in this organism, and it indicates that the separation range of the technique extends to DNA molecules as large as 9,000,000 base pairs. ...

journal_title：Nucleic acids research

authors： Smith CL,Matsumoto T,Niwa O,Klco S,Fan JB,Yanagida M,Cantor CR

更新日期：1987-06-11 00:00:00

abstract：:Proper DNA double-strand break (DSB) repair is essential for maintaining genome integrity. Microhomology-mediated end joining (MMEJ) is an error-prone repair mechanism, which introduces mutations at break sites and contributes to chromosomal translocations and telomere fusions, thus driving carcinogenesis. Mitotic kin...

journal_title：Nucleic acids research

authors： Wang H,Qiu Z,Liu B,Wu Y,Ren J,Liu Y,Zhao Y,Wang Y,Hao S,Li Z,Peng B,Xu X

更新日期：2018-11-16 00:00:00

abstract：:As opposed to the vast majority of prokaryotic repressors, the immunity repressor of temperate Escherichia coli phage P2 (C) recognizes non-palindromic direct repeats of DNA rather than inverted repeats. We have determined the crystal structure of P2 C at 1.8 Å. This constitutes the first structure solved from the fam...

journal_title：Nucleic acids research

authors： Massad T,Skaar K,Nilsson H,Damberg P,Henriksson-Peltola P,Haggård-Ljungquist E,Högbom M,Stenmark P

更新日期：2010-11-01 00:00:00

abstract：:A method for the facile preparation of oligoribonucleotide analogues containing beta-d-allofuranosyl nucleosides with additional functional groups tethered to the 6'-O positions is presented. It is based on the synthesis of two protected nucleosides carrying a 6'-O -bromopentyl and a 6'-O -methylaminopentyl substituen...

journal_title：Nucleic acids research

authors： Wu X,Pitsch S

更新日期：1998-10-01 00:00:00

abstract：:The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes,...

journal_title：Nucleic acids research

authors： Howe DG,Ramachandran S,Bradford YM,Fashena D,Toro S,Eagle A,Frazer K,Kalita P,Mani P,Martin R,Moxon ST,Paddock H,Pich C,Ruzicka L,Schaper K,Shao X,Singer A,Van Slyke CE,Westerfield M

更新日期：2021-01-08 00:00:00

abstract：:We report thermodynamic values for binding of the guanosine nucleophile to the ribozyme derived from the Anabaena group I intron, and find that they are similar to those measured previously for the structurally distinct Tetrahymena ribozyme. The free energy of binding guanosine 5'-monophosphate (pG) at 30 degrees C is...

journal_title：Nucleic acids research

authors： Kuo LY,Cech TR

更新日期：1996-10-01 00:00:00

abstract：:Arylsulfatase, produced by Chlamydomonas reinhardtii during sulfur-limited growth, is secreted into the periplasmic space and is readily assayed using a chromogenic substrate. To assess the usefulness of the gene encoding arylsulfatase (ars) as a reporter gene in C. reinhardtii, we have fused the promoter region of th...

journal_title：Nucleic acids research

authors： Davies JP,Weeks DP,Grossman AR

更新日期：1992-06-25 00:00:00

abstract：:A number of regulatory nascent peptides have been shown to regulate gene expression by causing programmed ribosome stalling during translation. Nascent peptide emerges from the ribosome through the exit tunnel, and one-third of the way along which β-loop structures of ribosomal proteins uL4 and uL22 protrude into the ...

journal_title：Nucleic acids research

authors： Takamatsu S,Ohashi Y,Onoue N,Tajima Y,Imamichi T,Yonezawa S,Morimoto K,Onouchi H,Yamashita Y,Naito S

更新日期：2020-02-28 00:00:00

abstract：:p16 is a key regulator of cellular senescence, yet the drivers of this stable state of proliferative arrest are not well understood. Here, we identify 22 senescence-associated microRNAs (SA-miRNAs) in normal human mammary epithelial cells. We show that SA-miRNAs-26b, 181a, 210 and 424 function in concert to directly r...

journal_title：Nucleic acids research

authors： Overhoff MG,Garbe JC,Koh J,Stampfer MR,Beach DH,Bishop CL

更新日期：2014-02-01 00:00:00