The fidelity of template-directed oligonucleotide ligation and its relevance to DNA computation.

abstract：:Highly toxic DNA double-strand breaks (DSBs) readily trigger the DNA damage response (DDR) in cells, which delays cell cycle progression to ensure proper DSB repair. In Saccharomyces cerevisiae, mitotic S phase (20-30 min) is lengthened upon DNA damage. During meiosis, Spo11-induced DSB onset and repair lasts up to 5 ...

journal_title：Nucleic acids research

authors： Woo TT,Chuang CN,Higashide M,Shinohara A,Wang TF

更新日期：2020-09-04 00:00:00

abstract：:The International Mouse Phenotyping Consortium (IMPC) web portal (http://www.mousephenotype.org) provides the biomedical community with a unified point of access to mutant mice and rich collection of related emerging and existing mouse phenotype data. IMPC mouse clinics worldwide follow rigorous highly structured and ...

journal_title：Nucleic acids research

authors： Koscielny G,Yaikhom G,Iyer V,Meehan TF,Morgan H,Atienza-Herrero J,Blake A,Chen CK,Easty R,Di Fenza A,Fiegel T,Grifiths M,Horne A,Karp NA,Kurbatova N,Mason JC,Matthews P,Oakley DJ,Qazi A,Regnart J,Retha A,Santos

更新日期：2014-01-01 00:00:00

abstract：:We previously constructed a multiribozyme expression vector by combining cis- and trans-acting ribozymes and we showed that several ribozymes, each directed against a different target in the HIV genome and acting independently in a 'shotgun' manner, markedly increased the efficiency of cleavage of HIV RNA in vitro [Oh...

journal_title：Nucleic acids research

authors： Yuyama N,Ohkawa J,Koguma T,Shirai M,Taira K

更新日期：1994-11-25 00:00:00

abstract：:Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generat...

journal_title：Nucleic acids research

authors： Rageul J,Park JJ,Jo U,Weinheimer AS,Vu TTM,Kim H

更新日期：2019-05-07 00:00:00

abstract：:A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase has been investigated. Gene mapping and complementation experiments placed the mutation to temperature-sensitivity within the alpha operon at 72 min. on the bacterial chromosome. The rate of RNA synthesis in vivo and the...

journal_title：Nucleic acids research

authors： Mehrpouyan M,Champney WS

更新日期：1990-06-25 00:00:00

abstract：:The D. melanogaster Adh gene is transcribed from two different promoters; a proximal (larval) promoter is active during late embryonic and larval stages, and a distal (adult) promoter is active primarily in third instar larvae and in adult flies (1). Genetic analyses suggest that several species of the mulleri subgrou...

journal_title：Nucleic acids research

authors： Fischer JA,Maniatis T

更新日期：1985-10-11 00:00:00

abstract：:The investigation of RNA structure, dynamics and biological function often requires the site-specific incorporation of non-natural moieties. Here we describe the functionalization of RNA transcripts by aldehyde-hydrazine chemistry using a simple initiator nucleotide that carries an acetal-protected aldehyde function. ...

journal_title：Nucleic acids research

authors： Pfander S,Fiammengo R,Kirin SI,Metzler-Nolte N,Jäschke A

更新日期：2007-01-01 00:00:00

abstract：:We report the first investigation of oligoribonucleotides containing a few 1-(2-deoxy-2-alpha-C-hydroxymethyl-beta-D-ribofuranosyl)thymine units (or 2'-hm-dT, abbreviated in this work as 'H'). Both the 2'-CH2O-phosphoramidite and 3'-O-phosphoramidite derivatives of H were synthesized and incorporated into both 2',5'-R...

journal_title：Nucleic acids research

authors： Peng CG,Damha MJ

更新日期：2005-12-23 00:00:00

abstract：:Mammalian antibody switch regions (∼1500 bp) are composed of a series of closely neighboring G4-capable sequences. Whereas numerous structural and genome-wide analyses of roles for minimal G4s in transcriptional regulation have been reported, Long G4-capable regions (LG4s)-like those at antibody switch regions-remain ...

journal_title：Nucleic acids research

authors： Williams JD,Houserova D,Johnson BR,Dyniewski B,Berroyer A,French H,Barchie AA,Bilbrey DD,Demeis JD,Ghee KR,Hughes AG,Kreitz NW,McInnis CH,Pudner SC,Reeves MN,Stahly AN,Turcu A,Watters BC,Daly GT,Langley RJ,Gillesp

更新日期：2020-06-19 00:00:00

abstract：:Re-sequencing, the identification of the specific variants in a sequence of interest compared with a known genomic sequence, is a ubiquitous task in today's biology. Universal arrays, which interrogate all possible oligonucleotides of a certain length in a target sequence, have been suggested for computationally deter...

journal_title：Nucleic acids research

authors： Pe'er I,Arbili N,Liu Y,Enck C,Gelfand CA,Shamir R

更新日期：2003-10-01 00:00:00

abstract：:A 12 bp long GCN4-binding, self-complementary duplex DNA d(CATGACGTCATG)(2) has been investigated by NMR spectroscopy to study the structure and dynamics of the molecule in aqueous solution. The NMR structure of the DNA obtained using simulated annealing and iterative relaxation matrix calculations compares quite clos...

journal_title：Nucleic acids research

authors： Khandelwal P,Panchal SC,Radha PK,Hosur RV

更新日期：2001-01-15 00:00:00

abstract：:A rearrangement of the mitochondrial genome of a long lived mutant of Podospora anserina is presented. It consists in the insertion of 191 bp of the LrDNA gene (coding for the large ribosomal RNA) at the junction between exon1 and intron alpha of gene co1 (coding for subunit 1 of cytochrome oxidase). This insertion is...

journal_title：Nucleic acids research

authors： Sainsard-Chanet A,Begel O

更新日期：1990-02-25 00:00:00

abstract：:Bulk replicative DNA synthesis in eukaryotes is highly accurate and efficient, primarily because of two DNA polymerases (Pols): Pols δ and ε. The high fidelity of these enzymes is due to their intrinsic base selectivity and proofreading exonuclease activity which, when coupled with post-replication mismatch repair, he...

journal_title：Nucleic acids research

authors： Korona DA,Lecompte KG,Pursell ZF

更新日期：2011-03-01 00:00:00

abstract：:As an approach to gene therapy for the respiratory manifestations of cystic fibrosis (CF), in vivo plasmid-mediated direct transfer of the normal CF transmembrane conductance regulator (CFTR) gene to the airway epithelium was investigated in mice. To evaluate the feasibility of this strategy, pRSVL, a plasmid composed...

journal_title：Nucleic acids research

authors： Yoshimura K,Rosenfeld MA,Nakamura H,Scherer EM,Pavirani A,Lecocq JP,Crystal RG

更新日期：1992-06-25 00:00:00

abstract：:Starting from a synthetic E. coli promoter with the consensus sequences at -35 and -10 regions, a sequence CAT frequently occurred in the RNA start points of natural promoters was introduced in the downstream of the consensus sequences, and the sequences around the RNA start points as well as the relative positions of...

journal_title：Nucleic acids research

authors： Aoyama T,Takanami M

更新日期：1985-06-11 00:00:00

abstract：:Nuclear factors NF90 and NF45 form a complex involved in a variety of cellular processes and are thought to affect gene expression both at the transcriptional and translational level. In addition, this complex affects the replication of several viruses through direct interactions with viral RNA. NF90 and NF45 dimerize...

journal_title：Nucleic acids research

authors： Wolkowicz UM,Cook AG

更新日期：2012-10-01 00:00:00

abstract：:The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-re...

journal_title：Nucleic acids research

authors： Tworowski D,Gorohovski A,Mukherjee S,Carmi G,Levy E,Detroja R,Mukherjee SB,Frenkel-Morgenstern M

更新日期：2021-01-08 00:00:00

abstract：:G-quadruplexes (G4s) are non-canonical nucleic acids secondary structures that form within guanine-rich strands of regulatory genomic regions. G4s have been extensively described in the human genome, especially in telomeres and oncogene promoters; in recent years the presence of G4s in viruses has attracted increasing...

journal_title：Nucleic acids research

authors： Ruggiero E,Richter SN

更新日期：2018-04-20 00:00:00

abstract：:Overexpressed in colon carcinoma-1 (OCC-1) is one of the earliest annotated long noncoding RNAs (lncRNAs) in colorectal cancer (CRC); however, its function remains largely unknown. Here, we revealed that OCC-1 plays a tumor suppressive role in CRC. OCC-1 knockdown by RNA interference promotes cell growth both in vitro...

journal_title：Nucleic acids research

authors： Lan Y,Xiao X,He Z,Luo Y,Wu C,Li L,Song X

更新日期：2018-06-20 00:00:00

abstract：:Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until ...

journal_title：Nucleic acids research

authors： Hüttenhofer A,Vogel J

更新日期：2006-01-25 00:00:00

abstract：:A nucleic acid affinity matrix containing a short oligodeoxynucleotide ligand has been prepared as an example of a material which can be used for the rapid and effective isolation of sequence specific DNA binding proteins. Two complementary oligodeoxynucleotides have been employed, one of which contains a small 5'-spa...

journal_title：Nucleic acids research

authors： Blanks R,McLaughlin LW

更新日期：1988-11-11 00:00:00

abstract：:Signal Transducers and Activators of Transcription (STAT) 5A/B regulate cytokine-inducible genes upon binding to GAS motifs. It is not known what percentage of genes with GAS motifs bind to and are regulated by STAT5. Moreover, it is not clear whether genome-wide STAT5 binding is modulated by its concentration. To cla...

journal_title：Nucleic acids research

authors： Zhu BM,Kang K,Yu JH,Chen W,Smith HE,Lee D,Sun HW,Wei L,Hennighausen L

更新日期：2012-05-01 00:00:00

abstract：:Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology a...

journal_title：Nucleic acids research

authors： Kelder T,van Iersel MP,Hanspers K,Kutmon M,Conklin BR,Evelo CT,Pico AR

更新日期：2012-01-01 00:00:00

abstract：:Synthesis and antisense activity of oligonucleotides modified with 2'-O-[2-[(N,N-dimethylamino)oxy] ethyl] (2'-O-DMAOE) are described. The 2'-O-DMAOE-modified oligonucleotides showed superior metabolic stability in mice. The phosphorothioate oligonucleotide 'gapmers', with 2'-O-DMAOE- modified nucleoside residues at t...

journal_title：Nucleic acids research

authors： Prakash TP,Johnston JF,Graham MJ,Condon TP,Manoharan M

更新日期：2004-02-03 00:00:00

abstract：:DNA2 nuclease/helicase is a structure-specific nuclease, 5'-to-3' helicase, and DNA-dependent ATPase. It is involved in multiple DNA metabolic pathways, including Okazaki fragment maturation, replication of 'difficult-to-replicate' DNA regions, end resection, stalled replication fork processing, and mitochondrial geno...

journal_title：Nucleic acids research

authors： Zheng L,Meng Y,Campbell JL,Shen B

更新日期：2020-01-10 00:00:00

abstract：:Affymetrix has recently developed whole-transcript GeneChips-'Gene' and 'Exon' arrays-which interrogate exons along the length of each gene. Although each probe on these arrays is intended to hybridize perfectly to only one transcriptional target, many probes match multiple transcripts located in different parts of th...

journal_title：Nucleic acids research

authors： Turro E,Lewin A,Rose A,Dallman MJ,Richardson S

更新日期：2010-01-01 00:00:00

abstract：:Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This pote...

journal_title：Nucleic acids research

authors： Cerdeño-Tárraga AM,Efstratiou A,Dover LG,Holden MT,Pallen M,Bentley SD,Besra GS,Churcher C,James KD,De Zoysa A,Chillingworth T,Cronin A,Dowd L,Feltwell T,Hamlin N,Holroyd S,Jagels K,Moule S,Quail MA,Rabbinowitsch E

更新日期：2003-11-15 00:00:00

abstract：:Amino acid sequences of 2 giant non-structural polyproteins (F1 and F2) of infectious bronchitis virus (IBV), a member of Coronaviridae, were compared, by computer-assisted methods, to sequences of a number of other positive strand RNA viral and cellular proteins. By this approach, juxtaposed putative RNA-dependent RN...

journal_title：Nucleic acids research

authors： Gorbalenya AE,Koonin EV,Donchenko AP,Blinov VM

更新日期：1989-06-26 00:00:00

abstract：:PPARγ2 is a critical lineage-determining transcription factor that is essential for adipogenic differentiation. Here we report characterization of the three-dimensional structure of the PPARγ2 locus after the onset of adipogenic differentiation and the mechanisms by which it forms. We identified a differentiation-depe...

journal_title：Nucleic acids research

authors： LeBlanc SE,Wu Q,Lamba P,Sif S,Imbalzano AN

更新日期：2016-06-20 00:00:00

abstract：:The hybridization of complementary strands of DNA is the underlying principle of all microarray-based techniques for the analysis of DNA variation. In this paper, we study how probe immobilization at surfaces, specifically probe density, influences the kinetics of target capture using surface plasmon resonance (SPR) s...

journal_title：Nucleic acids research

authors： Peterson AW,Heaton RJ,Georgiadis RM

更新日期：2001-12-15 00:00:00