Abstract:
:DNA polymerase mu is a member of the mammalian pol X family and reduces deletion during chromosome break repair by nonhomologous end joining (NHEJ). This biological role is linked to pol mu's ability to promote NHEJ of ends with noncomplementary 3' overhangs, but questions remain regarding how it performs this role. We show here that synthesis by pol mu in this context is often rapid and, despite the absence of primer/template base-pairing, instructed by template. However, pol mu is both much less active and more prone to possible template independence in some contexts, including ends with overhangs longer than two nucleotides. Reduced activity on longer overhangs implies pol mu is less able to synthesize across longer gaps, arguing pol mu must bridge both sides of gaps between noncomplementary ends to be effective in NHEJ. Consistent with this argument, a pol mu mutant defective specifically on gapped substrates is also less active during NHEJ of noncomplementary ends both in vitro and in cells. Taken together, pol mu activity during NHEJ of noncomplementary ends can thus be primarily linked to pol mu's ability to work together with core NHEJ factors to bridge DNA ends and perform a template-dependent gap fill-in reaction.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Davis BJ,Havener JM,Ramsden DAdoi
10.1093/nar/gkn164subject
Has Abstractpub_date
2008-05-01 00:00:00pages
3085-94issue
9eissn
0305-1048issn
1362-4962pii
gkn164journal_volume
36pub_type
杂志文章abstract::Understanding the molecular mechanisms that influence transposable element target site preferences is a fundamental challenge in functional and evolutionary genomics. Large-scale transposon insertion projects provide excellent material to study target site preferences in the absence of confounding effects of post-inse...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn563
更新日期:2008-11-01 00:00:00
abstract::A lac promotor mutant was constructed by filling in the protruding ends of the HpaII site located within the lac promotor. The mutation, named M42, is a two base pair insertion that changes the distance between the -10 and -35 regions from 18 to 20 residues. The activity of the mutant promotor measured in vivo is 15% ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.3.903
更新日期:1982-02-11 00:00:00
abstract::A UCSD Pascal program was developed which can analyze nucleic acid dot matrices of up to 9500 X 9500 in size on the Apple II computer. Although matrices of such size consume large amounts of computer memory, this program minimizes these problems by analyzing only small strips of the matrix at a time, and then transfer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.1part2.767
更新日期:1984-01-11 00:00:00
abstract::The behaviour of highly purified bacterial expressed rat O6-methylguanine-DNA methyltransferase (MGMT) towards the repair of CGCm6GAGCTCGCG and CGCe6GAGCTCGCG (km6G/ke6G = 1.45, where k is the second order repair rate constant determined, m6G and e6G are O6-methyl and O6-ethylguanine) is similar to that of E. coli 39k...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.9.1613
更新日期:1994-05-11 00:00:00
abstract::The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hy...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.18.7007
更新日期:1984-09-25 00:00:00
abstract::siRNAs confer sequence specific and robust silencing of mRNA. By virtue of these properties, siRNAs have become therapeutic candidates for disease intervention. However, their use as therapeutic agents can be hampered by unintended off-target effects by either or both strands of the siRNA duplex. We report here that u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq961
更新日期:2011-03-01 00:00:00
abstract::Pyrrole-imidazole polyamides targeted to the androgen response element were cytotoxic in multiple cell lines, independent of intact androgen receptor signaling. Polyamide treatment induced accumulation of S-phase cells and of PCNA replication/repair foci. Activation of a cell cycle checkpoint response was evidenced by...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku866
更新日期:2014-10-01 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
pub_type: 杂志文章
doi:10.1093/nar/29.2.407
更新日期:2001-01-15 00:00:00
abstract::Histone proteins are synthesized in large amounts during S-phase to package the newly replicated DNA, and are among the most stable proteins in the cell. The replication-dependent (RD)-histone mRNAs expressed during S-phase end in a conserved stem-loop rather than a polyA tail. In addition, there are replication-indep...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw620
更新日期:2016-11-02 00:00:00
abstract::The Protein Folding Database (PFD) is a publicly accessible repository of thermodynamic and kinetic protein folding data. Here we describe the first major revision of this work, featuring extensive restructuring that conforms to standards set out by the recently formed International Foldeomics Consortium. The database...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1007
更新日期:2007-01-01 00:00:00
abstract::The replication origin (oriC) of the Escherichia coli chromosome has been cloned and the region essential for chromosomal replication has been delimited to 245 base pairs. In previous studies the ability of recombinants between oriC and ColE1-type vectors, to transform E. coli polA- strains was used to determine which...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.22.8007
更新日期:1983-11-25 00:00:00
abstract::Calf lens messenger fractions have been purified on poly(dT)-cellulose. The purified RNA's have been analyzed as nucleosides by a method which can be used on a micro-scale with highly reproduceble results. Both the 10S and 14S lens mRNA contain poly A sequences. The poly A content found in 14S mRNA cannot account for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.2.245
更新日期:1974-02-01 00:00:00
abstract::Selection for amino acid affinity by elution of RNAs from tryptophan-Sepharose using free L-tryptophan evokes one sequence predominantly (K(D) = 12 microM), a symmetrical internal loop of 3 nt per side. Though we have also isolated larger sequences with affinity for tryptophan, successively squeezed selection in rando...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki861
更新日期:2005-09-25 00:00:00
abstract::GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1023
更新日期:2021-01-08 00:00:00
abstract::Natural oligopeptides may regulate nearly all vital processes. To date, the chemical structures of nearly 6000 oligopeptides have been identified from >1000 organisms representing all the biological kingdoms. We have compiled the known physical, chemical and biological properties of these oligopeptides--whether synthe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj008
更新日期:2006-01-01 00:00:00
abstract::Gene expression circuitries, which enable cells to detect precise levels within a morphogen concentration gradient, have a pivotal impact on biological processes such as embryonic pattern formation, paracrine and autocrine signalling, and cellular migration. We present the rational synthesis of a synthetic genetic cir...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq671
更新日期:2010-10-01 00:00:00
abstract::We have compiled the DNA sequence data for E. coli K12 available from the GENBANK and EMBO databases and over a period of several years independently from the literature. We have introduced all available genetic map data and have arranged the sequences accordingly. As far as possible the overlaps are deleted and a tot...
journal_title:Nucleic acids research
pub_type:
doi:10.1093/nar/17.suppl.r283
更新日期:1989-01-01 00:00:00
abstract::Using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar RNA (snoRNA) genes in the recently released draft sequence of the rice genome was carried out. This analysis identified 120 different box C/D snoRNA genes with a total of 346 gene variants, which were predicted to guide 135 2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg373
更新日期:2003-05-15 00:00:00
abstract::The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CR: ISPR/Cas9 O: ff-target P: rediction and I: dentification T: ool (CROP-IT) th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv575
更新日期:2015-10-15 00:00:00
abstract::The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa;...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx932
更新日期:2018-01-04 00:00:00
abstract::CRISPR/Cas9 is a powerful genome editing system but uncontrolled Cas9 nuclease expression triggers off-target effects and even in vivo immune responses. Inspired by synthetic biology, here we built a synthetic switch that self-regulates Cas9 expression not only in the transcription step by guide RNA-aided self-cleavag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1165
更新日期:2019-02-20 00:00:00
abstract::The topoisomerase I (TOP1) inhibitor irinotecan triggers cell death by trapping TOP1 on DNA, generating cytotoxic protein-linked DNA breaks (PDBs). Despite its wide application in a variety of solid tumors, the mechanisms of cancer cell resistance to irinotecan remains poorly understood. Here, we generated colorectal ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1026
更新日期:2017-02-17 00:00:00
abstract::Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.12.2607
更新日期:2001-06-15 00:00:00
abstract::A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt216
更新日期:2013-05-01 00:00:00
abstract::Search of interrelationships between the structural-functional protein organization and exon structure of encoding gene provides insights into issues concerned with the function, origin and evolution of genes and proteins. The functions of proteins and their domains are defined mostly by functional sites. The relation...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1187
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
pub_type: 杂志文章
doi:10.1093/nar/gkh220
更新日期:2004-02-03 00:00:00
abstract::A number of novel phosphate triester derivatives of the anti-cancer nucleoside analogue araC have been prepared by a rapid 2-step procedure, not necessitating prior sugar protection. Spectroscopic and lipophilicity data have been collected on these compounds. An in vitro assay indicated inhibition of thymidine incorpo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.18.7195
更新日期:1989-09-25 00:00:00
abstract::LOCtarget is a web server and database that predicts and annotates sub-cellular localization for structural genomics targets; LOCnet is one of the methods used in LOCtarget that can predict sub-cellular localization for all eukaryotic and prokaryotic proteins. Targets are taken from the central registration database f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh441
更新日期:2004-07-01 00:00:00
abstract::Cloned ribosomal DNA (rDNA) of Locusta migratoria was analyzed by restriction site mapping and SI nuclease experiments. The repeat unit is 18 kb long. The nontranscribed spacer region (NTS) is very large (11 kb) and homogeneous in length, but many of the restriction sites are heterogeneous among the repeat units. Two ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.4.1251
更新日期:1985-02-25 00:00:00
abstract::The nuclear receptor vitamin D receptor (VDR) is known to associate with two vitamin D response element (VDRE) containing chromatin regions of the insulin-like growth factor binding protein 3 (IGFBP3) gene. In non-malignant MCF-10A human mammary cells, we show that the natural VDR ligand 1α,25-dihydroxyvitamin D(3) (1...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq820
更新日期:2011-01-01 00:00:00