Abstract：
:Reactive oxygen species (ROS) have been implicated as the cause of cumulative damage to DNA, proteins and lipids that can ultimately result in cell death. A common problem when measuring oxidative DNA damage has been the introduction of modifications in the native state of the molecule by many DNA isolation methods. We circumvented this problem by employing direct PCR (DPCR) of whole cell lysates. DPCR of mouse lung fibroblasts performed better than PCRs containing template acquired by phenol/chloroform extraction or a commercially available genomic DNA isolation kit. We investigated the direct use of whole cell preparations in the polymerase chain reaction (PCR) to detect hydrogen peroxide (H(2)O(2))-mediated DNA damage. We observed a concentration-dependent decrease in amplification efficiency of a 4.3 kb mitochondrial (mt)DNA target in H(2)O(2)-treated mouse lung fibroblasts (MLFs). At low doses the efficiency of amplification returns to control levels over 24 h. We detected no change in amplification efficiency of a plasmid control containing our mtDNA target under any of the culture conditions employed in these studies. Treatment of MLFs with the catalytic antioxidant manganese(III) meso -tetrakis(4-benzoic acid)porphyrin (MnTBAP) attenuates the effects of H(2)O(2)exposure. When quantitated with an external standard the use of DPCR in tandem with a PCR amplification efficiency assay provides a powerful approach to assess oxidative mtDNA damage.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Milano J,Day BJdoi
10.1093/nar/28.4.968keywords:
subject
Has Abstractpub_date
2000-02-15 00:00:00pages
968-73issue
4eissn
0305-1048issn
1362-4962pii
gkd189journal_volume
28pub_type
杂志文章abstract：:Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins. While over the years, a large number of DNA and RNA binding proteins have been identified and extensively studied, it is still expected that many other proteins, some with y...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw454
更新日期：2016-07-08 00:00:00
abstract：:WebProAnalyst is a web-accessible analysis tool (http://wwwmgs.bionet.nsc.ru/mgs/programs/panalyst/) designed for scanning quantitative structure-activity relationships in protein families. The tool allows users to search correlations between protein activity and physicochemical characteristics (i.e. hydrophobicity or...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki421
更新日期：2005-07-01 00:00:00
abstract：:Cells internalized synthetic oligonucleotides (oligos) in culture. The hybridization of these molecules to target RNA in the living cell was subsequently detected and characterized after fixation of the cells, with or without previous detergent extraction. Hybridized oligo was distinguished from free oligo in the cell...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.24.4946
更新日期：1995-12-25 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：:We describe a method for the formation of hybrid genes by in vivo recombination between two genes with partial sequence homology. DNA structures consisting of plasmid vector sequences, flanked by the alpha 2 interferon gene on the one side and a portion of the alpha 1 interferon gene (homology about 80%) on the other,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.16.5661
更新日期：1983-08-25 00:00:00
abstract：:Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit to their host. They encode site-specific DNA endonucleases that perpetuate the element within a species population by homing and disseminate it between species by horizontal transfer. Several yeast species contain the VMA1 H...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh734
更新日期：2004-07-27 00:00:00
abstract：:Several derivatives of N2,N2-7-trimethylguanosine (m3(2,2,7G)-cap, which was found at the 5' ends of small nuclear RNAs, were synthesized by use of S-phenyl N2,N2,7-trimethylguanosine 5'-phosphorothioate (PhSpm3(2,2,7)G) as a key intermediate. This compound was activated by iodine in the presence of phosphoric acid an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.22.8979
更新日期：1989-11-25 00:00:00
abstract：:Little is known about the regulation of the DNA damage-mediated gene expression in archaea. Here we report that the addition of actinomycin D to Sulfolobus solfataricus cultures triggers the expression of the radA paralogue sso0777. Furthermore, a specific retarded band is observed when electrophoretic mobility shift ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm782
更新日期：2007-01-01 00:00:00
abstract：:Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. During tissue differentiation the level of MBNLs increases, while their functional insufficiency plays a crucial role in myotonic dystrophy (DM). Deep sequencing of RNA molecules cross-linked to immunoprecipitated protein particles (CLIP-seq) revealed...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1158
更新日期：2017-02-28 00:00:00
abstract：:This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transiti...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/15.23.9985
更新日期：1987-12-10 00:00:00
abstract：:The advent of RNA-sequencing and microarray technologies has led to rapid growth of transcriptome data generated for a wide range of organisms, under various cellular, organ and individual conditions. Since the number of possible combinations of intercellular and extracellular conditions is almost unlimited, catalogin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1155
更新日期：2019-01-08 00:00:00
abstract：:Positive control of the wild-type Klebsiella pneumoniae nifH promoter by the NifA protein requires that NifA is bound at the upstream activator sequence (UAS). By introducing base substitutions at -15 to -17 in the RNA polymerase recognition sequence of the nifH promoter, positive control by a form of NifA unable to b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.7.2597
更新日期：1989-04-11 00:00:00
abstract：:Apolipoprotein B (apoB) is a major protein component of low density and very low density lipoproteins. Because of its large size and heterogeneity, molecular studies of apoB have been difficult, and its structure and regulation remain poorly understood. We now report the identification of human apoB cDNA clones by ant...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.19.6937
更新日期：1985-10-11 00:00:00
abstract：:The dhp1+ gene of Schizosaccharomyces pombe is a homolog of Saccharomyces cerevisiae HKE1/RAT1/TAP1 gene that is involved in RNA metabolism such as RNA trafficking and RNA synthesis. dhp1+ is also related to S. cerevisiae DST2 (SEP1) that encodes a DNA strand exchange protein required for sporulation and homologous re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.3.357
更新日期：1995-02-11 00:00:00
abstract：:The Rat Genome Database (RGD, http://rgd.mcw.edu) was developed to provide a core resource for rat researchers combining genetic, genomic, pathway, phenotype and strain information with a focus on disease. RGD users are provided with access to structured and curated data from the molecular level through to the level o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn842
更新日期：2009-01-01 00:00:00
abstract：:p53 as an effector of nucleolar stress is well defined, but p53 independent mechanisms are largely unknown. Like p53, the NF-κB transcription factor plays a critical role in maintaining cellular homeostasis under stress. Many stresses that stimulate NF-κB also disrupt nucleoli. However, the link between nucleolar func...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky455
更新日期：2018-07-06 00:00:00
abstract：:Synthesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end of the gag gene performing a programmed -1 ribosomal frameshift event to enter the overlapping pol gene. In vitro studies here show that at the same shift motif HIV reverse transcriptase generates -1 and +1 indels...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx690
更新日期：2017-09-29 00:00:00
abstract：:The nature of mammalian origins of DNA replication remains controversial and this is primarily because two-dimensional gel replicon mapping techniques have identified broad zones of replication initiation whereas several other techniques, such as quantitative PCR, have disclosed more discrete sites of initiation at th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.10.2313
更新日期：1998-05-15 00:00:00
abstract：:Competition binding and UV melting studies of a DNA model system consisting of three, four or five mutually complementary oligonucleotides demonstrate that unpaired bases at the branch point stabilize three- and five-way junction loops but destabilize four-way junctions. The inclusion of unpaired nucleotides permits t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.12.2212
更新日期：1995-06-25 00:00:00
abstract：:The use of the ammonia deprotection step to introduce (15)N labels at specific exocyclic amino positions of adenine, cytosine, guanine or 2-aminopurine of oligodeoxynucleotides is described. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.15.2982
更新日期：1994-08-11 00:00:00
abstract：:The transmission of genetic information relies on Watson-Crick base pairing between nucleoside phosphates and template bases in template-primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequenc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku314
更新日期：2014-06-01 00:00:00
abstract：:The vitamin D receptor mediates the signal of 1 alpha, 25-dihydroxyvitamin D3 by binding to vitamin D responsive elements in DNA as a homodimer or as a heterodimer composed of one vitamin D receptor subunit and one retinoid X receptor subunit. We have mapped the dimerization interfaces of the vitamin D receptor that i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.4.606
更新日期：1995-02-25 00:00:00
abstract：:During mitosis the chromatin undergoes dramatic architectural changes with the halting of the transcriptional processes and evacuation of nearly all transcription associated machinery from genes and promoters. Molecular bookmarking of genes during mitosis is a mechanism of faithfully transmitting cell-specific transcr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1223
更新日期：2016-03-18 00:00:00
abstract：:OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1119
更新日期：2017-01-04 00:00:00
abstract：:Translation initiation in eukaryotes is mediated by assembly of the eIF4F complex over the m(7)GTP cap structure at the 5'-end of mRNAs. This requires an interaction between eIF4E and eIF4G, two eIF4F subunits. The Leishmania orthologs of eIF4E are structurally diverged from their higher eukaryote counterparts, since ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp190
更新日期：2009-06-01 00:00:00
abstract：:Dnmt3a and Dnmt3b are paralogous enzymes responsible for de novo DNA methylation but with distinguished biological functions. In mice, disruption of Dnmt3b but not Dnmt3a causes global DNA hypomethylation, especially in repetitive sequences, which comprise the large majority of methylated DNA in the genome. By measuri...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq456
更新日期：2010-10-01 00:00:00
abstract：:An oligodeoxyribonucleotide, d(GCTCACAAT-X-ATTGTGAGC), where X represents a hexaethylene glycol chain, was studied using circular dichroism spectroscopy. Its conformation and conformational stability were compared to those of compounds where X was replaced by four thymines and to the duplex of same sequence without lo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.21.6353
更新日期：1990-11-11 00:00:00
abstract：:A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' U...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn1064
更新日期：2009-04-01 00:00:00
abstract：:The prime mechanism by which p53 acts as a tumor suppressor is as a transcription factor regulating the expression of diverse downstream genes. The DNA-binding domain of p53 (p53DBD) interacts with defined DNA sites and is the main target for mutations in human primary tumors. Here, we show that the CWWG motif, found ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1044
更新日期：2011-03-01 00:00:00
abstract：:Protein species interacting with newly replicated DNA were analyzed using a photo cross-linking technique. Nascent DNA was labeled in vitro with [alpha-32P]dCTP and BrdUTP in SV40-infected CV-1 cells made permeable with saponin. The labeled cells were then irradiated with UV light (254 nm) and were treated extensively...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.14.4793
更新日期：1983-07-25 00:00:00
