Abstract:
:An investigation of the mobility of short duplexes of DNA -octamers and decamers-on polyacrylamide gels is presented, showing that molecules containing less than one helical turn exhibit sequence dependent mobilities. Analysis of chains with different sequences indicates that any arrangement of two or more adjacent A.T base pairs causes a duplex to move more slowly than does any combination of isolated A.T pairs This behavior appears to be an intrinsic property of these sequences, since the anomaly persists in the absence of magnesium or presence of spermine and is not due to strand dissociation. In two decamers we studied, the position of A.T tracts within a duplex can be shown to influence mobility: the sequence GA4T4C associated with bending or curvature of the helix axis when ligated into polymers migrates more slowly than the corresponding sequence GT4A4C, polymers of which migrate as linear B DNA.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chen JH,Seeman NC,Kallenbach NRdoi
10.1093/nar/16.14.6803subject
Has Abstractpub_date
1988-07-25 00:00:00pages
6803-12issue
14Beissn
0305-1048issn
1362-4962journal_volume
16pub_type
杂志文章abstract::The specific recognition of homopurine-homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Alkylation of nucleobases with functionalized TFOs would have the potential for site-directed mutagenesis. Recently, we demonstrated that a T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng031
更新日期:2003-03-15 00:00:00
abstract::The nucleotide sequence of the celD gene, encoding the previously crystallized endoglucanase D of Clostridium thermocellum, is reported. The enzyme shares a conserved, reiterated domain with the COOH-terminal end of endoglucanases A and B from the same organism. The overexpression in Escherichia coli of celD subcloned...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.21.8605
更新日期:1986-11-11 00:00:00
abstract::Among a collection of 74 aprt mutations induced by treatment of plateau phase Chinese hamster ovary CHO cells with the radiomimetic DNA double-strand cleaving agent neocarzinostatin, nine were large-scale rearrangements. Molecular analysis indicated that all nine were highly conservative, non-homologous reciprocal exc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf369
更新日期:2002-06-15 00:00:00
abstract::Communication between distantly spaced genomic regions is one of the key features of gene regulation in eukaryotes. Chromatin per se can stimulate efficient enhancer-promoter communication (EPC); however, the role of chromatin structure and dynamics in this process remains poorly understood. Here we show that nucleoso...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1240
更新日期:2017-04-07 00:00:00
abstract::Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn470
更新日期:2008-09-01 00:00:00
abstract::The eukaryotic mismatch repair protein Msh6 shares five domains in common with other MutS members. However, it also contains several hundred additional residues at its N-terminus. A few of these residues bind to PCNA, but the functions of the other amino acids in the N-terminal region (NTR) are unknown. Here we demons...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm409
更新日期:2007-01-01 00:00:00
abstract::In this study, we demonstrate that the lack of retinoic acid-related orphan receptor (ROR) γ or α expression in mice significantly reduced the peak expression level of Cry1, Bmal1, E4bp4, Rev-Erbα and Per2 in an ROR isotype- and tissue-selective manner without affecting the phase of their rhythmic expression. Analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks630
更新日期:2012-09-01 00:00:00
abstract::We examined the mechanism regulating the cellular levels of PNKP, the major kinase/phosphatase involved in the repair of oxidative DNA damage, and find that it is controlled by ATM phosphorylation and ubiquitylation-dependent proteasomal degradation. We discovered that ATM-dependent phosphorylation of PNKP at serines ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks909
更新日期:2012-12-01 00:00:00
abstract::Glucocorticoid (GC) signaling synchronizes the circadian rhythm of individual peripheral cells and induces the expression of circadian genes, including Period1 (Per1) and Period2 (Per2). However, no GC response element (GRE) has been reported in the Per2 promoter region. Here we report the molecular mechanisms of Per2...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt307
更新日期:2013-07-01 00:00:00
abstract::Gel migration and uranyl photoprobing have been used to study the effects of inosine and 2,6-diaminopurine (2,6-DAP) substitution on adenine-tract (A-tract) induced DNA curvature. Using a 10mer repeated sequence including five inosines we show by uranyl photoprobing that a narrow minor groove varying in phase with the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.17.3497
更新日期:1997-09-01 00:00:00
abstract::The ability of Deinococcus radiodurans to recover from extensive DNA damage is due in part to its ability to efficiently repair its genome, even following severe fragmentation by hundreds of double-strand breaks. The single-strand annealing pathway plays an important role early during the recovery process, making use ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt759
更新日期:2013-11-01 00:00:00
abstract::In vitro enzymatic amplification of nucleic acids by PCR or other techniques is a very sensitive method to detect rare DNA segments. We present here a protocol that allows the rapid, sensitive and precise quantification of DNA molecules using PCR amplification run to saturation. The DNA (or cDNA) to be assayed is co-a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.3.577
更新日期:1993-02-11 00:00:00
abstract::The mini-exon, a short segment found at the 5' end of trypanosome mRNAs, is contributed by a small RNA, the mini-exon donor (medRNA). In vivo 32P-labeled medRNA, a set of smaller RNAs related to it, and mRNA, were purified from Trypanosoma brucei by hybrid selection and gel electrophoresis. Using RNA fingerprinting an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.23.9861
更新日期:1987-12-10 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::In Escherichia coli transcription of individual genes generally requires concomitant translation, and thus the decay of mRNAs cannot be studied without the complication of translation. Here we have used T7 RNA polymerase to transcribe in vivo lacZ genes carrying ribosome binding sites of variable efficiency. We show t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.19.5787
更新日期:1990-10-11 00:00:00
abstract::Genetic screens in Saccharomyces cerevisiae have identified the roles of ribosome components, tRNAs and translation factors in translational fidelity. These screens rely on the suppression of altered start codons, nonsense codons or frameshift mutations in genes involved in amino acid or nucleotide metabolism. Many of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki765
更新日期:2005-08-12 00:00:00
abstract::Treatment of cells with DNA damaging agents leads to induction of a variety of genes involved in different cellular processes. We have applied a lacZ-based gene trap strategy to search for new mammalian genes induced by genotoxic stress. A population of 32 x 10(3) neo r clones stably transfected with a gene trap vecto...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.23.4803
更新日期:1997-12-01 00:00:00
abstract::A highly polymorphic locus associated with the variable tandem repetition of a 35 bp consensus sequence was mapped to chromosome 10, band q26. Examination of leukocyte DNA from a cancer patient revealed the twenty-fold amplification of one allelic fragment of this locus, while the other allelic fragment demonstrated a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.20.7929
更新日期:1986-10-24 00:00:00
abstract::The sequential arrangement of histones along DNA in nucleosome core particles was determined between 0.5 and 600 mM salt and from 0 to 8 M urea. These concentrations of salt and urea up to 6 M had no significant effect on the linear order of histones along DNA but 8 M urea caused the rearrangement of histones. Conform...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.5.1053
更新日期:1981-03-11 00:00:00
abstract::Topoisomerase II, purified from chicken erythrocytes, was reacted with a large number of different DNA fragments and cleavages were catalogued in the presence and absence of drugs that stabilize the cleavage intermediate. Cleavages were sequenced to derive a consensus for topoisomerase II that predicts catalytic sites...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.12.5533
更新日期:1988-06-24 00:00:00
abstract::The secondary structure of an adenovirus associated low molecular weight RNA (VAI-RNA) has been studied by partial digestion with T1-RNase and S1-endonuclease followed by T1-fingerprint analysis. The empirical secondary structure has been compared with two computer generated models based on minimal free energy of the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.17.4239
更新日期:1981-09-11 00:00:00
abstract::We have developed general methods for joining together, via cleavable disulfide bonds, either two unprotected polynucleotides or a polynucleotide and a peptide or protein. To join two oligonucleotides, each is first converted to an adduct in which cystamine is joined to the 5'-terminal phosphate of the oligonucleotide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.9.3671
更新日期:1988-05-11 00:00:00
abstract::Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr903
更新日期:2012-02-01 00:00:00
abstract::Primer extension studies have shown that the Y-family DNA polymerase IV (Dpo4) from Sulfolobus solfataricus P2 can preferentially insert C opposite N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) [F. Boudsocq, S. Iwai, F. Hanaoka and R. Woodgate (2001) Nucleic Acids Res., 29, 4607-4616]. Our goal is to elucidate...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj479
更新日期:2006-02-01 00:00:00
abstract::Transcription factor IIIA (TFIIIA) is specifically required for transcription of 5S rRNA genes and is the archetypal C2H2 zinc finger protein. All known vertebrate TFIIIAs have a similar organization: nine zinc fingers, followed by a C-terminal domain of unknown structure. The zinc fingers of Saccharomyces cerevisiae ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkf385
更新日期:2002-07-01 00:00:00
abstract::The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing infor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl793
更新日期:2007-01-01 00:00:00
abstract::Reverse transcription of HIV-1 RNA is primed by a tRNA3(Lys) molecule bound at the primer binding site (PBS). Complex intermolecular interactions were proposed between tRNA3(Lys) and the RNA of the HIV-1 Mal isolate. Recently, an alternative interaction was proposed between the TPsiC stem of tRNA3(Lys) and a primer ac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg187
更新日期:2003-02-01 00:00:00
abstract::To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1273
更新日期:2014-03-01 00:00:00
abstract::The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.2.555
更新日期:1988-01-25 00:00:00
abstract::The conditions under which Drosophila melanogaster are grown markedly influence the amount of the hypermodified nucleoside Q found in certain tRNAs. This effect on Q biosynthesis was found in both the wild-type and the suppressor of sable [su(s)2] mutant. Suppressed vermilion flies [su(s)2v; bw] with 78% of the tyrosi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.11.3919
更新日期:1977-11-01 00:00:00