Abstract:
:Large-scale cooperative helix opening has been previously observed in A + T rich sequences contained in supercoiled DNA molecules at elevated temperatures. Since it is well known that helix melting of linear DNA is suppressed by addition of salt, we have investigated the effects of added salts on opening transitions in negatively supercoiled DNA circles. We have found that localised large-scale stable melting in supercoiled DNA is strongly suppressed by modest elevation of salt concentration, in the range 10 to 30 mM sodium. This has been shown in a number of independent ways: 1. The temperature required to promote cruciform extrusion by the pathway that proceeds via the coordinate large-scale opening of an A + T rich region surrounding the inverted repeat (the C-type pathway, first observed in the extrusion of the ColE1 inverted repeat) is elevated by addition of salt. The temperature required for extrusion was increased by about 4 deg for an addition of 10 mM NaCl. 2. A + T rich regions in supercoiled DNA exhibit hyperreactivity towards osmium tetroxide as the temperature is raised; this reactivity is strongly suppressed by the addition of salt. At low salt concentrations of added NaCl (10 mM) we observe that there is an approximate equivalence between reducing the salt concentration, and the elevation of temperature. Above 30 mM NaCl the reactivity of the ColE1 sequences is completely supressed at normal temperatures. 3. Stable helix opening transitions in A + T rich sequences may be observed with elevated temperature, using two-dimensional gel electrophoresis; these transitions become progressively harder to demonstrate with the addition of salt. With the addition of low concentrations of salt, the onset of opening transitions shifts to higher superhelix density, and by 30 mM NaCl or more, no transitions are visible up to a temperature of 50 degrees C. Statistical mechanical simulation of the data indicate that the cooperativity free energy for the transition is unaltered by addition of salt, but that the free energy cost for opening each basepair is increased. These results demonstrate that addition of even relatively low concentrations of salt strongly suppress the large-scale helix opening of A + T rich regions, even at high levels of negative supercoiling. While the opening at low salt concentrations may reveal a propensity for such transitions, spontaneous opening is very unlikely under physiological conditions of salt, temperature and superhelicity, and we conclude that proteins will therefore be required to facilitate opening transitions in cellular DNA.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bowater RP,Aboul-ela F,Lilley DMdoi
10.1093/nar/22.11.2042subject
Has Abstractpub_date
1994-06-11 00:00:00pages
2042-50issue
11eissn
0305-1048issn
1362-4962journal_volume
22pub_type
杂志文章abstract::The effect of [Na+] on the stability and conformation of penicillium chrysogenum mycophage dsRNA (PCMdsRNA) was investigated using CD and UV optical techniques. Thermal melting profiles reveal prominent fine structure attributed to at least four regions of structural dissimilarity. A constant increased thermal stabili...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.6.759
更新日期:1975-06-01 00:00:00
abstract::The nematode Caenorhabditis elegans contains a small family of vitellogenin genes which is expressed abundantly, but only in the intestine of the adult hermaphrodite worm. In order to identify possible regulatory elements, we have sequenced the DNA surrounding the 5' ends of five of the six genes. Contained within reg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.14.5283
更新日期:1985-07-25 00:00:00
abstract::Bacteria core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Promoters recognized by the sigma(54) (or sigma(N)) associated RNA polymerase are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site. Using DNA microarra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1123
更新日期:2010-03-01 00:00:00
abstract::The nucleotide sequence of the promoter region and the first five genes of the atp (or unc) operon of Escherichia coli has been determined. The first proposed gene in the operon contains four AUA codons and may be poorly expressed; it encodes a basic but yet hydrophobic protein which could function as a pilot protein ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.16.3919
更新日期:1981-08-25 00:00:00
abstract::Endonucleases that generate double-strand breaks in DNA often possess two identical subunits related by rotational symmetry, arranged so that the active sites from each subunit act on opposite DNA strands. In contrast to many endonucleases, Type IIP restriction enzyme BcnI, which recognizes the pseudopalindromic seque...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr588
更新日期:2011-11-01 00:00:00
abstract::The active and inactive state of transcription factors in growing cells is usually directed by allosteric physicochemical signals or metabolites, which are in turn either produced in the cell or obtained from the environment by the activity of the products of effector genes. To understand the regulatory dynamics and t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm743
更新日期:2007-01-01 00:00:00
abstract::Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv469
更新日期:2015-06-23 00:00:00
abstract::Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting so...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx389
更新日期:2017-07-03 00:00:00
abstract::Cisplatin analogues were synthesised that consisted of platinum(II) diamine complexes tethered via a polymethylene chain ( n = 3, 5, 8 and 10) to a phenanthridinium cation. Both chloro and iodo leaving groups were examined. DNA adduct formation was quantitatively analysed using a linear amplification system with the p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.17.3933
更新日期:1998-09-01 00:00:00
abstract::Transcription of 5S RNA gene in Xenopus oocytes requires a 38 kDa transcription factor TFIIIA, which interacts with the 50 bp internal control region of the gene. We looked for TFIIIA-like polypeptides in the extracts of adult Xenopus tissues on the basis of their antigenic cross-reactivity to anti-TFIIIA antibody. Se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.14.5597
更新日期:1989-07-25 00:00:00
abstract::A multivariate statistical method called correspondence analysis was used to examine the codon usage of one-hundred-and-one nuclear genes of maize (Zea mays L.). Forty percent of the variation in codon usage was due to bias toward G or C-ending versus A or U-ending codons. Differences in levels of G-ending codons show...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.23.5294
更新日期:1993-11-25 00:00:00
abstract::We describe a cell-free chromatin assembly system derived from the yeast Saccharomyces cerevisiae, which efficiently packages DNA into minichromosomes in a reaction dependent on exogenous core histones and an ATP-regenerating system. Both supercoiled and relaxed plasmid DNA serve as templates for nucleosomal loading i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh107
更新日期:2004-07-28 00:00:00
abstract::Identification of MHC-binding peptides is a prerequisite in rational design of T-cell based peptide vaccines. During the past decade a number of computational approaches have been introduced for the prediction of MHC-binding peptides, efficiently reducing the number of candidate binders that need to be experimentally ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl284
更新日期:2006-07-01 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
pub_type: 杂志文章
doi:10.1093/nar/9.19.4879
更新日期:1981-10-10 00:00:00
abstract::DNA polymerase delta (Pol δ) is responsible for the elongation and maturation of Okazaki fragments in eukaryotic cells. Proliferating cell nuclear antigen (PCNA) recruits Pol δ to the DNA and serves as a processivity factor. Here, we show that PCNA also stimulates the catalytic rate of Saccharomyces cerevisiae Pol δ b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1321
更新日期:2019-02-28 00:00:00
abstract::The Transcription Regulatory Regions Database (TRRD) is a curated database designed for accumulation of experimental data on extended regulatory regions of eukaryotic genes, the regulatory elements they contain, i.e., transcription factor binding sites, promoters, enhancers, silencers, etc., and expression patterns of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.303
更新日期:1999-01-01 00:00:00
abstract::We developed an integrated method to identify aptamers with only 10 fixed nucleotides through ligation and removal of primer binding sites within the systematic evolution of ligands by exponential enrichment (SELEX) process. This Tailored-SELEX approach was validated by identifying a Spiegelmer ('mirror-image aptamer'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng130
更新日期:2003-11-01 00:00:00
abstract::Yeast co-expressing rat APOBEC-1 and a fragment of human apolipoprotein B (apoB) mRNA assembled functional editosomes and deaminated C6666 to U in a mooring sequence-dependent fashion. The occurrence of APOBEC-1-complementing proteins suggested a naturally occurring mRNA editing mechanism in yeast. Previously, a hidde...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.8.1772
更新日期:2001-04-15 00:00:00
abstract::Polyadenylation is a co-transcriptional process that modifies mRNA 3'-ends in eukaryotes. In yeast, CF IA and CPF constitute the core 3'-end maturation complex. CF IA comprises Rna14p, Rna15p, Pcf11p and Clp1p. CF IA interacts with the C-terminal domain of RNA Pol II largest subunit via Pcf11p which links pre-mRNA 3'-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr800
更新日期:2012-02-01 00:00:00
abstract::Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2723
更新日期:1998-06-01 00:00:00
abstract::The covalent attachment of thiol-modified DNA oligomers; to self-assembled monolayer silane films on fused silica and oxidized silicon substrates is described. A heterobifunctional crosslinking molecule bearing both thiol- and amino-reactive moieties was used to tether a DNA oligomer (modified at its terminus with a t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.15.3031
更新日期:1996-08-01 00:00:00
abstract::Point mutations in mitochondrial tRNA genes are responsible for individual subgroups of mitochondrial encephalomyopathies. We have recently reported that point mutations in the tRNA(Leu)(UUR) and tRNA(Lys) genes cause a defect in the normal modification at the first nucleotide of the anticodon. As part of a systematic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.19.3779
更新日期:2000-10-01 00:00:00
abstract::Fundamental aspects of the biochemistry of Type III restriction endonucleases remain unresolved despite being characterized by numerous research groups in the past decades. One such feature is the subunit stoichiometry of these hetero-oligomeric enzyme complexes, which has important implications for the reaction mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku122
更新日期:2014-04-01 00:00:00
abstract::The reactivities of the two cysteine thiol groups of calf thymus F3 histone were investigated using 5,5'-dithiobis-[2- nitrobenzoic acid], (DTNB). In isolated histone, both thiol groups were available for reaction. However, analysis of reaction profiles of native deoxyribonucleohistone, (DNH), in various solvent condi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.2.203
更新日期:1974-02-01 00:00:00
abstract::Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an addi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr054
更新日期:2011-06-01 00:00:00
abstract::We have determined the nucleotide sequence at the 3' end of the vesicular stomatitis virus (VSV) polymerase or L gene and compared it to that obtained from a defective interfering particle (DI) RNA generated by this virus. The latter (DI 0.50) contains a large internal deletion within this gene. The deletion begins ex...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.21.6919
更新日期:1982-11-11 00:00:00
abstract::Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the fi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj454
更新日期:2006-01-31 00:00:00
abstract::Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose dependent equal inhibition of the synthesis of rRNA, 5.8S, 5S and tRNA. Similar results were obtained with 3-carbethoxy-8-methox...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.3.921
更新日期:1987-02-11 00:00:00
abstract::Loading of the replicative ring helicase onto the origin of replication (oriC) is the final outcome of a well coordinated series of events that collectively constitute a primosomal cascade. Once the ring helicase is loaded, it recruits the primase and signals the switch to the polymerization mode. The transient nature...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh628
更新日期:2004-06-01 00:00:00
abstract::Triethylammonium uridine-3',5'-cyclic phosphorothioate crystallizes in space group P2(1)2(1)2(1), a = 7.177(1), b = 13.155(6), c = 21.114(7) A, C15H26N3O7PS, MW 423.4, Z = 4, dx = 1.41g/cm3. The crystal structure was solved by direct methods on the basis of 1493 counter X-ray diffraction data (CuK alpha) and refined t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.12.4945
更新日期:1987-06-25 00:00:00