Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “DNA structure”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources
PubMedDate not supplied

[Genotoxic and radioprotective properties of 2,5-diphenyloxazole and its derivatives on mice DNA structure in vivo].

The effects of 2,5-diphenyloxazole ad its derivatives suggested as nontraditional radioprotectors on mice spleen DNA structure were studied. The effects of these compounds were studied on intraperitoneal injection with and without subsequent X-ray exposure of mice to a dose of 12 cGy. The formation of double-strand breaks and DNA conformation change (by adsorption on NC filters) were recorded. A genotoxic effect of 2,5-diphenyloxazole and its derivatives, a nonlinearity of their dose-response relationships and different effects depending on the substance concentration were found. Some of the compounds exhibited radioprotective properties in certain concentration.

Animals↗
PubMed2003

Raman microspectroscopic study of effects of Na(I) and Mg(II) ions on low pH induced DNA structural changes.

In this work a confocal Raman microspectrometer is used to investigate the influence of Na(+) and Mg(2+) ions on the DNA structural changes induced by low pH. Measurements are carried out on calf thymus DNA at neutral pH (7) and pH 3 in the presence of low and high concentrations of Na(+) and Mg(2+) ions, respectively. It is found that low concentrations of Na(+) ions do not protect DNA against binding of H(+). High concentrations of monovalent ions can prevent protonation of the DNA double helix. Our Raman spectra show that low concentrations of Mg(2+) ions partly protect DNA against protonation of cytosine (line at 1262 cm(-1)) but do not protect adenine and guanine N(7) against binding of H(+) (characteristic lines at 1304 and 1488 cm(-1), respectively). High concentrations of Mg(2+) can prevent protonation of cytosine and protonation of adenine (disruption of AT pairs). By analyzing the line at 1488 cm(-1), which obtains most of its intensity from a guanine vibration, high magnesium salt protect the N(7) of guanine against protonation. A high salt concentration can prevent protonation of guanine, cytosine, and adenine in DNA. Higher salt concentrations cause less DNA protonation than lower salt concentrations. Magnesium ions are found to be more effective in protecting DNA against binding of H(+) as compared with calcium ions presented in a previous study. Divalent metal cations (Mg(2+), Ca(2+)) are more effective in protecting DNA against protonation than monovalent ions (Na(+)).

Animals↗
PubMed1989

A self-consistent formulation for analysis and generation of non-uniform DNA structures.

A fully self-consistent formulation is described here for the analysis and generation of base-pairs in non-uniform DNA structures, in terms of various local parameters. It is shown that the internal "wedge parameters" are mathematically related to the parameters describing the base-pair orientation with respect to an external helix axis. Hence any one set of three translation and three rotation parameters are necessary and sufficient to completely describe the relative orientation of the base-pairs comprising a step (or doublet). A general procedure is outlined for obtaining an average or global helix axis from the local helix axes for each step. A graphical representation of the local helix axes in the form of a polar plot is also shown and its application for estimating the curvature of oligonucleotide structures is illustrated, with examples of both A and B type structures.

Algorithms↗
PubMed1988

Insertion sequence IS5 contains a sharply curved DNA structure at its terminus.

It was demonstrated that insertion sequence IS5 contains a sequence-directed bent (sharply curved) DNA structure at its terminus, close to one of its 16 bp terminal repeats. The minimal number of copies of IS5 related sequences and the locations of the latter on the Escherichia coli K12 W3110 chromosome were determined. Evidence is presented of the occurrence of IS5 mediated translocation and duplication of a large DNA segment on the E. coli chromosome.

Bacteriophage lambda↗
PubMed1995

DNA structural reorganization upon conversion of a psoralen furan-side monoadduct to an interstrand cross-link: implications for DNA repair.

We have used 1H NMR spectroscopy to determine the structural changes induced in the DNA oligomer d(5'-GCGTACGC-3')2 upon conversion of the 4'-hydroxy-methyl-4,5',8-trimethylpsoralen-DNA furan-side monoadduct (MAf) to the interstrand cross-link (XL). The MAf is a photochemical intermediate on the path to interstrand XL and has the psoralen intercalated into the helix. The local DNA structure is distorted in both adducts, but it returns to normal within three base pairs. The formation of XL requires displacement of the psoralen toward the initially unmodified strand, accompanied by a change in the hybridization of the thymine C-5 and C-6 carbons and a change in the local helix twist. The MAf is intercalated in the helix. There is no significant bend in the helix axis of either the MAf or XL. There are significant changes in the local helix dynamics upon photoadduct formation that may be recognized by cellular DNA repair enzyme systems. We hypothesize that the repair enzymes target lesions by detecting the conformational flexibility of the sugar-phosphate backbone induced by DNA-damaging agents.

Base Sequence↗
PubMed2006

Human RECQ5beta helicase promotes strand exchange on synthetic DNA structures resembling a stalled replication fork.

The role of the human RECQ5beta helicase in the maintenance of genomic stability remains elusive. Here we show that RECQ5beta promotes strand exchange between arms of synthetic forked DNA structures resembling a stalled replication fork in a reaction dependent on ATP hydrolysis. BLM and WRN can also promote strand exchange on these structures. However, in the presence of human replication protein A (hRPA), the action of these RecQ-type helicases is strongly biased towards unwinding of the parental duplex, an effect not seen with RECQ5beta. A domain within the non-conserved portion of RECQ5beta is identified as being important for its ability to unwind the lagging-strand arm and to promote strand exchange on hRPA-coated forked structures. We also show that RECQ5beta associates with DNA replication factories in S phase nuclei and persists at the sites of stalled replication forks after exposure of cells to UV irradiation. Moreover, RECQ5beta is found to physically interact with the polymerase processivity factor proliferating cell nuclear antigen in vitro and in vivo. Collectively, these findings suggest that RECQ5beta may promote regression of stalled replication forks to facilitate the bypass of replication-blocking lesions by template-switching. Loss of such activity could explain the elevated level of mitotic crossovers observed in RECQ5beta-deficient cells.

Adenosine Triphosphatases↗
PubMed1994

DNA structural patterns and nucleosome positioning.

There is no clear picture to date of the mechanisms determining nucleosome positioning. Generally, local DNA sequence signals (sequence-dependent positioning) or non-local signals (e.g. boundary effects) are possible. We have analyzed the DNA sequences of a series of positioned and mapped nucleosome cores in a systematic search for local sequence signals. The data set consists of 113 mapped nucleosome cores, mapped in vivo, in situ, or in reconstituted chromatin. The analysis focuses on the periodic distribution of sequence elements implied by each of six different published DNA structural models. We have also investigated the periodic distribution of all mono-, di-, and trinucleotides. An identical analysis was performed on a set of isolated chicken nucleosome cores (nucleosome data from the literature) that are presumably positioned due to local sequence signals. The results show that the sequences of the isolated nucleosome cores have a number of characteristic features that distinguish them clearly from randomly chosen reference DNA. This confirms that the positioning of these nucleosomes is mainly sequence-dependent (i.e., dependent on local octamer-DNA interactions) and that our algorithms are able to detect these patterns. Using the same algorithms, the sequences of the mapped nucleosome cores, however, are on average very similar to randomly chosen reference DNA. This suggests that the position of the majority of these nucleosomes can not be attributed to the sequence patterns implemented in our algorithms. The arrangement of positioned nucleosomes seems to be the result of a dynamic interplay of octamer-DNA interactions, nucleosome-nucleosome interactions and other positioning signals with varying relative contributions along the DNA.

Algorithms↗
PubMed1987

Use of site-specific recombination as a probe of DNA structure and metabolism in vivo.

We used site-specific recombination catalyzed by the bacteriophage lambda Int system to probe DNA structure and metabolism in vivo. In vitro, the complexity of catenated products was linearly proportional to substrate supercoil density. A system was developed that gave efficient, controlled Int recombination in Escherichia coli cells. From a comparison of the data obtained in vitro and in vivo, we conclude that Int recombination does have the same mechanism in vivo as it has in vitro, but that only 40% of the plasmid DNA linking deficit in E. coli cells may be in the interwound supercoil form demonstrated in vitro. We suggest that this is the effective level of supercoiling in vivo, because the remaining DNA is constrained in alternative forms by protein binding. The study of Int recombination in vivo also provides an assay for enzymes that decatenate circular molecules, such as those formed during DNA replication. We find that DNA gyrase is the principal decatenase in E. coli and that it acts spontaneously and rapidly.

Attachment Sites, Microbiological↗
PubMedDate not supplied

[Occurrence of DNA structures which differ from the canonic B-form in sites of highly specific interaction with chromatin proteins].

According to the three-dimensional structure of DNase I and the mechanism of its action on linear double-stranded DNA, helix regions in conformations considerably different from the canonical B-form should be resistant to endonucleolysis. A number of DNA sequences specifically bound by nonhistone factors within 5'-flanking regions of the chicken beta A-globin, beta H-globin and c-myc genes are shown to contain short DNase I-resistant DNA domains. Several examples of the occurrence of such DNase I-resistant domains within the sites for high-specific recognition by different proteins are given. The role of the DNA structural polymorphism in site-specific interaction with protein factors is discussed.

Animals↗
PubMed2002

Effects of DNA structure on oxopropenylation by the endogenous mutagens malondialdehyde and base propenal.

Malondialdehyde (MDA) and nucleobase propenals can transfer oxopropenyl groups to guanine residues of DNA to yield pyrimodopurinone (M(1)G) adducts. The DNA structural requirements for reaction with alpha,beta-unsaturated aldehydes were explored. We found that single-stranded DNA is more sensitive to oxopropenylation than double-stranded DNA, and supercoiled plasmid DNA is more sensitive than linearized plasmid DNA. Increasing ionic strength inhibits oxopropenylation, especially by adenine propenal. The intercalating agents ethidium bromide and 9-aminoacridine enhanced oxopropenylation by severalfold. In contrast, actinomycin D, which both intercalates and binds in the minor groove, inhibited oxopropenylation. The anthracycline drugs daunorubicin and doxorubicin enhanced oxopropenylation by MDA up to 3-fold and by adenine propenal up to 7-fold in a concentration-dependent manner. The minor groove binders netropsin and distamycin inhibited oxopropenylation, but methyl green, a major groove binder, had little effect. These data suggest that steric access to the target nucleophile located in the minor groove of DNA is critical for adduct formation by the endogenous mutagens MDA and base propenals.

Acrolein↗
PubMed2004

Position- and orientation-specific enhancement of topoisomerase I cleavage complexes by triplex DNA structures.

Topoisomerase I (Top1) activities are sensitive to various endogenous base modifications, and anticancer drugs including the natural alkaloid camptothecin. Here, we show that triple helix-forming oligonucleotides (TFOs) can enhance Top1-mediated DNA cleavage by affecting either or both the nicking and the closing activities of Top1 depending on the position and the orientation of the triplex DNA structure relative to the Top1 site. TFO binding 1 bp downstream from the Top1 site enhances cleavage by inhibiting religation and to a lesser extent DNA nicking. In contrast, TFO binding 4 bp downstream from the Top1 site enhances DNA nicking especially when the 3' end of the TFO is proximal to the Top1 site. However, when the orientation of the triplex is inverted, with its 5' terminus 4 bp downstream from the Top1 site, religation is also inhibited. These position- and orientation-dependent effects of triplex structures on the Top1-mediated DNA cleavage and religation are discussed in the context of molecular modeling and effects of TFO on DNA twist and mobility at the duplex/triplex junction.

Base Sequence↗
PubMed1993

Abolition of intrinsically bent DNA structure components in AT clusters by netropsin interaction; titration viscometric investigations.

It is argued that the enhancement of the apparent DNA contour length by the specifically binding non-intercalating drug netropsin (Nt) (Reinert et al., NAR 9, 2335, 1981) at very low Nt/DNA-phosphate ratios essentially is the result of an abolition of periodically arranged intrinsic helix bends in A.T rich tracts of base pairs. In the preceding paper the existence of pronounced DNA tertiary structure components has been postulated for (two species of) natural eukaryotic DNA. The resulting model suggests local apparent solenoid-related DNA tertiary structure components at high sodium ion concentration cs, partly/totally molten out at 45/60 C. With decreasing cs the tertiary structure components have been found to be gradually reduced, at least below cs = 0.010 M, as titration viscometrically revealed by a gradual rise of the apparent DNA contour length (Reinert et al., JBSD 9, 537, 1991). Hence, we performed titration viscometric analyses about Nt interaction with calf thymus DNA (ctDNA) at cs = 0.075 M, 0.010 M and 0.004 M Na+. The concomitant DNA conformational changes are quantitatively described in terms of the relative changes of both DNA persistence length and hydrodynamically operative apparent DNA contour length for the three first resolved interaction modes below a Nt/DNA-P ratio of 0.03. These experiments, together with previous respective analyses at cs = 0.20 M Na+ and different temperatures (l.c.), suggest that those DNA sites binding Nt most strongly predominantly are responsible for the formation of solenoid-related DNA tertiary structure components. Most probably these are A tract-containing sequences. As the essential factor for their apparent elongation effect at low Na+ concentrations, a gradual alteration of the number of base pairs per helix turn seems to occur below cs = 0.010 M Na+ and, concomitantly, a change in phasing between intrinsic helix bends and helix screw.

Adenine↗
PubMed1987

Monoclonal antibodies to cruciform DNA structures.

Two monoclonal antibodies, 2D3 and 4B4, have been raised against a cruciform structure in a heteroduplex DNA molecule. Antibody binding to DNA fragments was determined by a radioimmunoassay in which DNA--antibody complexes were separated from unbound DNA by acrylamide gel electrophoresis. These antibodies seem to recognize conformational determinants specific to cruciform structures. 2D3 and 4B4 antibodies do not bind to linear double-stranded homoduplex DNA fragments, linear single-stranded DNA or single-stranded simian virus 40 DNA containing a stem--loop structure, but do bind to the original cruciform and to a different cruciform with one shortened arm. 2D3 also bound to a T-shaped double-stranded DNA molecule, while 4B4 binding to this structure was weak. The monoclonal antibodies 2D3 and 4B4 were found to be immunoglobulin G1 and immunoglobulin M, respectively.

Animals↗
PubMed2005

Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo.

Telomere end-binding proteins (TEBPs) bind to the guanine-rich overhang (G-overhang) of telomeres. Although the DNA binding properties of TEBPs have been investigated in vitro, little is known about their functions in vivo. Here we use RNA interference to explore in vivo functions of two ciliate TEBPs, TEBPalpha and TEBPbeta. Silencing the expression of genes encoding both TEBPs shows that they cooperate to control the formation of an antiparallel guanine quadruplex (G-quadruplex) DNA structure at telomeres in vivo. This function seems to depend on the role of TEBPalpha in attaching telomeres in the nucleus and in recruiting TEBPbeta to these sites. In vitro DNA binding and footprinting studies confirm the in vivo observations and highlight the role of the C terminus of TEBPbeta in G-quadruplex formation. We have also found that G-quadruplex formation in vivo is regulated by the cell cycle-dependent phosphorylation of TEBPbeta.

Animals↗
PubMed2000

Influence of DNA structure on hypoxanthine and 1,N(6)-ethenoadenine removal by murine 3-methyladenine DNA glycosylase.

3-Methyladenine DNA glycosylases initiate base excision repair by flipping the nucleotide bearing the target base out of double-stranded DNA into an active site pocket for glycosylic bond cleavage and base release. Substrate bases for the murine 3-methyladenine DNA glycosylase (other than 3-methyladenine) include hypoxanthine and 1,N(6)-ethenoadenine, two mutagenic adducts formed by both endogenous and exogenous agents. Using double-stranded DNA oligonucleotides containing damaged bases at specific sites, we studied the relative removal rates for these two adducts when located in different sequence contexts. One of the sequence contexts was an A:T tract, chosen because DNA secondary structure is known to change along the length of this tract, due to a progressive narrowing of the minor groove. Here we report that removal rates for hypoxanthine, but not for 1,N(6)-ethenoadenine, are dramatically affected by its location within the A:T tract. In addition, the removal rates of hypoxanthine and 1,N(6)-ethenoadenine when paired opposite thymine or cytosine were examined, and in each sequence context hypoxanthine removal decreased by at least 20-fold when paired opposite cytosine versus thymine. In contrast, 1, N(6)-ethenoadenine removal was unaffected by the identity of the opposing pyrimidine. We conclude that the removal of certain bases by the mouse 3-methyladenine DNA glycosylase can be modulated by both adjacent and opposing sequence contexts. The influence of DNA sequence context upon DNA repair rates, such as those described here, may contribute to the creation of mutational hot spots in mammalian cells.

Adenine↗
PubMed1984

Supercoil-dependent features of DNA structure at Drosophila locus 67B1.

We have analyzed the pattern of supercoil-dependent, single strand-specific nuclease cleavage sites across 11.6 kb (11.6 X 10(3) base-pairs) of cloned Drosophila melanogaster DNA from locus 67B1. This region contains coding sequences for the heat shock proteins hsp23, hsp26 and hsp28 as well as for a 1.6 kb developmentally regulated transcript (R). Two major sites are detected on digestion with S1 nuclease or mung bean nuclease. The most prominent site maps 100 base-pairs upstream of hsp26 in a very pyrimidine-rich region adjacent to a known region of chromatin DNAase I hypersensitivity. The other site is located approximately 800 base-pairs upstream of hsp28 in an area devoid of such chromatin-specific features. BAL31 nuclease produces a different array, with three to six strong cleavages located in the spacer DNA approx. 0.1 to 1.0 kb upstream of the DNAase I hypersensitive sites of hsp28, hsp23 and R. Thus, for each gene in the cluster a localized sequence sensitive to the winding state of the DNA is observed 5' to the gene. However, there is no precise coincidence of any of the major sites sensitive to BAL31 nuclease in the supercoiled plasmid with the sequences sensitive to DNAase I in chromatin. While all of the enzymes utilized in this study have prominent single strand-specific endonucleolytic activity, it is clear that they recognize different variants in the DNA structure induced by supercoiling. At least two classes of DNA perturbation have been detected.

Animals↗
PubMed2000

15N-enriched 5-fluorocytosine as a probe for examining unusual DNA structures.

A new method is presented for the synthesis of oligonucleotides containing 15N-enriched 5-fluorocytosine (FC). Due to the reduced pK of FC, the amino protons of an unpaired FC residue may be observed at lower values of solution pH. The labeled FC residue has been placed as a template base at a model DNA replication fork. The amino protons of the FC residue have been identified in isotope-edited NMR spectra. Data is presented for a template FC residue unpaired, paired with guanine, and mispaired with adenine. These studies demonstrate the utility of labeled FC in examining unusual DNA structures.

DNA↗