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At least 919 records · Page 51Linked to original sources
PubMed1999

High-resolution A-DNA crystal structures of d(AGGGGCCCCT). An A-DNA model of poly(dG) x poly(dC).

A-DNA conformation is favored by guanine-rich sequences, such as (dG)n x (dC)n, or under low-humidity conditions. Earlier A-DNA crystal structures revealed some conformational variations which may be the result of sequence-dependent effects and/or crystal packing forces. Here we report the high-resolution crystal structure of d(AGGGGCCCCT) in two crystal forms (either in the P212121 or the P6122 space group) to gain insights into the conformation and dynamics of the (dG)n x (dC)n sequence. The P212121 form has been analyzed using data to 1.1 A resolution by the anisotropic temperature factor refinement procedure of the SHELX97 program. Such analysis affords us with the detailed geometric, conformational and motional property of an A-DNA structure. The backbone torsional angles fall in a narrow range, except for the alpha/gamma angles which have two distinct combinations (gauche-/gauche+ or trans/trans). An A-DNA model of poly(dG) x poly(dC) has been constructed using the conformational parameters derived from the crystal structure of the P212121 form. In the crystal structure of the P6122 space group, the central eight base pairs of the decamer adopt A-DNA conformation with the two terminal nucleotides flipped out to form base pairs with the neighboring nucleotides. Comparison of the A-DNA structure of the same sequence from two different crystal forms, reinforced the conclusion that molecules crystallized in the same space group have a more similar conformation, whereas the same molecule crystallized in different space groups has different (local) conformations.

DNA↗
PubMed1984

DNA supercoiling and its effects on the structure of DNA.

In prokaryotic organisms, there is strong evidence that the DNA is underwound or negatively supercoiled. The degree of supercoiling of intracellular DNA is less certain, and various estimates that can be made from existing data place the specific linking difference (superhelical density) of intracellular DNA in prokaryotes around -0.04. The effects of negative supercoiling on DNA structure are illustrated by the flipping of alternating C-G or T-G sequences from right-handed B-helical form to the left-handed Z-helical form. For a plasmid containing a 42 base-pair alternating C-G insert, the B-to-Z transition occurs at a specific linking difference of 0.031 in a dilute aqueous buffer; the same transition occurs at a specific linking difference of -0.041 for a plasmid containing a 42 base-pair alternating T-G insert. The probing of the structure of a particular sequence of intracellular DNA is discussed.

Base Sequence↗
PubMed2000

New insights into the structure of abasic DNA from molecular dynamics simulations.

Abasic (AP) sites constitute a common form of DNA damage, arising from the spontaneous or enzymatic breakage of the N-glycosyl bond and the loss of a nucleotide base. To examine the effects of such damage on DNA structure, especially in the vicinity of the abasic sugar, four 1.5 ns molecular dynamics simulations of double-helical DNA dodecamers with and without a single abasic (tetrahydrofuran, X) lesion in a 5'-d(CXT) context have been performed and analyzed. The results indicate that the abasic site does not maintain a hole or gap in the DNA, but instead perturbs the canonical structure and induces additional flexibility close to the abasic site. In the apurinic simulations (i.e., when a pyrimidine is opposite the AP site), the abasic sugar flipped in and out of the minor groove, and the gap was water filled, except during the occurrence of a novel non-Watson-Crick C-T base pair across the abasic site. The apyrimidinic gap was not penetrated by water until the abasic sugar flipped out and remained extrahelical. Both AP helices showed kinks of 20-30 degrees at the abasic site. The Watson-Crick hydrogen bonds are more transient throughout the DNA double helices containing an abasic site. The abasic sugar displayed an unusually broad range of sugar puckers centered around the northern pucker. The increased motion of the bases and backbone near the abasic site appear to correlate with sequence-dependent helical stability. The data indicate that abasic DNA contorts more easily and in specific ways relative to unmodified DNA, an aspect likely to be important in abasic site recognition and hydrolysis.

Apurinic Acid↗
PubMed1986

[Relation between the changes in the structure and synthesis of DNA in the cells of mouse leukemia L1210 induced by 1-methyl-1-nitrosourea and 1,3-bis(2-chloroethyl)-1-nitrosourea].

The damage of DNA structure and synthesis in murine leukemia L1210 cells upon single administration in therapeutic doses of antitumour agents of N-nitrosourea type, such as 1-methyl-1-nitrosourea (MNU) and 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) was studied. MNU and BCNU were characterized by stronger inhibitory effects on de novo DNA synthesis compared to additional pathway of DNA synthesis in leukemia L1210 cells in vivo. Centrifugation in alkaline sucrose density gradients of L1210 cell lysates has revealed persistent single-strand breaks and alkaline-labile sites in newly replicated DNA. Parental DNA structure was more stable to damaging drug effects than that of newly replicated DNA. The results are consistent with our previous data on the differences in the mechanisms of MNU and BCNU action and the absence of complete cross resistance between the drugs.

Animals↗
PubMed2005

[Evaluating the harmfulness of copper in aquatic environment by measuring the supercoiled structure change of plasmid DNA].

The interaction of cupric ions with supercoiled DNA was investigated by agarose gel electrophoresis. Experimental results indicate that cupric ions could convert DNA structure from supercoiled to relaxed forms outside the cells in distilled water medium. At the levels of 10(-3) mol/L and 10(-4) mol/L copper, supercoiled DNA was totally converted into other forms of DNA after 24 hours. At a lower cupric level of 10(-6) mol/L, 52% supercoiled DNA was converted to other forms after 24 h and the relaxed form increased by 17% at 48h. Supercoiled form of DNA relaxed and gradually disappeared with the increase of incubation period of copper ions with the plasmid DNA. Supercoiled DNA degraded into other forms more rapidly at higher copper concentration. The percentages of different forms of DNA were related to copper concentration and incubation time. These results suggested that changes in supercoiled DNA structure may provide a rapid and sensitive method to assess the harmfulness of copper in aquatic environment.

Copper↗
PubMed2000

Theoretical analysis of DNA branch migration in the presence of a slow reversible initiation step.

Branched DNA structures include several DNA regions connected by three- or four-way DNA junctions. Branched DNAs can be intermediates in DNA replication and recombination in living organisms and in sequence-specific DNA targeting in vitro. Branched DNA structures are usually metastable and irreversibly dissociate to non-branched products via a DNA strand exchange process commonly known as DNA branch migration. The key parameter in the DNA dissociation process is its characteristic time, which depends on the length of the dissociating DNA structure. Here, we predict that the presence of a slow reversible initiation step, which precedes DNA branch migration, can alter, to almost linear dependence, the "classic" quadratic dependence of the dissociation time on the length of the dissociating DNA structure. This prediction can be applied to dissociation of Y-like DNA structures and double D-loop DNA hybrids, which are DNA structures similar to replication bubbles. In addition, the slow initiation step can increase the effect of DNA sequence heterologies within the structure on its kinetic stability. Applications of our analysis for genetic manipulations with branched DNA structures are discussed.

Algorithms↗
PubMed2003

Influence of DNA aptamer structure on the specificity of binding to Taq DNA polymerase.

The secondary structure of DNA aptamer to Taq DNA polymerase was established as a hairpin. Both stem and loop structures of DNA ligand were shown to be involved in the interaction with Taq DNA polymerase. Moreover, the structure and sequence of DNA aptamer that was the most effective inhibitor of DNA polymerase activity were established. This crucial structure was evaluated as a GC-rich stem longer than 17 bp, and a loop consisting of 12 bases with strictly determined nucleotide sequence. It was demonstrated that nucleotide in position 23 counting from the 5;-end of DNA ligand was involved in direct contact with Taq DNA polymerase. The ability of optimized DNA aptamer TQ21-11 to form a complex with the enzyme was increased 5-fold in comparison to the initial aptamer.

Base Sequence↗
PubMed1994

Preexisting nuclear architecture defines the intranuclear location of herpesvirus DNA replication structures.

Herpes simplex virus DNA replication proteins localize in characteristic patterns corresponding to viral DNA replication structures in the infected cell nucleus. The intranuclear spatial organization of the HSV DNA replication structures and the factors regulating their nuclear location remain to be defined. We have used the HSV ICP8 DNA-binding protein and bromodeoxyuridine labeling as markers for sites of herpesviral DNA synthesis to examine the spatial organization of these structures within the cell nucleus. Confocal microscopy and three-dimensional computer graphics reconstruction of optical series through infected cells indicated that viral DNA replication structures extend through the interior of the cell nucleus and appear to be spatially separate from the nuclear lamina. Examination of viral DNA replication structures in infected, binucleate cells showed similar or virtually identical patterns of DNA replication structures oriented along a twofold axis of symmetry between many of the sister nuclei. These results demonstrate that HSV DNA replication structures are organized in the interior of the nucleus and that their location is defined by preexisting host cell nuclear architecture, probably the internal nuclear matrix.

Animals↗
PubMed2001

Sequence-structure relationships in DNA oligomers: a computational approach.

A collective-variable model for DNA structure is used to predict the conformation of a set of 30 octamer, decamer, and dodecamer oligomers for which high-resolution crystal structures are available. The model combines an all-atom base pair representation with an empirical backbone, emphasizing the role of base stacking in fixing sequence-dependent structure. We are able to reproduce trends in roll and twist to within 5 degrees across a large database of both A- and B-DNA oligomers. A genetic algorithm approach is used to search for global minimum structures and this is augmented by a grid search to identify local minimums. We find that the number of local minimums is highly sequence dependent, with certain sequences having a set of minimums that span the entire range between canonical A- and B-DNA conformations. Although the global minimum does not always agree with the crystal structure, for 24 of the 30 oligomers, we find low-energy local minimums that match the experimental step parameters. Discrepancies throw some light on the role of crystal packing in determining the solid-state conformation of double-helical DNA.

Algorithms↗
PubMed2000

DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected].

Non-coding apurinic/apyrimidinic (AP) sites in DNA are continually created in cells both spontaneously and by damage-specific DNA glycosylases. The biologically critical human base excision repair enzyme APE1 cleaves the DNA sugar-phosphate backbone at a position 5' of AP sites to prime DNA repair synthesis. Here we report three co-crystal structures of human APE1 bound to abasic DNA which show that APE1 uses a rigid, pre-formed, positively charged surface to kink the DNA helix and engulf the AP-DNA strand. APE1 inserts loops into both the DNA major and minor grooves and binds a flipped-out AP site in a pocket that excludes DNA bases and racemized beta-anomer AP sites. Both the APE1 active-site geometry and a complex with cleaved AP-DNA and Mn2+ support a testable structure-based catalytic mechanism. Alanine substitutions of the residues that penetrate the DNA helix unexpectedly show that human APE1 is structurally optimized to retain the cleaved DNA product. These structural and mutational results show how APE1 probably displaces bound glycosylases and retains the nicked DNA product, suggesting that APE1 acts in vivo to coordinate the orderly transfer of unstable DNA damage intermediates between the excision and synthesis steps of DNA repair.

Aminopeptidases↗
PubMed1989

[An analysis of DNA secondary structure during lymphocyte activation by mitogens].

The DNA structure of human peripheral blood lymphocytes was studied following activation by concanavalin A in vitro. DNA strand breaks were measured by the fluorometric method after DNA alkaline denaturation in cell lysates. Stimulation of lymphocytes proliferation was controlled by 3H-thymidine and 3H-uridine incorporation. It was shown that 1-3 hours after the addition of mitogens the quantity of alkali-labile sites in DNA increased. Cultivation of lymphocytes in vitro without mitogens was accompanied by gradual accumulation of alkali-labile sites in DNA and in 18-72 hours the DNA structure of lymphocytes in the culture was the same. It is possible that the rapid disturbances in the DNA secondary structure of lymphocytes following activation by mitogens is determined by the transmembrane signal transduction and is the one of the early events in genome activation.

Cells, Cultured↗
PubMed2005

Topoisomerase II-DNA complexes trapped by ICRF-193 perturb chromatin structure.

DNA topoisomerase II (topo II) is involved in unlinking replicating DNA and organizing mitotic chromosomes. Topo II is the target of many antitumour drugs. Topo II inhibition results in extensive catenation of newly replicated DNA and may potentially perturb chromatin assembly. Here, we show that the topo II inhibitor ICRF-193 does not prevent the bulk of nucleosome deposition, but perturbs nucleosome spacing in Xenopus egg extracts. This is due to the trapping of topo II-closed clamps on the DNA rather than increased DNA catenation. Inhibition of replicative DNA decatenation has in itself little or no effect on nucleosome deposition and spacing, suggesting that DNA can easily accommodate the sharp bending constraints imposed by the co-habitation of nucleosomes and catenane nodes. Chromatin perturbation by topo II clamps may explain some dominant cellular effects of ICRF-193. Nucleosome-driven bending of precatenane nodes may facilitate their unlinking by topo II during unperturbed replication.

Animals↗
PubMed2005

Mutant p53 proteins bind DNA in a DNA structure-selective mode.

Despite the loss of sequence-specific DNA binding, mutant p53 (mutp53) proteins can induce or repress transcription of mutp53-specific target genes. To date, the molecular basis for transcriptional modulation by mutp53 is not understood, but increasing evidence points to the possibility that specific interactions of mutp53 with DNA play an important role. So far, the lack of a common denominator for mutp53 DNA binding, i.e. the existence of common sequence elements, has hampered further characterization of mutp53 DNA binding. Emanating from our previous discovery that DNA structure is an important determinant of wild-type p53 (wtp53) DNA binding, we analyzed the binding of various mutp53 proteins to oligonucleotides mimicking non-B DNA structures. Using various DNA-binding assays we show that mutp53 proteins bind selectively and with high affinity to non-B DNA. In contrast to sequence-specific and DNA structure-dependent binding of wtp53, mutp53 DNA binding to non-B DNA is solely dependent on the stereo-specific configuration of the DNA, and not on DNA sequence. We propose that DNA structure-selective binding of mutp53 proteins is the basis for the well-documented interaction of mutp53 with MAR elements and for transcriptional activities mediates by mutp53.

DNA↗
PubMed1989

A dual-circular plasmid structure dependent on DNA replication generated in monkey COS7 cells and cell extracts.

When monkey COS7 cells are transfected with plasmids pSVod or pSV2-neo, a DNA structure can be detected consisting of two circular forms linked by a duplex bridge. Generation of this structure is enhanced by camptothecin, an inhibitor of DNA topoisomerase I. Generation of dual-circles in vitro, using a DNA replication system with added T-antigen, requires template DNA with an SV40 origin. Heterogeneous dual-circles can be visualized involving two initially independent molecules of different size. Implications for in vitro studies of certain types of recombination are discussed.

Animals↗