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At least 523 records · Page 29Linked to original sources
PubMed1991

Drosophila topoisomerase II-DNA interactions are affected by DNA structure.

The binding of purified Drosophila topoisomerase II to the highly bent DNA segments from the SV40 terminus of replication and C. fasciculata kinetoplast minicircle DNA (kDNA) was examined using electron microscopy (EM). The probability of finding topoisomerase II positioned at or near the bent SV40 terminus and Crithidia fasciculata kDNA was two- and threefold higher, respectively, than along the unbent pBR325 DNA into which the elements had been cloned. Closer examination demonstrated that the enzyme bound preferentially to the junction between the bent and non-bent sequences. Using gel electrophoresis, a cluster of strong sodium dodecyl sulfate-induced topoisomerase II cleavage sites was mapped to the SV40 terminus DNA, and two weak cleavage sites to the C. fasciculata kDNA. As determined by EM, Drosophila topoisomerase II foreshortened the apparent length of DNA by only 15 base-pairs when bound, arguing that it does not wrap DNA around itself. When bound to pBR325 containing the C. fasciculata kDNA and the SV40 terminus, topoisomerase II often produced DNA loops. The size distribution was that predicted from the known probability of any two points along linear DNA colliding. In vitro mapping of topoisomerase II on DNA whose ends were blocked by avidin protein revealed that binding is enhanced at sites located near a blocked end as compared to a free end. These observations may contribute towards establishing a framework for understanding topoisomerase II-DNA interactions.

Animals↗
PubMed1992

DNA associations: packing calculations in A-, B-, and Z-DNA structures.

A detailed theoretical study has been carried out to examine the modes of DNA-DNA interactions on the basis of hard-sphere contact criteria. Two helices of identical structure and length are oriented side-by-side and their relative positions are controlled by translations along and rotations about specific axes. Short atomic contacts between pairs of atoms in the structures are assessed and contact-free configurations are compiled. The computed contact-free arrangements of A, B, and Z double helices are found to be remarkably similar to the packing motifs observed in DNA crystals and stretched fibers. Equally interesting in the study are the broad ranges of sterically acceptable arrangements that preserve the overall packing morphology of neighboring duplexes: Among the most notable morphological features in the helical complexes are extended "super" major and minor grooves which might facilitate the wrapping and packaging of DNA chains in supramolecular assemblies. The hard-sphere computations, however, are insufficient for quantitative interpretation of the packing of DNA helices in the solid state. The results are, nevertheless, a useful starting point for energy based studies as well as relevant to the analysis of long-range interactions in DNA supercoils and cruciforms.

DNA↗
PubMed2005

More than just strand breaks: the recognition of structural DNA discontinuities by DNA-dependent protein kinase catalytic subunit.

The DNA-dependent protein kinase (DNA-PK) is a trimeric factor originally identified as an enzyme that becomes activated upon incubation with DNA. Genetic defects in either the catalytic subunit (DNA-PK(CS)) or the two Ku components of DNA-PK result in immunodeficiency, radiosensitivity, and premature aging. This combined phenotype is generally attributed to the requirement for DNA-PK in the repair of DNA double strand breaks during various biological processes. However, recent studies revealed that DNA-PK(CS), a member of the growing family of phosphatidylinositol 3-kinases, participates in signal transduction cascades related to apoptotic cell death, telomere maintenance and other pathways of genome surveillance. These manifold functions of DNA-PK(CS) have been associated with an increasing number of protein interaction partners and phosphorylation targets. Here we review the DNA binding properties of DNA-PK(CS) and highlight its ability to interact with an astounding diversity of nucleic acid substrates. This survey indicates that the large catalytic subunit of DNA-PK functions as a sensor of not only broken DNA molecules, but of a wider spectrum of aberrant, unusual, or specialized structures that interrupt the standard double helical conformation of DNA.

Catalytic Domain↗
PubMed2003

AFM studies of DNA structures on mica in the presence of alkaline earth metal ions.

As counterions of DNA on mica, Mg(2+), Ca(2+), Sr(2+) and Ba(2+) were used for clarifying whether DNA molecules equilibrate or are trapped on mica surface. End to end distance and contour lengths were determined from statistical analysis of AFM data. It was revealed that DNA molecules can equilibrate on mica when Mg(2+), Ca(2+) and Sr(2+) are counterions. When Ba(2+) is present, significantly crossovered DNA molecules indicate that it is most difficult for DNA to equilibrate on mica and the trapping degree is different under different preparation conditions. In the presence of ethanol, using AFM we have also observed the dependence of B-A conformational transition on counterion identities. The four alkaline earth metal ions cause the B-A transition in different degrees, in which Sr(2+) induces the greatest structural transition.

Adsorption↗
PubMed1985

Regularities in formation of the spine of hydration in the DNA minor groove and its influence on the DNA structure.

Computer calculations as well as an analysis of space-filling models and literature data allowed the following conclusions to be made: an ordered spine of water in the DNA minor groove, similar to that revealed in the CGCGAATTCGCG crystal, seems to exist in DNA crystals, fibers and solutions; it is shown that this spine may be formed on A/T runs containing no TA step while on the TA step the spine is disrupted; the existence of this spine changes the double helix structure stabilizing a definite DNA conformation; the spine of hydration makes the DNA more stable to conformational transitions. These conclusions permit us to interpret a large body of experimental data on DNA crystals, fibers and solutions. The role of water bridges constituting the first hydration shell of the ordered spine of water is discussed in connection with the B-to-A transition.

Base Composition↗
PubMed1969

Probes of DNA structure and interactions. Effects of copper II on ultraviolet-induced pyrimidine dimer formation.

Cu(II) affects the yield of cyclobutyl dimers induced in DNA by 254 nm radiation. The effects are a function of r, the ratio of Cu(II) to DNA phosphate, and of the ultraviolet (UV) fluence; they seem to reflect two types of copper complexes with DNA. The first probably involves "exterior" binding to the bases of native DNA and increases [unk]TT formation (without affecting [unk]UT yield) by raising the energy levels of bases other than thymine. The second seems to occur only at high ratios (rs) and only after the structure has been opened locally by UV radiation; it involves "interior" binding of Cu(II) to the bases. This complex tends to decrease dimer yield by holding the bases apart and/or by lowering the energy levels of bases other than thymine. These results illustrate the potential use of DNA photoproducts and ligands to probe the structure and interactions of DNA in vitro and perhaps also in vivo.

Carbon Isotopes↗
PubMed1999

Thermodynamic basis of the enhanced specificity of structured DNA probes.

Molecular beacons are DNA probes that form a stem-and-loop structure and possess an internally quenched fluorophore. When they bind to complementary nucleic acids, they undergo a conformational transition that switches on their fluorescence. These probes recognize their targets with higher specificity than probes that cannot form a hairpin stem, and they easily discriminate targets that differ from one another by only a single nucleotide. Our results show that molecular beacons can exist in three different states: bound to a target, free in the form of a hairpin structure, and free in the form of a random coil. Thermodynamic analysis of the transitions between these states reveals that enhanced specificity is a general feature of conformationally constrained probes.

Base Sequence↗
PubMed2006

Synthesis, crystal structure, DNA binding and photo-induced DNA cleavage activity of (S-methyl-L-cysteine)copper(II) complexes of heterocyclic bases.

Ternary S-methyl-L-cysteine (SMe-l-cys) copper(II) complexes [Cu(SMe-L-cys)(B)(H(2)O)](X) (1-4), where the heterocyclic base B is 2,2'-bipyridine (bpy, 1), 1,10-phenanthroline (phen, 2), dipyridoquinoxaline (dpq, 3) and dipyridophenazine (dppz, 4), and X is ClO(4)(-) (1-3) or NO(3)(-) (4), are prepared and their DNA binding and cleavage properties studied. Complexes 2 and 4 are structurally characterized by X-ray crystallography. Both the crystal structures show distorted square-pyramidal (4+1) CuN(3)O(2) coordination geometry of the complexes in which the N,O-donor S-methyl-L-cysteine and N,N-donor heterocyclic base bind at the basal plane with a water molecule as the axial ligand. In addition, the dppz structure shows the presence of a 1D-chain formed due to covalent linkage of the carboxylate oxygen atom belonging to another molecule at the elongated axial site. The crystal structures show chemically significant non-covalent interactions like hydrogen bonding involving the axial aqua ligand and pi-pi interactions between dppz ligands. The complexes display a d-d band in the range of 605-654 nm in aqueous dimethylformamide (DMF) solution (9:1 v/v). The redox active complexes show quasireversible cyclic voltammetric response near 0.1 V in DMF assignable to the Cu(II)/Cu(I) couple. The complexes show good binding affinity to calf thymus (CT) DNA giving the order: 4 (dppz)>3 (dpq)>2 (phen)>>1 (bpy). The intrinsic binding constants, obtained from UV-visible spectroscopic studies, are 1.3x10(4) and 2.15 x 10(4) M(-1) for 3 and 4, respectively. Control DNA cleavage experiments using pUC19 supercoiled (SC) DNA and minor groove binder distamycin suggest major groove binding propensity for the dppz complex, while the phen and dpq complexes bind at the minor groove of DNA. Complexes 2-4 show DNA cleavage activity in dark in the presence of a reducing agent 3-mercaptopropionic acid (MPA) via a mechanistic pathway involving formation of hydroxyl radical as the reactive species. The complexes also show efficient photo-induced DNA cleavage activity on irradiation with a monochromatic UV light of 365 nm in absence of any external reagent. The cleavage efficiency follows the order: 3>4>2. The complexes exhibit significant DNA cleavage activity on irradiation with visible light of 633 nm. Control experiments show inhibition of cleavage in presence of singlet oxygen quenchers like sodium azide, histidine and enhancement of cleavage in D(2)O, suggesting formation of singlet oxygen as a reactive species in a type-II process. The photosensitizing effect of the thiomethyl group of the amino acid is evidenced from the observation of significant DNA photocleavage activity of the phen complex 2 as the phen ligand itself is not a photosensitizer.

Animals↗
PubMed2005

DNA structural similarity in the 2:1 complexes of the antitumor drugs trabectedin (Yondelis) and chromomycin A3 with an oligonucleotide sequence containing two adjacent TGG binding sites on opposing strands.

Yondelis (trabectedin) is an antitumor ecteinascidin that binds covalently to the 2-amino group of the central guanine in the minor groove of selected DNA pyrimidine-G-G and purine-G-C triplets. Chromomycin A3 is an aureolic acid derivative that binds noncovalently to the DNA minor groove in G/C-rich triplet sites as a metal-chelated dimer. Despite their different binding modes, the cytotoxicity profiles of these two drugs, as assessed in the COMPARE analysis carried out by the National Cancer Institute on data from 60 human tumor cell lines, are highly correlated (Pearson's correlation coefficient of 0.96). We now report that in an oligonucleotide containing the "natural bending element" TGGCCA, the structural distortions inflicted by the tail-to-tail bonding of two trabectedin molecules to adjacent target sites on opposing strands are strikingly similar to those observed in a crystal containing d(TTGGCCAA)2 and two bound chromomycin A3 molecules arranged in a head-to-tail orientation in the minor groove. In both complexes, the double helix is characterized by being considerably unwound and possessing a notably widened minor groove. Binding of the drugs to this sequence could be favored by the distinct bends at each of the TpG steps that are already present in the free oligonucleotide. Simultaneous drug binding to the two strands in the manner described here is proposed to stabilize the helical structure of duplex DNA to prevent or hamper strand separation and stall replication and transcription forks.

Antineoplastic Agents↗
PubMed1988

DNA structural alterations in the SV40 enhancer region are retained in vivo.

Psoralen accessibility in the SV40 regulatory region has been analyzed in vivo on viral minichromosomes and extracellular virus particles using a psoralen mapping technique which we have recently described. This approach takes advantage of the fact that lambda exonuclease digestion of double-stranded DNA is inhibited by the presence of 5-methylisopsoralen monoadducts. Previous analysis of purified restriction fragments from this region irradiated in vitro revealed a region of psoralen hypersensitivity which encompassed the repeated 72-base-pair (bp) enhancers and sequences 150 bp upstream toward the late region. The studies reported here demonstrate that changes in the structure of the DNA helix due to supercoiling do not affect the pattern of psoralen accessibility in this region. Additionally, no significant difference in the precise pattern of the psoralen hypersensitive domain is observed between late nucleoprotein complexes and extracellular virus. Finally, virus particles that have been through a freeze-thaw cycle, a process which we have shown eliminates the preferential photoaddition of the regulatory region in chromatin, also exhibit the same pattern of psoralen hypersensitivity.

DNA, Viral↗
PubMed1992

Chromatin structure, DNA methylation, and gene expression at sites of viral integration in human fibroblasts. Implications for chromosomal fragility.

We analyzed the structural and functional properties of a chromosomal region in which a recombinant hybrid virus adenovirus 5/SV40 preferentially integrates. Our results demonstrated that the structure of the cellular targets for DNA and RNA viruses is very similar and that the cellular sequence flanking the integrated virus possesses, simultaneously, all the features postulated to be the molecular basis for chromosomal fragility.

Adenoviridae↗
PubMed2000

Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal.

Protein-directed reorganization of DNA underlies mechanisms of transcription, replication, and recombination. A molecular model for DNA reorganization in the regulation of gene expression is provided by the sequence-specific high-mobility-group (HMG) box. Structures of HMG-box complexes with DNA are characterized by expansion of the minor groove, sharp bending toward the major groove, and local unwinding of the double helix. The Raman vibrational signature of such DNA reorganization has been identified in a study of the SRY HMG box, encoded by the human male-determining region of the Y chromosome. We observe in the human SRY-HMG:DNA complex extraordinarily large perturbations to Raman bands associated with vibrational modes of the DNA backbone and accompanying large increases in intensities of Raman bands attributable to base unstacking. In contrast, DNA major-groove binding, as occurs for the bZIP protein GCN4 [Benevides, J. M., Li, T., Lu, X.-J., Srinivasan, A. R., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochemistry 39, 548-556], perturbs the Raman signature of DNA only marginally. Raman markers of minor-groove recognition in the human SRY-HMG:DNA complex are due primarily to perturbation of specific vibrational modes of deoxyribose moieties and presumably reflect desolvation at the nonpolar interface of protein and DNA. These Raman markers may be diagnostic of protein-induced DNA bending and are proposed as a baseline for comparative analysis of mutations in SRY that cause human sex reversal.

Amino Acid Sequence↗
PubMed1988

Detection of intercalation-induced changes in DNA structure by reaction with diethyl pyrocarbonate or potassium permanganate. Evidence against the induction of Hoogsteen base pairing by echinomycin.

Binding of the bis-intercalators echinomycin and N,N'-di(9-acridinyl)spermidine or the mono-intercalators 9-aminoacridine and ethidium to DNA induces hypersensitivity of adenines towards reaction with diethyl pyrocarbonate. It is proposed that this hyperreactivity is due to the DNA helix unwinding and extension induced by intercalation, thereby exposing N7 in the major groove, and not as previously suggested to the formation of Hoogsteen base pairing. Hypersensitivity of thymines towards oxidation with permanganate is also induced upon binding of these drugs (especially the bis-intercalators) to DNA. This thymine hyperreactivity is both sequence- and intercalator-dependent, thereby indicating the potential of KMnO4 as a useful probe for analyzing the structure of intercalator-DNA complexes in solution.

Base Composition↗