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PubMed1994

The maize chromosomal HMGa protein recognizes structural features of DNA and increases DNA flexibility.

The abundant maize high-mobility group protein HMGa belongs to the chromosomal, non-histone proteins and consists of a basic region containing the HMG-box DNA-binding domain and a highly acidic carboxy-terminal tail. The full-length HMGa protein and a truncated version lacking the acidic tail were synthesized in Escherichia coli and tested for their ability to induce DNA-bending in a ligase mediated circularization assay with short DNA fragments. It is shown that the recombinant HMGa protein as well as its truncated form efficiently cause circularization of the tested DNA fragments without an obvious requirement for stable DNA-binding. They bind furthermore preferentially to A/T-rich linear DNA or bent DNA structures such as four-way junctions and DNA minicircles. The DNA-binding properties and the ability to increase DNA flexibility suggest a general role of the HMGa protein in assisting the formation of nucleoprotein complexes, possibly by facilitating interactions of proteins bound to adjacent DNA sites.

Base Sequence↗

PubMed2002

Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy.

We report here the direct evidence for the formation of alternative DNA structures in a plasmid DNA, termed pTIR10, containing a 0.23-kb pyrimidine/purine-biased (Pyr/Pur) stretch isolated from the rat genome. Long Pyr/Pur sequences are abundant in eukaryotic genomes, and they may modulate the biological activity of genes and genomes via formation of various types of triplex-related structures. The plasmid DNA in sodium acetate buffer (pH 4.35) was deposited on APS-modified mica, and after drying it was imaged with an atomic force microscope in air. Various types of thick protrusions have been observed on pTIR10 DNA. Structural parameters (width and height) of DNA molecules suggest that the alternative structures observed here are variations on the theme of an intramolecular triplex. The biological relevance of the structural features within Pyr/Pur stretches is discussed.

DNA↗

PubMedDate not supplied

[Characteristics of the structural state of DNA in chromatin with short linker].

Various fragments of pigeon brain neuron chromatin with very short linker DNA have been studied by circular dichroism (CD). The DNA structure in core particles of the brain and thymus chromatins is very similar. Linker DNA and a part of core DNA in the mononucleosomes of brain chromatin is extended. This conclusion follows from increasing CD amplitude of the brain mononucleosomes as compared with the corresponding value for thymus mononucleosomes. The internucleosome interactions stabilized the compactness of core DNA in the brain oligonucleosomes. The whole linker DNA of the brain chromatin unlike thymus chromatin is extended at low ionic strength. This fact can explain the brain chromatin ability to form a compact structure with increasing ionic strength.

Animals↗

PubMed1995

Coherent potential approximation approach to electronic structure of DNA.

The electronic structure of DNA is theoretically investigated by use of the coherent potential approximation. Even when the sequence of the four kinds of bases is nonperiodic, guanine block forms the persistent highest valence band edge, and adenine block forms the persistent lowest conduction band edge state. According to the calculated joint density-of-states energy profiles, the site first attacked by the lowest excitation is adenine block. After this excitation, electrons are generated at adenine sites, and holes are generated at guanine sites. The resulting electronic structures of the valence band and conduction band suggest that the base complementarity in DNA produces the complementarity in the density-of-states divergences of the excited electrons and holes. This complementarity lowers the excitation instability in the DNA chains.

DNA↗

PubMedDate not supplied

[Mechanism of the radiation effect at the level of the supramolecular structures of eukaryotic DNA].

The methods of viscosimetry and light scattering were used to study the radiosensitivity of the supramolecular DNA (SM DNA) structure in vivo. Irreversible lesions were found in SM DNA 2 min after gamma-irradiation of rats with a dose of 10 Gy. They were associated with the damage to the RNA-lipoprotein component (a linker) and with the dissociation of SM DNA to fragments of different molecular weight, that is, 109 +/- 25 X 10(6), 51 +/- 15 X 10(6), and 47 +/- 21 X 10(6) D for liver, spleen, and thymus, respectively, which correlated with the radiosensitivity of these organs.

Animals↗

PubMed2006

Non-B DNA structure-induced genetic instability.

Repetitive DNA sequences are abundant in eukaryotic genomes, and many of these sequences have the potential to adopt non-B DNA conformations. Genes harboring non-B DNA structure-forming sequences increase the risk of genetic instability and thus are associated with human diseases. In this review, we discuss putative mechanisms responsible for genetic instability events occurring at these non-B DNA structures, with a focus on hairpins, left-handed Z-DNA, and intramolecular triplexes or H-DNA. Slippage and misalignment are the most common events leading to DNA structure-induced mutagenesis. However, a number of other mechanisms of genetic instability have been proposed based on the finding that these structures not only induce expansions and deletions, but can also induce DNA strand breaks and rearrangements. The available data implicate a variety of proteins, such as mismatch repair proteins, nucleotide excision repair proteins, topoisomerases, and structure specific-nucleases in the processing of these mutagenic DNA structures. The potential mechanisms of genetic instability induced by these structures and their contribution to human diseases are discussed.

Base Sequence↗

PubMed1977

Studies on a defective variant of simian virus 40 that is substituted with DNA sequences derived from monkey. II. Structure of DNA.

The structure of a substituted, reiterated defective variant of the simian virus 40 genome has been analyzed. The DNA of the defective variant is a closed circular duplex resistant to restriction endonuclease R-EcoRI and slightly shorter than the genome of wild type simian virus 40. Analysis of the double-stranded DNA segments produced by the action of a variety of restriction endonucleases on the defective genome allow description of the molecule as follows. (a) The full DNA molecule contains four tandem repeats of a DNA segment containing both SV40 and monkey DNA sequences. (b) Three out of the four segments are identical and are about 23% of the wild type genome in length: one segment of the four is larger and contains an additional peice of DNA about 4.3% of a wild type genome in length, but is otherwise identical with the other three segments. (c) Portions of the defective variant that contain monkey DNA can be isolated as discrete segments by restriction endonuclease digestion. (d) Some of the sequences originating from monkey DNA are derived from the highly reiterated class of monkey DNA sequences; others may represent sequences derived from infrequently reiterated or single copy monkey sequences.

Animals↗

PubMed1998

Structure of a DNA base-excision product resembling a cisplatin inter-strand adduct.

Base-excision of a self-complementary oligonucleotide with central G:T mismatches by the G:T/U-specific mismatch DNA glycosylase (MUG), generates an unusual DNA structure which is remarkably similar in conformation to an interstrand DNA adduct of the anti-tumor drug cis-diamminedichloroplatinum. The abasic sugars generated by excision of the mismatched thymines are extruded from the double-helix, and the 'widowed' deoxyguanosines rotate so that their N7 and O6 groups protrude into the minor groove of the duplex and restack in an interleaved intercalative geometry, generating a kink in the helix axis.

Bacterial Proteins↗

PubMed1980

HMG proteins (1 + 2) form beaded structures when complexed with closed circular DNA.

Structures bearing a resemblance to nucleosomes can be assembled by incubating calf thymus High Mobility Group proteins (1 + 2) with closed circular DNA. These HMG proteins are capable of forming beads and inducing superhelicity when bound to DNA. However, they do not protect from nuclease digestion the discrete DNA fragments characteristic of nucleosomes. The relationship between HMGs (1 + 2) and the "primitive" histone-like DNA-packaging proteins from prokaryotes and mitochondria is discussed.

Animals↗

PubMed2003

Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential.

Oxidative damage to DNA generates 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG). During DNA replication and repair synthesis, 8-oxodG can pair with cytosine or adenine. The ability to accurately replicate through this lesion depends on the DNA polymerase. We report the first structure of a polymerase with a promutagenic DNA lesion, 8-oxodG, in the confines of its active site. The modified guanine residue is in an anti conformation and forms Watson-Crick hydrogen bonds with an incoming dCTP. To accommodate the oxygen at C8, the 5'-phosphate backbone of the templating nucleotide flips 180 degrees. Thus, the flexibility of the template sugar-phosphate backbone near the polymerase active site is one parameter that influences the anti-syn equilibrium of 8-oxodG. Our results provide insights into the mechanisms employed by polymerases to select the complementary dNTP.

Binding Sites↗

PubMedDate not supplied

[Structural characteristics of DNA from sarcoma 45].

It is shown that thermodynamical parameters of thermal melting and the content of 5-methylcytosine for tumor DNA of sarcoma 45 differ from DNA in the norm. The reason of such difference is the presence of regions with changed DNA structure in sarcoma 45, which occurs apparently owing to hypermethylation of cytosine in tumor DNA.

5-Methylcytosine↗

PubMed2004

Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA.

We show that intracellular transcription of G-rich regions produces novel DNA structures, visible by electron microscopy as large (150-500 bp) loops. These G-loops are formed cotranscriptionally, and they contain G4 DNA on one strand and a stable RNA/DNA hybrid on the other. G-loop formation requires a G-rich nontemplate strand and reflects the unusual stability of the rG/dC base pair. G-loops and G4 DNA form efficiently within plasmid genomes transcribed in vitro or in Escherichia coli. These results establish that G4 DNA can form in vivo, a finding with implications for stability and maintenance of all G-rich genomic regions.

Base Pairing↗

PubMed2002

Polyamine-nucleic acid interactions and the effects on structure in oriented DNA fibers.

Fibrous oriented calf thymus DNA containing the natural polyamines spermidine (Spd) and putrescine (Put), and the degradation polyamines cadaverine (Cad) and 1,3-diaminopropane (DAP), have been investigated at different water contents using nuclear magnetic resonance (NMR) methods, fiber X-ray diffraction and gravimetric measurements. When judged by X-ray only the DAP and Spd samples seem to undergo a B-A-form transition at reduced water activity. Solid-state two-dimensional rotor-synchronized magic angle spinning (2D-syncMAS) 31P-NMR, however, shows the A-form to be present also in the Put sample, and it appears that the separation between the amine units of diamines is correlated with the amount of A-form present. In addition, the solid-state NMR data show the polyamine-bound DNA samples to have a significant deviation from the ordinary B-form DNA structure, displaying similar amounts of BI and BII nucleotide conformations. The low water content of the samples suggest that the polyamines themselves act as hydrators of DNA. Water 2H-NMR results are in agreement with this observation. The quadrupolar splittings of the polyamine 2H signals for samples at low water content indicate some preferential spatial orientations of the polyamines in the ordered DNA environment. The polyamines show relatively fast macroscopic diffusion as detected by NMR self-diffusion measurements.

Animals↗

PubMed1979

Structure models for DNA in filamentous viruses with phosphates near the center.

DNA structure models deduced from X-ray and physicochemical data for Pfl, Xf, and fd viruses have two antiparallel chains wound in helices of approximately 15 A pitch with the phosphates near the structure axes and the bases directed outward. The models, which differ for each virus, are used to interpret ultraviolet absorbance and fluorescence data in terms of DNA protein interactions.

DNA, Viral↗

PubMed2005

Pre-organized structure of viral DNA at the binding-processing site of HIV-1 integrase.

The integration of the human immunodeficiency virus type 1 DNA into the host cell genome is catalysed by the viral integrase (IN). The reaction consists of a 3'-processing [dinucleotide released from each 3' end of the viral long terminal repeat (LTR)] followed by a strand transfer (insertion of the viral genome into the human chromosome). A 17 base pair oligonucleotide d(GGAAAATCTCTAGCAGT), d(ACTGCTAGAGATTTTCC) reproducing the U5-LTR extremity of viral DNA that contains the IN attachment site was analysed by NMR using the classical NOEs and scalar coupling constants in conjunction with a small set of residual dipolar coupling constants (RDCs) measured at the 13C/15N natural abundance. The combination of these two types of parameters in calculations significantly improved the DNA structure determination. The well-known features of A-tracts were clearly identified by RDCs in the first part of the molecule. The binding/cleavage site at the viral DNA end is distinguishable by a loss of regular base stacking and a distorted minor groove that can aid its specific recognition by IN.

Binding Sites↗

PubMed2002

Structural analysis of hemicatenated DNA loops.

BACKGROUND: We have previously isolated a stable alternative DNA structure, which was formed in vitro by reassociation of the strands of DNA fragments containing a 62 bp tract of the CA-microsatellite poly(CA).poly(TG). In the model which was proposed for this structure the double helix is folded into a loop, the base of the loop consists of a DNA junction in which one of the strands of one duplex passes between the two strands of the other duplex, forming a DNA hemicatenane in a hemiknot structure. The hemiknot DNA structures obtained with long CA/TG inserts have been imaged by AFM allowing us to directly visualize the loops. RESULTS: Here we have analyzed this structure with several different techniques: high-resolution gel electrophoresis, probing by digestion with single stranded DNA-specific nucleases or with DNase I, modification with chemicals specific for unpaired bases, and atomic force microscopy. The data show a change in DNA structure localized to the CA/TG sequence and allow us to better understand the structure of this alternative conformation and the mechanism of its formation. CONCLUSIONS: The present work is in good agreement with the model of hemicatenated DNA loop proposed previously. In the presence of protein HMGB1, shifted reassociation of the strands of DNA fragments containing a tract of the poly(CA).poly(TG) microsatellite leads to the formation of DNA loops maintained at their base by a hemicatenated junction located within the repetitive sequence. No mobility of the junction along the DNA molecule could be detected under the conditions used. The novel possibility to prepare DNA hemicatenanes should be useful to further study this alternative DNA structure and its involvement in replication or recombination.

DNA, Catenated↗

PubMed2002

Effect of tetrahydrocortisol-apolipoprotein A-I complex on the secondary structure of eukaryotic DNA and its interaction with RNA-polymerase.

The in vitro effect of tetrahydrocortisol-apolipoprotein A-I complex on native adult rat liver DNA results in the formation of S1 nuclease sensitive fragments that are irregularly distributed throughout a genome. Low-angle X-ray scattering showed that after the interaction with the tetrahydrocortisol-apolipoprotein A-I complex, DNA can bind to RNA-polymerase with a high and dose-dependent cooperativity. This indicates that the effect of tetrahydrocortisol-apolipoprotein A-I complex on secondary eukaryotic DNA structure causes a local denaturation of the double helix, promoting high cooperativity of binding to RNA-polymerase. The reduced form of the hormone, tetrahydrocortisol, previously considered as an inactive metabolite, when complexed with apolipoprotein A-I, promotes a biological function similar to that of a transcription factor.

Animals↗

PubMed1988

Multiple DNA secondary structures in perfect inverted repeat inserts in plasmids. Right-handed B-DNA, cruciforms, and left-handed Z-DNA.

The capabilities of five recombinant plasmids, containing relatively long (approximately 60-100 base pairs) perfect inverted repeat (IR) inserts, to support supercoil stabilized non-B-DNA structures were studied in vitro. The IRs were also alternating purine-pyrimidine sequences, thus, each could form either left-handed Z-DNA or cruciforms. Single-strand specific endonucleases, restriction endonucleases and methylases, and OsO4 modifications were used to characterize the DNA structures. Two-dimensional gel electrophoretic studies indicated that three of the five IRs formed both cruciforms and Z-DNA. (C-G) containing inserts preferred to form Z-DNA, whereas (T-G) sequences favored cruciforms. In vivo supercoil relaxation experiments demonstrated the existence of cruciforms in Escherichia coli. The physiological significance of these structures is discussed.

Base Sequence↗