DNA structure, gene expression and protein synthesis.
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DNA↗
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[Application of spin labels in studying DNA structure and function].
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DNA↗
DNA structures and radiation injury.
In the present paper experimental results from radiobiological investigations of the sedimentation behaviour of damaged and restored DNA-subunits attached to the nuclear membrane have been summarized. The studies were carried out preferably with Chinese Hamster cells V79-4 irradiated with different kinds of radiation (gamma-rays, neutrons and carbon ions) using the nucleoid sedimentation technique. Single-strand breaks relax the supercoiled DNA in the subunits resulting in a decreased sedimentation velocity. Rejoining leads to a correct restoration of the structure as can be studied by means of postincubation irradiation. Double-strand breaks release DNA fragments, again leading to an increased sedimentation velocity. If the average number of the induced double-strand breaks per subunit increases to a number higher than one, the measured results suggest that the structures should not be restored completely. The results are compatible with a new repair model developed in our laboratory on the assumption that, firstly, the single DNA subunits are the sensitive target rather than the whole DNA and, secondly, the repair of DNA damage takes place independently in each subunit.
Animals↗
DNA structure in the nucleoprotein complex that activates replication of phage phi 29.
Initiation of phage phi 29 DNA replication is activated by the viral protein p6 which forms a nucleoprotein complex at the replication origins, located at the linear genome ends. The complex consists of a DNA right-handed superhelix wrapped around a multimeric protein core. We have determined the superhelical path of the DNA in the complex, measuring the change in linking number induced by the protein, the surface-related helical repeat and the compaction of the DNA. One superhelical turn has approximately 63 bp (2.6 p6 dimers). Furthermore, we have determined that the DNA binding domain of protein p6 is located at the N-terminal region, predicted to form an amphipathic alpha-helix. We have obtained, by site-directed mutagenesis, protein p6 mutants in the polar side of the putative helix in which their DNA binding and replication activation properties were impaired or undetectable, in agreement with in vivo results.
Bacillus Phages↗
A site-targeted recombinant nuclease probe of DNA structure.
A genetically engineered lac repressor/T7 endonuclease hybrid protein shows repressor-like binding toward restriction fragments carrying the lac operator. In addition, fragments carrying the operator near a particular pBR322 sequence are cleaved into specific products. Cleavage occurs at precise positions within that sequence, is independent of the orientation of the operator, is inhibited by isopropyl-1-thio-beta-D-galactopyranoside, and is observed when the target is separated from the operator by at least as few as 150 and as many as 240 base pairs. This evidence indicates that the hybrid protein is a site-directed nuclease that requires the following two structural elements for activity: the lac operator and a target. Repressor-like binding directs the enzyme to the operator and nearby single-stranded DNA targets. The discovery of an unusual target in a well-studied DNA sequence is evidence of the power of this approach for probing unusual structures in non-supercoiled duplex DNA.
Binding, Competitive↗
NAMOT2--a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures.
Using a new set of reduced coordinates developed for describing regular and unusual nucleic acid structures, we have revised our nucleic acid modeling tool NAMOT2. NAMOT2 is general in terms of modeling different nucleic acid structures. A set of modifiable libraries allows users to customize their modeling environment. With this set of libraries, NAMOT2 can be used to model non-canonical structures such as parallel-stranded, triple-stranded and quadruple-stranded nucleic acid molecules. For modeling irregular structures (junctions, hairpin loops, etc.), we introduce a structural recipe approach. The complete procedure using NAMOT2 to construct the structure of a specific molecule is treated as the recipe for that structural motif. The existing recipes can be modified to generate new recipes for different structural motifs. Several examples of nucleic acids with non-canonical structures were modeled using NAMOT2. These examples include a DNA-drug complex, a DNA cube, a six-arm junction and a curved DNA molecule.
Base Sequence↗
A distinct intron-DNA structure in simian virus 40 T-antigen and adenovirus 2 E1A genes.
Distinct structures delineating the introns of simian virus 40 T-antigen and adenovirus 2 E1A genes have been discovered. The structures, which are centered around the branch points of the genes inserted in supercoiled double-stranded plasmids, are specifically targeted through photoactivated strand cleavage by the metal complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III). The DNA sites that are recognized lack sequence homology but are similar in demarcating functionally important sites on the RNA level. The single-stranded DNA fragment corresponding to the coding strand of the E1A gene was also found to fold into a structure apparently identical to that in the supercoiled E1A gene based on the recognition by the metal complex. Further investigation of different single-stranded DNA fragments showed that the structure requires the sequences at both ends of the intron plus the flanking sequences but not the middle of the intron. These results provide direct evidence that the positions of these introns are structurally encoded on the DNA level.
Adenovirus E1A Proteins↗
Diethyl pyrocarbonate can detect a modified DNA structure induced by the binding of quinoxaline antibiotics.
The reactivity of the 160 bp tyrT DNA fragment towards diethyl pyrocarbonate (DEPC) has been investigated in the presence of bis-intercalating quinoxaline antibiotics and the synthetic depsipeptide TANDEM. At moderate concentrations of each ligand, specific purine residues (mainly adenosines) exhibit enhanced reactivity towards the probe, and several sites of enhancement appear to be related to the sequence selectivity of drug binding. Further experiments were performed with echinomycin at pH 5.5 and 4.6 to facilitate the protonation of cytosine required for formation of Hoogsteen GC base pairs. No significant increase in reactivity was observed under these conditions. Additionally, no protection of deoxyguanosine residues from methylation by dimethyl sulphate was observed in the presence of echinomycin. We conclude that the structural anomaly giving rise to drug-dependent enhanced DEPC reaction is not simply the formation of Hoogsteen base pairs adjacent to antibiotic binding sites. Nor is it due to a general unwinding of the double helix, since we show that conditions which are supposed to unwind the helix lead to a uniform increase in purine reactivity, regardless of the surrounding nucleotide sequence.
Anti-Bacterial Agents↗
Altered dinucleotide content within the latently transcribed regions of the DNA of alpha herpes viruses--implications for latent RNA expression and DNA structure.
The alphaherpesviruses establish latent infections in sensory neuronal cells, during which a number of latency-associated RNA transcripts (LATs) are produced. The reasons for the production of the LATs, however, and the mechanism by which the LAT region of the genome remains active during latency are unknown. Here we have analysed alphaherpesvirus sequences in an attempt to assess any differences between latently active regions of the genomes and the genomes as a whole which might be necessary for this differential expression pattern or for the LAT function, whatever that might be. We show that the LAT regions of all of the four alphaerpesviruses examined exhibit a previously unidentified and marked increase in CC + GG dinucleotides within the region and that three of the four viruses examined also show a marked decrease in CG + GC dinucleotides. The CC + GG increase was shown to occur throughout the LAT regions of these viruses, but the GC + CG decrease was shown to be confined only to LATs which are thought to be expressed as introns, and also to the intron sequences of the IE1 genes (at least for herpes simplex viruses 1 and 2), which overlap the LAT region. Bovine herpesvirus, the virus which did not show the GC + CG reduction in its LAT region but did show the GG + CC increase, is thought not to express LATs by a mechanism involving splicing, again indicating that the CG + GC reduction may be an intron-related phenomenon and also further suggesting that the two effects of CG + GC decrease and GG + CC increase may be independent of one another. Possible reasons for these unusual dinucleotide frequencies within the latently active regions of the alphaherpesviruses relating to DNA and RNA structure and to LAT function are discussed.
Base Sequence↗
Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. I. Computational analysis.
The tendency for relatively short (less than 500 base-pair) DNA molecules to circularize in the presence of DNA ligase is a sensitive function of both the lateral and torsional flexibilities of the molecules being studied. This tendency is reflected in a quantity known as the j-factor, which is determined experimentally by measuring the relative rates of circle and linear dimer formation at a specified concentration of linear monomer. Shimada & Yamakawa have provided an analytical representation of j that takes account of DNA molecules whose ends are not torsionally aligned. Their approach, however, assumes that contributions from helix writhe are small. Using a Monte Carlo approach for the determination of j, thereby avoiding any assumptions regarding writhe, we demonstrate that the computed, torsion angle-averaged quantity, [j], is exactly reproduced by the corresponding Shimada & Yamakawa quantity for all lengths examined. However, for DNA molecules having lengths that are substantially greater than the persistence length, P, the analysis of experimental ring-closure data using j (Shimada & Yamakawa) may lead to underestimates for the torsional elastic constant C. We demonstrate that no single set of values for P, C and the helical repeat (hR) can produce a reasonable fit of the computed j curve to the experimental values of Shore et al. This observation suggests that P, C and/or hR vary within the set of DNA molecules studied by those authors. The current computational analysis considers the effects on j of single or multiple bends in the helix axis. For single, centrally located bends, the shift in the distribution of end-to-end separations to smaller values is nearly offset by the less favorable polar alignment of the ends of the chain; the net effect being a modest change in j that is not a monotonic function of the bend angle. In contrast, polar alignment, and hence j, can be enhanced dramatically for molecules containing multiple, phased bends. However, for studies of the distribution of circle sizes formed from ligation of bend-containing DNA oligomers, the DNA lengths giving rise to maximal j values are smaller than predicted on the basis of the number of bends and the per-bend angle. This last result suggests that such studies may yield apparent bend angles that are too large.
Chemical Phenomena↗
Chemical probes of DNA structure in chromatin.
Understanding the way genes work requires detailed knowledge of the organization of DNA in the chromatin complex. The difficulties associated with the study of this large macromolecular assembly present an interesting challenge to both biologists and chemists.
Chromatin↗
RecG helicase activity at three- and four-strand DNA structures.
The RecG helicase of Escherichia coli is necessary for efficient recombination and repair of DNA in vivo and has been shown to catalyse the unwinding of DNA junctions in vitro. Despite these findings, the precise role of RecG remains elusive. However, models have been proposed in which RecG promotes the resolution of linked duplexes by targeting three-strand junctions present at D-loops. One such model postulates that RecG catalyses the formation of four-strand (Holliday) junctions from three-strand junctions. To test this model, the DNA binding and unwinding activities of RecG were analysed using synthetic three- and four-strand junctions. The substrate specificity of RecG was found to depend critically on the concentrations of ATP and MgCl(2)and under certain conditions RecG preferentially unwound three-strand junction DNA. This was at least partly due to the larger inhibitory effect of MgCl(2)on the binding of four-strand as opposed to three-strand junctions by RecG. Thus RecG may be targeted to three-strand junctions in vivo whilst still being able to branch migrate the four-strand junctions formed as a result of the initial helicase reaction. The increase in the dissociation constant of RecG on conversion of a three-strand into a four-strand junction may also facilitate resolution of the four-strand junction by the RuvABC complex.
Adenosine Triphosphate↗
Artificial metallo-DNA: structural control and discrete metal assembly.
To array Cu2+ ions within a double-stranded DNA along the helix axis in a controllable manner, a series of artificial oligonucleotides, d(5'-GHnC-3') (n = 1-5), were synthesized, where H is a hydroxypyridone nucleobase. Right-handed double helices of the oligonucleotides, nCu2+ x d(5'-GHnC-3')2 (n = 1-5), were quantitatively formed through Cu2+-mediated metallo-base pairing (H-Cu2+-H). The Cu2+ ions incorporated into each duplex were aligned along the helix axes with the Cu2+-Cu2+ distance of 3.7 +/- 0.1 A. The unpaired d electrons of the Cu2+ ions were coupled ferromagnetically with one another to form magnetic chains.
DNA↗
[State of DNA structural alkalinity in tissue of rats of different ages].
The single-strand breaks in DNA of cell nuclei of the normal and regenerating liver and kidneys are studied depending on the rat age by the sedimentation analysis within the gradient of alkaline sucrose without previous purification and isolation of the preparations. It is found that DNA of tissues under study in the six-month rats sedimentates, forming one fraction of high-molecular DNA (molecular mass 1.3-1.5 x 10(8) Daltons). In sedimentograms of DNA of the same tissues of 24-month rats there appear additional peaks which correspond to the fractions with the low molecular mass (1.6 x 10(7) and 1.2 x 10(5) Daltons), which evidences for the presence of single-strand breaks in DNA of old animals.
Aging↗
Intercalation complex of proflavine with DNA: structure and dynamics by solid-state NMR.
The structure of the complex formed between the intercalating agent proflavine and fibrous native DNA was studied by one- and two-dimensional high-resolution solid-state nuclear magnetic resonance (NMR). Carbon-13-labeled proflavine was used to show that the drug is stacked with the aromatic ring plane perpendicular to the fiber axis and that it is essentially immobile. Natural abundance carbon-13 NMR of the DNA itself shows that proflavine binding does not change the puckering of the deoxyribose ring. However, phosphorus-31 NMR spectra show profound changes in the orientation of the phosphodiester grouping on proflavine binding, with some of the phosphodiesters tilting almost parallel to the helix axis, and a second set almost perpendicular. The first group to the phosphodiesters probably spans the intercalation sites, whereas the tilting of the second set likely compensates for the unwinding of the DNA by the intercalator.
Acridines↗
Tumor DNA structure in plant cells transformed by A. tumefaciens.
Crown gall tumors are induced in plants by infection with the soil bacterium Agrobacterium tumefaciens. Because the tumor induction involves transfer of a portion of the tumor-inducing (Ti) plasmid DNA from the bacterium to the plant cells, this system is of interest for the study of genetic exchange as well as tumor induction. The boundaries of the transferred DNA (T-DNA) have been cloned from transformed plant cells of tobacco. Detailed mapping with restriction enzymes and nucleotide sequence analysis of two independent clones were used to study the molecular structure of the ends of the T-DNA. One clone contains the two ends of the T-DNA joined together; the other contains one end of the T-DNA joined to repetitive plant DNA sequences. These studies provide direct evidence that the T-DNA can be integrated into the plant genome. In addition, the data suggest that in the plant, T-DNA can be tandemly repeated. Sequence analysis of the junction of crown gall clone 1 reveals several direct repeats as well as an inverted repeat; these structures may be involved in the transfer of the DNA from Agrobacterium to plant cells.
Base Sequence↗
Using hydroxyl radical to probe DNA structure.
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Animals↗
Hydroxylamine and methoxylamine as probes of DNA structure.
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Animals↗