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 1,117 records · Page 62Linked to original sources
PubMed1986

Ecotropic and mink cell focus-forming murine leukemia viruses integrate in mouse T, B, and non-T/non-B cell lymphoma DNA.

Structures of somatically acquired murine leukemia virus (MuLV) genomes present in the DNA of a large panel of MuLV-induced C57BL and BALB/c B and non-T/non-B cell lymphomas were compared with those present in MuLV-induced T-cell lymphomas induced in the same low-"spontaneous"-lymphoma-incidence mice. Analyses were performed with probes specific for the gp70, p15E, and U3-long terminal repeat (LTR) regions of ecotropic AKV MuLV and a mink cell focus-forming virus (MCF)-LTR probe annealing with U3-LTR sequences of a unique endogenous xenotropic MuLV, which also hybridizes with U3-LTR sequences of a substantial portion of somatically acquired MCF genomes in spontaneous AKR thymomas. The DNAs of both T- and B-cell tumors induced by neonatal inoculation with the highly oncogenic C57BL-derived MCF 1233 virus predominantly contain integrated MCF proviruses. In contrast, the DNAs of more slowly developing B and non-T/non-B cell lymphomas induced by poorly oncogenic ecotropic or MCF C57BL MuLV isolates mostly contain somatically acquired ecotropic MuLV genomes. Approximately 50% of the spontaneous C57BL lymphoma DNAs contain somatically acquired MuLV genomes. None of the integrated MuLV proviruses annealed with the MCF-LTR probe, which indicates a clear difference in LTR structure with a substantial portion of the somatically acquired MuLV genomes present in the DNA of spontaneous AKR thymomas. This study stresses a dominant role of MuLV with ecotropic gp70 and LTR sequences in the development of slowly arising MuLV-induced B and non-T/non-B cell lymphomas.

Animals↗
PubMed1998

Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.

New levels in the understanding of DNA replication have been achieved from recent crystal structure determinations of several DNA polymerases and their substrate complexes. The structure of an alpha family DNA polymerase from bacteriophage RB69 shows some similarities, but also considerable differences in structure and organization from the pol I family DNA polymerases. Also, the functions of three polymerase domains and their conserved residues have been clarified by studying structures of pol I family DNA polymerases complexed to their substrates. These structures also confirm that an identical two-metal ion catalytic mechanism proposed previously is used by both the nonhomologous pol I and pol beta family DNA polymerases.

Amino Acid Sequence↗
PubMedDate not supplied

[Effect of supporting substrates on the structure of DNA and DNA-trivaline complexes studied by atomic force microscopy].

Linear DNA, circular DNA, and circular DNA complexes with trivaline (TV), a synthetic oligopeptide, were imaged by atomic force microscopy (AFM) using mica as a conventional supporting substrate and modified highly ordered pyrolytic graphite (HOPG) as an alternative substrate. A method of modifying the HOPG surface was developed that enabled the adsorption of DNA and DNA-TV complexes onto this surface. On mica, both purified DNA and DNA-TV complexes were shown to undergo significant structural distortions: DNA molecules decrease in height and DNA-TP displays substantial changes in the shape of its circular compact structures. Use of the HOPG support helps preserve the structural integrity of the complexes and increase the measured height of DNA molecules up to 2 nm. AFM with the HOPG support was shown to efficiently reveal the particular points of the complexes where, according to known models of their organization, a great number of bent DNA fibers meet. These results provide additional information on DNA organization in its complexes with TV and are also of methodological interest, since the use of the modified HOPG may widen the possibilities of AFM in studying DNA and its complexes with various ligands.

Adsorption↗
PubMed2004

T-DNA locus structure in a large population of soybean plants transformed using the Agrobacterium-mediated cotyledonary-node method.

Designing transformation experiments for either functional genomics or crop improvement requires knowledge of the transgene locus structure, number, transmission and expression resulting from a specific transformation method. We recently reported an improvement to the soybean [Glycine max (L.) Merrill] cotyledonary-node transformation method that resulted in the efficient production of transgenic plants. To characterize the transgene loci resulting from this method, we analysed 270 independent T0 plants and 95 randomly selected T1 progenies for T-DNA locus complexity using Southern analysis. The lines were transformed with Agrobacterium tumefaciens strains LBA4404 or EHA105 carrying the binary plasmids pGPTV, pTOK233, pCAMBIA1303 or pCAMBIA1309, and regenerated in medium supplemented with or without silver nitrate (AgNO3). Analysis in the T0 generation showed that the number of hpt-hybridizing fragments per plant ranged from 1-15, with 31.5% of the lines having a single hpt-hybridizing fragment. Each primary soybean transformant had, on average, 2.0 unlinked transgene loci and that half of the segregating loci in the T1 progenies were single, simple T-DNA insertions. Of the loci containing multiple T-DNA fragments, a low frequency had tandem and inverted repeat T-DNA structures. Integration of binary plasmid backbone sequences occurred in 37% of primary transformants. A. tumefaciens strain, binary plasmid and thiol treatment had no significant effect on transgene locus structure, numbers or expression. Interestingly, exposure of soybean explants to AgNO3 throughout shoot induction and elongation increased T-DNA locus complexity in the primary transformants and decreased silencing of gusA expression in the T1 generation.

Journal Article↗
PubMed1998

Role of DNA definite structural elements in interaction with repair enzyme uracil-DNA glycosylase.

Interaction of different oligodeoxyribonucleotides (oligos), their analogs and oligonucleopeptide with uracil-DNA glycosylase (UDG) from human placenta was investigated. It is shown that there is no considerable contribution of heterocyclic bases of DNA to UDG-substrate binding but the UDG interaction with some DNA phosphate groups is necessary for enzyme-substrate recognition. However the phosphate group adjacent to single dU from the 3'-end in oligo is not involved into the electrostatic contact with UDG. It is found that UDG has the high affinity to its reaction product. An oligonucleotide containing a single 2'-deoxy-2'-aminouridine is a non-hydrolyzable substrate analog for UDG.

DNA↗
PubMed2001

X-ray analysis of d(GCGAACGC); intra-duplex and inter-duplex hand-in-pocket motifs.

The structure of DNA octamer with the sequence d(GCGAACGC) has been determined by the X-ray crystallography to investigate the specific DNA structural motifs that are useful for designing various functional DNA molecules. Two kinds of interaction motifs for the bulged out adenosine residues have been found. One is an intra-duplex and the other is an inter-duplex hand-in-pocket motif. These interactions consist of the novel A:G pairs that have never been found so far in any crystal and solution studies on DNA molecules.

Base Sequence↗
PubMed2003

The octaplex structure of d(GCGAGAGC) with I-motif of guanine quartet, controlled by potassium concentration.

Crystal structures of DNA octamer with the sequence d(GCGAGAGC) have been determined by X-ray analyses to investigate the specific DNA structural motifs that are useful for designing various functional DNA molecules. The octamers are assembled to form an octaplex with G-quartets and water-mediated A-quartets. At relatively high potassium concentration, however, the octaplex is split into two quadruplexes, each of which contains two G-duets. The two crystal forms suggest a dynamic formation of an octaplex from two quadruplexes in solution.

Crystallography, X-Ray↗
PubMedDate not supplied

[DNA interaction with low molecular weight ligands of different structure. III. DNA complexes with distactins].

The DNA complexes with distactins have been investigated by means of spectrophotometry, viscosimetry and flow birefringence methods. The distactins are actinocin's derivatives containing in the 1,9 positions of the phenoxazone moiety oligopyrrolcarboxamide groups (like those of distamycin A), which have from one to three fragments of 1-methyl-4-amino-2-pyrrolic acid. The mode of DNA-distactins binding in water solution depends on the quantity of the methylpyrrole rings in the oligopeptide groups. The ligand with oligopeptide groups containing three methylpyrrole rings joins the DNA double helix only from outside by means of oligopeptide groups. The compounds with one and two methylpyrrole rings form two kinds of complexes with DNA: external binding and intercalation. In the latter case both chromophore and methylpyrrole fragments, interact with DNA.

Animals↗
PubMedDate not supplied

[Spatial structure of DNA complex with the oligopeptide dansyl hydrazide trivaline].

The structure of complexes between double-stranded DNA and oligopeptide dansyl hydrazide trivaline was studied by linear dichroism, electron microscopy and hydrodynamical methods. The results show that the binding of the oligopeptide to DNA is a cooperative process that leads to the formation of particles significantly differing in the structure from free DNA. The linear dichroism studies were carried out in a wide range of flow-speed gradients. From the theoretical analysis of these data a conclusion can be drawn that the DNA-oligopeptide complexes possesses a higher rigidity as compared with that of free DNA. The hydrodynamical behaviour of these particles is consistent with the rigid rod-like structure of the particles with a long axis nearly parallel to the DNA helix axis in the complexes. The sedimentation patterns of the complexes suggest the existence of the fast and slow sedimenting species. The sedimentation coefficient measured for a fast sedimenting species is about 3 times higher than that of free DNA. The linear dichroism spectra obtained for the floworiented DNA-oligopeptide complexes correlate with the existence of a superhelical organization of DNA in the complex. This offers a possibility for the determining of the angle of the DNA local axis inclination with respect to the superhelix axis. On electron micrographs the DNA-oligopeptide complexes look like rod-shaped structures with the thickness of about 180 A and 80 A on the rotatory-shadowed preparations and on the uranylacetate stained preparations, respectively. The rod-shaped structures are formed by two interwound DNA molecules. The superhelix has a pitch of about 150 A with an angle of twist inclination of about 40 degrees. These values are in good agreement with the optical anisotropic data. It is suggested that the complex structure is stabilized by periodically spaced hydrophobic contacts between the dimeric oligopeptide species bound to the DNA molecules.

DNA↗
PubMedDate not supplied

Chromatin structure: from nuclei to genes (review).

Characterization of native nuclei by new unharmful biophysical methods, coupled both with the determination of lower order structures in DNA and isolated chromatin, by a variety of sophisticated physicochemical probes and with the intranuclear DNA distribution monitored in situ by high resolution image analysis, recently, point to a unique organization of chromatin-DNA from the secondary up to the quinternary level. Based on the wide range of experimental findings, hereby reviewed in details, a three-dimensional model for DNA structure is proposed from the nuclear level down to the genes, functional units hereby associated with specific structural repeating units. This "fibrosome" model not only accounts for many of the independent observations on the physical and chemical properties of chromatin-DNA, and on the nuclear scaffold and pores, but also accounts for most recent, yet unexplained, discoveries on eukaryotic gene structure, mapping and coding, suggesting a mechanism by which gene expression and cell function may be controlled.

Animals↗
PubMed2005

Whole-genome views of chromatin structure.

DNA in eukaryotes is packed into chromatin. The basic component of chromatin is the nucleosome consisting of DNA wrapped around a histone octamer. Inside the cell nucleus, chromatin is folded into higher-order structures through various mechanisms, including repositioning of nucleosomes along the DNA, packing of nucleosomes into more condensed 3-dimensional configurations, looping of chromatin fibres, and tethering of chromosomal regions to nuclear structures. Over the past few years, new microarray-based methods have been developed for the genome-wide mapping of various aspects of chromatin structure. These methods are beginning to provide insights into the different types of chromatin and the architectural principles that govern the 3-dimensional organisation of the genome inside the nucleus.

Cell Nucleus↗
PubMedDate not supplied

[RNA-recognizing function of the DNA-recognizing structure helix-turn-helix in ribosomal proteins S4 and S7 of Escherichia coli and plant chloroplasts].

The segments which satisfy the necessary requirements for DNA-recognizing structure helix-turn-helix coding have been found in amino acid sequences of RNA-recognizing E. coli ribosomal proteins S4 and S7. It has appeared that among these segments there are those that in chloroplasts S4 and S7 homologues satisfy these necessary requirements also: S4-97-121 and 108-132 (Ec), 91-115 and 102-126 (Zea mays); S7-109-133 (Ec) 110-134 (Euglena gracilis, Glycine max). Such segments have been confronted with known experimental data on 16S rRNA-binding region localization. It has appeared: 1) the segment 97-121 of S4 is localized in RNA-recognizing fragment 46-124 and one of two RNA-binding regions of this fragment containing Lys-120--belongs to the predicted DNA-recognizing structure; the segment 109-133 of S7 includes the only RNA-binding region of S7-113-117. It is concluded that E. coli ribosomal proteins S4 and S7 and their homologues from plant chloroplasts have a DNA-recognizing structure helix-turn-helix performing the RNA-recognizing function.

Amino Acid Sequence↗
PubMed1995

A BC200-derived element and Z-DNA as structural markers in annexin I genes: relevance to Alu evolution and annexin tetrad formation.

We have identified two types of structural elements in genomic DNA for annexin I that provide physical evidence of genetic events leading to conserved changes in gene structure. The sequence upstream of the transcribed region in human annexin I contained a rare, Alu-like repetitive element with flanking direct repeats, probably derived from the active BC200 gene via germline retroposition. Nucleotide substitutions in this BC200 insert relative to the 7SL gene and its absence in rodent annexins I identified it as a recent primate pseudogene. Phylogenetic analysis showed that the BC200 gene represents a new clade of primate Alu evolution that branched near the time of appearance of the progenitor to the free left Alu monomer, FLAM-C. Separate analysis identified a Z-DNA motif in pigeon annexin I intron 7 that may represent the vestigial recombination site involved in primordial assembly of the annexin tetrad. These distinct structural features in annexin I genes provide insight into the evolution of Alu repeats and the mechanism of annexin tetrad formation.

Animals↗
PubMed1991

Detection of triple-helix related structures adopted by poly(dG)-poly(dC) sequences in supercoiled plasmid DNA.

Negative superhelical strain induces the poly(dG)-poly(dC) sequence to adopt two totally different types of triple-helices, either a dG.dG.dC triplex in the presence of Mg(+)+ at both neutral and acidic pHs or a protonated dC+.dG.dC triplex in the absence of Mg(+)+ ions at acidic pH (1). To examine whether there are still other types of non-B DNA structures formed by the same sequence, we constructed supercoiled plasmid DNAs harboring varying lengths of the poly(dG) tract, and the structures adopted by each supercoiled plasmid DNA were studied with a chemical probe, chloroacetaldehyde. The potential of a poly(dG)-poly(dC) sequence to adopt non-B DNA structures depends critically on the length of the tract. Furthermore, in the presence of Mg(+)+ and at a mildly acidic pH, in addition to the expected dG.dG.dC triplex detected for the poly(dG) tracts of 14 to 30 base pairs (bp), new structures were also detected for the tracts longer than 35 bp. The structure formed by a poly(dG) tract of 45 bp revealed chemical reaction patterns consistent with a dG.dG.dC triplex and protonated dC+.dG.dC triple-helices fused together. This structure lacks single-stranded stretches typical of intramolecular triplexes.

Acetaldehyde↗
PubMed2000

Translesion replication by DNA polymerase beta is modulated by sequence context and stimulated by fork-like flap structures in DNA.

Mutations in the human genome are clustered in hot-spot regions, suggesting that some sequences are more prone to accumulate mutations than others. These regions are therefore more likely to lead to the development of cancer. Several pathways leading to the creation of mutations may be influenced by the DNA sequence, including sensitivity to DNA damaging agents, and repair mechanisms. We have analyzed sequence context effects on translesion replication, the error-prone repair of single-stranded DNA regions carrying lesions. By using synthetic oligonucleotides containing systematic variations of sequences flanking a synthetic abasic site, we show that translesion replication by the repair polymerase DNA polymerase beta is stimulated to a moderate extent by low stacking levels of the template nucleotides downstream of the lesion, combined with homopolymeric runs flanking the lesion both upstream and downstream. A strong stimulation of translesion replication by DNA polymerase beta was seen when fork-like flap structures were introduced into the DNA substrate downstream of the lesion. Unlike for gapped substrates, this stimulation was independent of the presence of a phosphate group at the 5' terminus of the flap. These results suggest that DNA polymerase beta may participate in cellular DNA transactions involving higher order structures. The significance of these results for in vivo translesion replication is discussed.

Binding Sites↗
PubMed1988

Structural bases of a long-stretched deletion: completing the lambda plac5 DNA primary structure.

In studying molecular mechanisms of specialised transduction, the lacI (E. coli)-Ea47 (lambda) DNA junction in transducing bacteriophage lambda plac 5 has been structurally elucidated, thus yielding the complete sequence of lambda plac 5 DNA including the lac5 substitution, a well-known segment of lambdoid vectors. The lambda plac5 DNA is shown to consist of 19368 bp (lambda left arm) + 3924 bp (lac5 substitution) + 25353 bp (lambda right arm), totally amounting to 48645 bp. The presence of the phage rho bL promoter near to the right end of the lac5 insert is shown. The lacI gene distal end in lambda plac5 proved to be much longer than it was postulated earlier, coding for 224 C-terminal amino acid residues of lac repressor. Both the recombination studied in this paper and the earlier studied abnormal prophage excision (2, 3) occur near to Chi-like structures (chi*lacI and chi*lom, respectively). On the basis of the data obtained, a key role of the E. coli RecBCD system and Chi-like sequences in the formation of deletions in bacterial cells is suggested.

Bacteriophage lambda↗
PubMed1997

Switching of DNA secondary structure in proenkephalin transcriptional regulation.

Proper transcriptional regulation of the proenkephalin gene requires a switch between distinct factor binding sites that cannot exist at the same time. Each of the sites is formed from a nearly palindromic region that contains two functionally defined cAMP response elements. The region can switch between cruciform and linear duplex. Formation of the cruciform creates an alternative binding site for mediators of second messenger-directed transcription and abolishes the site present in the native duplex form. Use of the cruciform site has been shown to correlate with activated transcription. Analysis of DNA structure, protein binding, and gene expression from plasmids with mutant enhancers shows, however, that both sites are required for regulation of transcription. The two distinct structures form within the same enhancer. Shifting the balance between the two alters transcriptional response.

Base Sequence↗