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At least 379 records · Page 21Linked to original sources
PubMed1998

DNA structure in human RNA polymerase II promoters.

The fact that DNA three-dimensional structure is important for transcriptional regulation begs the question of whether eukaryotic promoters contain general structural features independently of what genes they control. We present an analysis of a large set of human RNA polymerase II promoters with a very low level of sequence similarity. The sequences, which include both TATA-containing and TATA-less promoters, are aligned by hidden Markov models. Using three different models of sequence-derived DNA bendability, the aligned promoters display a common structural profile with bendability being low in a region upstream of the transcriptional start point and significantly higher downstream. Investigation of the sequence composition in the two regions shows that the bendability profile originates from the sequential structure of the DNA, rather than the general nucleotide composition. Several trinucleotides known to have high propensity for major groove compression are found much more frequently in the regions downstream of the transcriptional start point, while the upstream regions contain more low-bendability triplets. Within the region downstream of the start point, we observe a periodic pattern in sequence and bendability, which is in phase with the DNA helical pitch. The periodic bendability profile shows bending peaks roughly at every 10 bp with stronger bending at 20 bp intervals. These observations suggest that DNA in the region downstream of the transcriptional start point is able to wrap around protein in a manner reminiscent of DNA in a nucleosome. This notion is further supported by the finding that the periodic bendability is caused mainly by the complementary triplet pairs CAG/CTG and GGC/GCC, which previously have been found to correlate with nucleosome positioning. We present models where the high-bendability regions position nucleosomes at the downstream end of the transcriptional start point, and consider the possibility of interaction between histone-like TAFs and this area. We also propose the use of this structural signature in computational promoter-finding algorithms.

Algorithms↗
PubMed1983

Characterization of DNA structures by Raman spectroscopy: high-salt and low-salt forms of double helical poly(dG-dC) in H2O and D2O solutions and application to B, Z and A-DNA.

Raman spectra of poly(dG-dC) . poly(dG-dC) in D2O solutions of high (4.0M NaCl) and low-salt (0.1M NaCl) exhibit differences due to different nucleotide conformations and secondary structures of Z and B-DNA. Characteristic carbonyl modes in the 1600-1700 cm-1 region also reflect differences in base pair hydrogen bonding of the respective GC complexes. Comparison with A-DNA confirms the uniqueness of C = O stretching frequencies in each of the three DNA secondary structures. Most useful for qualitative identification of B, Z and A-DNA structures are the intense Raman lines of the phosphodiester backbone in the 750-850 cm-1 region. A conformation-sensitive guanine mode, which yields Raman lines near 682, 668, or 625 cm-1 in B (C2'-endo, anti), A (C3'-endo, anti) or Z (C3'-endo, syn) structures, respectively, is the most useful for quantitative analysis. In D2O, the guanine line of Z-DNA is shifted to 615 cm-1, permitting its detection even in the presence of proteins.

DNA↗
PubMed1996

Details of T-DNA structural organization from a transgenic Petunia population exhibiting co-suppression.

Analysis of Agrobacterium-transferred DNA (T-DNA) revealed strong correlations between transgene structures and floral pigmentation patterns from chalcone synthase (chs) co-suppression among 47 Petunia transformants. Presented here are the full details of T-DNA structural organization in that population. Sixteen transformants (34%) carried one T-DNA copy while 31 (66%) carried 106 complete and partial T-DNA elements in 54 linkage groups. Thirty linkage groups contained multiple T-DNA copies; 15 of these contained only contiguously repeated copies, 8 contained only dispersed copies and 7 contained both. Right-border inverted repeats were three times more frequent than left-border inverted or direct repeats. Large fragments of binary-vector sequences were linked to the T-DNA in seven plants.

Blotting, Southern↗
PubMed2006

Effect of DNA structural flexibility on promoter strength--molecular dynamics studies of E. coli promoter sequences.

To study possible correlations between promoter activity and the structural flexibility of the DNA helix, we have carried out unrestrained molecular dynamics simulations of the -10 consensus region sequence and five variants forming the -10 region of various Escherichia coli promoter sequences. Analyses of the trajectories obtained from the simulations show that the consensus sequence has a pattern of two structurally flexible nucleotide steps sandwiched between two stiff steps. In the other sequences, this pattern varies in consonance with the change in the sequence. The variations in the patterns show correlation with the promoter strength.

Base Sequence↗
PubMed2006

The complex of ethidium bromide with genomic DNA: structure analysis by polarized Raman spectroscopy.

Structural properties of the complex formed between genomic DNA and the intercalating drug ethidium bromide (EtBr) have been determined by use of a Raman microscope equipped with near-infrared laser excitation. The polarized spectra, which were obtained from oriented fibers of the EtBr:DNA complex, are interpreted in terms of the relative orientations of the phenanthridinium ring of EtBr and bases of DNA. Quantification of structure parameters of EtBr and DNA in the complex were assessed using Raman tensors obtained from polarized Raman analyses of oriented specimens of EtBr (single crystal) and DNA (hydrated fiber). We find that the phenanthridinium plane is tilted by 35+/-5 degrees from the plane perpendicular to the fiber (DNA helix) axis. Assuming coplanarity of the phenanthridinium ring and its immediate base neighbors at the intercalation site, such bases would have a tilt angle closer to that of A-DNA (20 degrees) than to that of B-DNA (6 degrees). The average base tilt in stretches of DNA between intercalation sites remains that of B-DNA.

Binding Sites↗
PubMed1990

The selective binding of HMG1 to the cruciform DNA structure and the subsequent resumption of transcription.

The binding of DNA binding protein HMG1 to palindromic sequences that can form the cruciform structure in supercoiled DNA and the subsequent effects on the transcription of the sequence were examined. The results show that the cruciform structure formed under negative supercoiling is a block to transcription and that HMG1, which bound selectively to single-stranded region within the cruciform, can remove the block by altering DNA conformation to allow the stalled RNA polymerase at the block to resume transcription.

DNA, Superhelical↗
PubMed1994

Molecular recognition of DNA structure by proteins that mediate genetic recombination.

The latter half of genetic recombination is mediated by proteins that recognise the structure of the four-way DNA junction, and manipulate this structure. In solution the four-way junction adopts a stacked X-structure in the presence of metal ions. The folding is brought about by the pairwise coaxial stacking of helices in a right-handed antiparallel X-shaped structure. The four-way junction is cleaved by structure-selective resolving enzymes that have been isolated from a wide variety of sources, from eubacteria and their phages through to mammals. In addition, another class of proteins accelerate the branch migration of the junction. These proteins all appear to be divisible into a component that recognises structure and another that carries out a reaction on the junction. Thus the ability of structure-selective binding to the four-way DNA junction is a key feature of enzymes important in genetic recombination.

Animals↗
PubMed1978

Analysis of DNA structure by hydroxyapatite columns and ethidium bromide fluorescence techniques. A comparative study and effect on DNA binding.

Seven duplex DNA preparations have been structurally analyzed by hydroxyapatite column chromatography and an ethidium bromide fluorescence technique. Significant contamination of one preparation with single-stranded DNA was detected by hydroxyapatite column chromatography. Five of the other six preparations were found to contain significant single-stranded regions by the ethidium bromide fluorescence technique. Synthetic poly dAT was found to be duplex in structure. The presence of single-stranded regions considerably influenced DNA binding results in a radioimmunoassay.

Antibodies↗
PubMed1981

Carcinogen-induced alteration of DNA structure.

We have prepared covalent complexes between defined length DNA fragments and a diol epoxide derivative of the carcinogenic polycyclic aromatic hydrocarbon, benzo(a)pyrene. We have studied the structure of these complexes, using transient electric dichroism, circular dichroism, fluorescence quenching, thermal denaturation, polyacrylamide gel electrophoresis, and nuclease digestion. Our observations suggest that th covalently bound carcinogen is intercalated within the helix, forming a wedge-shaped complex. Binding of the carcinogen distorts the structure of the DNA over a region extending beyond the immediate binding site. The most striking aspect of this distortion is that it produces a bend in the helix.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1998

Links between chromatin structure, DNA repair and chromosome fragility.

This paper is a brief overview of the studies we have recently conducted to unravel how chromatin structure and DNA repair modulate the fragility of diverse chromosomes and chromosomal regions. We have employed a combination of molecular cytogenetic techniques, including interphase and metaphase multicolour FISH, reverse FISH with CpG-rich probes or repaired DNA fractions, and several combinations of FISH and immunocytogenetics with antibodies against acetylated histones. The targets of our investigation were human constitutive and facultative heterochromatin, chromosomes with high and low gene density and human and hamster fragile sites. The role of DNA repair was investigated by using DNA repair deficient mutants and DNA repair inhibitors. We found that intragenomic heterogeneity in DNA repair and chromatin structure may explain a substantial part of the differential fragility of diverse chromosomes and chromosomal regions.

Animals↗
PubMed2000

Fluorescence energy transfer analysis of DNA structures containing several bulges and their interaction with CAP.

DNA molecules with three bulges separated by double-stranded helical sections of B-DNA were constructed to be used as substrates for DNA-protein binding assays. Fluorescence resonance energy transfer (FRET) between dye molecules attached to the 5'-ends of the DNA molecules is used to monitor the protein binding. The A5 bulge, which consists of five unpaired adenine nucleotides, alters the direction of the helical axis by approximately 80 to 90 at every bulge site. Computer molecular modeling facilitated a pre-selection of suitable helix lengths that bring the labeled ends of the three-bulge DNA molecules (60 to 70 base-pairs long) into close proximity. The FRET experiments verified that the labeled ends of the helices of these long molecules were indeed close. A series of FRET experiments was carried out with two A5 and two A7 bulge molecules. The relative positions of the bulges were varied along the central helical DNA sequence (between the bulges) in order to determine the relative angular juxtapositions of the outlying helical arms flanking the central helical region. The global structural features of the DNA molecules are manifested in the FRET data. The FRET experiments, especially those of the two-bulge series, could be interpreted remarkably well with molecular models based on the NMR structure of the A5 bulge. These models assume that the DNA molecules do not undergo large torsional conformational fluctuations at the bulge sites. The magnitude of the FRET efficiency attests to a relatively rigid structure for many of the long 5'-end-labeled molecules. The changes in the FRET efficiency of three-bulge structures containing the specific binding sequence of the catabolite activator protein (CAP) demonstrated significant deformation of the DNA upon binding of CAP. No direct interaction of CAP with the dyes was observed.

Adenine↗
PubMed1987

Equine herpesvirus type 1 defective-interfering (DI) particle DNA structure: the central region of the inverted repeat is deleted from DI DNA.

The inverted repeat (IRs) component of the genome of equine herpesvirus type 1 (EHV-1) is an important region of structure and function. It is a major constituent of the DNA of EHV-1 defective-interfering (DI) particles which have been shown to mediate the coestablishment of oncogenic transformation and persistent infection of hamster embryo cells. In addition, the IRs encodes the single EHV-1 immediate early gene and the 31.5K very early protein. DNA sequences encompassing EHV-1 internal IRs and the joint between the long (L) and short (S) regions were subcloned into the plasmid vectors pBR322 and pUC12. A total of 22 subclones were derived, including six Sa/l subclones in pBR322 and 12 SmaI subclones in pUC12. Individual subclones were employed in Southern blot hybridizations to define subclone homology to repeated, unique, or heterogeneous (het) DNA sequences within the EHV-1 genome. These studies revealed that the EHV-1 het region is contained entirely within the unique long region of the viral genome and is separated from the L/S junction by approximately 1.8 MDa of completely unique DNA sequences. Furthermore, these IRs subclones were employed in blot hybridizations to analyze the integrity of IRs DNA sequences within the cloned DNA of EHV-1 DI particles. These analyses demonstrated that IRs DNA sequences present in DI DNA were extensively rearranged and contained major deletions (0.80-0.83 map units) which removed a large portion of the single EHV-1 immediate early gene (0.78-0.83 and 0.95-1.00 map units) located in the IRs. Thus, these data and those previous studies (R. P. Baumann et al., 1984, J. Virol. 50, 13-21; R. P. Baumann, J. Staczek, and D. J. O-Callaghan, 1986, Virology 153, 188-200) indicate that the major subunits of the DI DNA molecule are comprised of selected sequences from the IRs component and a highly conserved short sequence located at the terminus of the L region of the standard viral genome.

Animals↗
PubMed1991

Effect of ultraviolet light on DNA structure in 5-iodo-2'-deoxyuridine-substituted HSV-1 DNA.

Herpes simplex virus type-1 (HSV-1) was grown in the presence of 5-iodo-2'-deoxyuridine (IdUrd), and the virion-DNA was isolated by isopycnic centrifugation in CsCl. Irradiation of IdUrd-containing HSV DNA with either 302 nm or 254 nm ultraviolet (UV) light introduced strand breakage into the DNA in a dose-dependent manner when analyzed by alkaline sucrose density gradient sedimentation. Irradiation of unsubstituted HSV DNA under similar conditions produced little strand breakage. These observations are in agreement with the proposed mechanism for photochemical generation of strand breakage in 5-halo-2'-deoxyuridine-containing DNA. Irradiation of IdUrd-substituted virions followed by analysis of the isolated DNA indicated less strand breakage than irradiation of isolated IdUrd-substituted DNA under equivalent conditions. The dosage of irradiation required to introduce DNA strand breakage in IdUrd-substituted virions was equivalent to that employed to affect greater than 99% loss of infectious virus activity in both control and IdUrd-containing virions. It is suggested that the relative UV insensitivity of IdUrd-substituted HSV may be due to the microstructure environment of the substituted HSV DNA which may favor recombination of the photochemically formed halogen-uracil radical pairs.

DNA Damage↗
PubMed1993

B-DNA to Z-DNA structural transitions in the SV40 enhancer: stabilization of Z-DNA in negatively supercoiled DNA minicircles.

During replication and transcription, the SV40 control region is subjected to significant levels of DNA unwinding. There are three, alternating purine-pyrimidine tracts within this region that can adopt the Z-DNA conformation in response to negative superhelix density: a single copy of ACACACAT and two copies of ATGCATGC. Since the control region is essential for both efficient transcription and replication, B-DNA to Z-DNA transitions in these vital sequence tracts may have significant biological consequences. We have synthesized DNA minicircles to detect B-DNA to Z-DNA transitions in the SV40 enhancer, and to determine the negative superhelix density required to stabilize the Z-DNA. A variety of DNA sequences, including the entire SV40 enhancer and the two segments of the enhancer with alternating purine-pyrimidine tracts, were incorporated into topologically relaxed minicircles. Negative supercoils were generated, and the resulting topoisomers were resolved by electrophoresis. Using an anti-Z-DNA Fab and an electrophoretic mobility shift assay, Z-DNA was detected in the enhancer-containing minicircles at a superhelix density of -0.05. Fab saturation binding experiments demonstrated that three, independent Z-DNA tracts were stabilized in the supercoiled minicircles. Two other minicircles, each with one of the two alternating purine-pyrimidine tracts, also contained single Z-DNA sites. These results confirm the identities of the Z-DNA-forming sequences within the control region. Moreover, the B-DNA to Z-DNA transitions were detected at superhelix densities observed during normal replication and transcription processes in the SV40 life cycle.

DNA, Superhelical↗
PubMed1999

Topology effect for DNA structure of cisplatin: topological transformation of cisplatin-closed circular DNA adducts by DNA topoisomerase I.

The reaction of cis-Pt(NH3)2Cl2(cis-DDP)-closed circular DNA adducts with DNA topoisomerse I(topo I) were studied by electron microscopy. We identified unique topoisomers such as a singly-linked catenane (2(1)2), trefoil (3(1), and dimetric catenane (2(1)2), etc., by analysis with electron micrographs. These unique recombination products resulted from cis-DDP-intra-twisting looped DNA adducts by DNA topo I, and the products could be explained a new mechanism based on an odd-even number rule. Our results suggest a new model on the working mechanisms for DNA topology of cis-DDP which enhances the recombination of DNA. Based on our results, we propose the topological idea that the yields of a mini closed circular DNA and pseudo trefoil DNA, etc., can be expected by reaction of cis-DDP-DNA-histone complexes with DNA topo I in the body.

Antineoplastic Agents↗
PubMedDate not supplied

[Effect of water on DNA structure in a model microemulsion system].

The physical state of water in a system of reversed micelles at different molar rations of H2O and a nonionic surfactant (tetraethylene glycol monododecyl ether, Brij 30) was studied by NMR spectroscopy. In addition, the effect of water on the structure of the intramicellar DNA was investigated using the intercalator ethidium bromide. It was shown by NMR diffusometry that the state of water inside micelles can be considered as supercooled. It was found that the condensation of DNA inside micelles takes place only at definite ratios of water and Brij 30 (from 1.26 to 5). If free water is absent and if the percentage of free water inside in reversed micelles is more than 50%, the process of DNA condensation is disturbed. It is assumed that the molecular memory inherent in the supercooled state of water affects the formation and stabilization of the condensed state of DNA.

DNA↗