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At least 577 records · Page 32Linked to original sources
PubMed1999

DNA structure and novel amino and carboxyl termini of the Chlamydia sigma 70 analogue modulate promoter recognition.

Genes from the eubacterium Chlamydia typically do not share promoter consensus sequences with those of Escherichia coli and are not expressed when cloned in E. coli; nevertheless, the major sigma-subunit identified from Chlamydia trachomatis has nearly identical amino acid sequence to E. coli sigma 70 in regions that contact DNA. Following expression of the chlamydial sigma-subunit gene in E. coli, expression was specifically initiated from chlamydial promoter regions. Selective recognition of chlamydial promoters by holoenzyme was dependent upon the structure of the promoter DNA coupled with novel amino- and carboxyl-terminal extensions of the chlamydial sigma-subunit.

Bacterial Outer Membrane Proteins↗
PubMed1995

In vivo binding of trimethylpsoralen detects DNA structural alterations associated with transcribing regions in the human beta-globin cluster.

In order to increase our knowledge about the mechanisms that regulate expression of human beta-like globin genes, we have used a novel technique to analyze the chromatin structure in living cells. This approach allowed us to detect specific DNA regions in vivo where nucleosome folding or unconstrained DNA supercoiling in erythroid cells differs from that in non-erythroid cells. In this method, we use 4,5',8-trimethylpsoralen (TMP) as a probe capable of detecting altered chromatin conformations. Our results show that TMP binds to DNA with a higher affinity over the regions in the locus that are actively expressed, including both the promoter and the transcribed region. This higher affinity detected when comparing erythroid cells with non-erythroid cells does not extend to other regions inside the beta-globin cluster. Our data suggest that the observed effect is likely due to nucleosome displacement. Alternatively, it could result from localized DNA supercoiling, but not from widespread torsional stress across the entire beta-like globin locus as hypothesized previously.

Base Sequence↗
PubMed1991

Ribosomal DNA structure in Aedes mosquitoes (Diptera: Culicidae) and their cell lines.

The molecular organization of the ribosomal DNA repeat unit in laboratory colonies of Aedes albopictus (Skuse) and Aedes aegypti (L.) and in continuous cell lines derived from these species was examined using restriction enzyme mapping and Southern blotting techniques. In the rRNA coding regions, restriction enzyme sites were conserved in Ae. aegypti and Ae. albopictus. In particular, sites that had been mapped in rDNA cloned from the Mauritius strain of Ae. albopictus mosquitoes were confirmed in cloned DNA from cultured Ae. alboptictus cells. The intergenic spacer region of the ribosomal DNA repeat unit in Ae. albopictus was longer than that in Ae. aegypti; contained multiple recognition sites for AluI, SstI, PvuI, and XhoI; and was more heterogeneous in DNA from cultured cells than in DNA from inbred laboratory mosquitoes. The rDNA copy number was 3- to 4-fold lower in cell lines from both Ae. albopictus and Ae. aegypti than in the corresponding adult mosquitoes.

Aedes↗
PubMed2003

Modeling DNA structure, elasticity, and deformations at the base-pair level.

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between the neighboring base pairs. The sugar-phosphate backbones are taken into account by semirigid harmonic springs with a nonzero spring length. The competition between these two interactions and the introduction of a simple geometrical constraint lead to a stacked right-handed B-DNA-like conformation. The mapping of the presented model to the Marko-Siggia and the stack-of-plates model enables us to optimize the free model parameters so as to reproduce the experimentally known observables such as persistence lengths, mean and mean-squared base-pair step parameters. For the optimized model parameters, we measured the critical force where the transition from B- to S-DNA occurs to be approximately 140 pN. We observe an overstretched S-DNA conformation with highly inclined bases which partially preserves the stacking of successive base pairs.

Base Composition↗
PubMed1990

The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure.

We have determined the domains of the mammalian high mobility group (HMG)I chromosomal proteins necessary and sufficient for binding to the narrow minor groove of stretches of A.T-rich DNA. Three highly conserved regions within each of the known HMG-I proteins is closely related to the consensus sequence T-P-K-R-P-R-G-R-P-K-K. A synthetic oligopeptide corresponding to this consensus "binding domain" (BD) sequence specifically binds to substrate DNA in a manner similar to the intact HMG-I proteins. Molecular Corey-Pauling-Koltun model building and computer simulations employing energy minimization programs to predict structure suggest that the consensus BD peptide has a secondary structure similar to the antitumor and antiviral drugs netropsin and distamycin and to the dye Hoechst 33258. In vitro these ligands, which also preferentially bind to A.T-rich DNA, have been demonstrated to effectively compete with both the BD peptide and the HMG-I proteins for DNA binding. The BD peptide also contains novel structural features such as a predicted Asx bend or "hook" at its amino-terminal end and laterally projecting cationic Arg/Lys side chains or "bristles" which may contribute to the binding properties of the HMG-I proteins. The predicted BD peptide structure, which we refer to as the "A.T-hook," represents a previously undescribed DNA-binding motif capable of binding to the minor groove of stretches of A.T base pairs.

Adenine↗
PubMed2004

DNA structural changes as the basis for a nanomolecular device.

There is currently great interest in the design of nanodevices that are capable of performing movements. Protein molecular machines are abundant in biology but it has recently been proposed that nucleic acids could also act as nanomolecular machines in model systems. Several types of movements have been described with DNA machines: rotation, extension-contraction and "scissor-like" opening and closing. Here we analyze the properties of a simple and robust device composed of a single 21-base-long oligonucleotide which relies on a duplex/quadruplex equilibrium fueled by the sequential addition of DNA single-strands, generating a DNA duplex as a by-product. The interconversion between two well-defined topological states induces a five nanometer two-stroke, linear motor type movement, which is detected by FRET spectroscopy.

Computers, Molecular↗
PubMed2006

Site-specific phosphorylation of a checkpoint mediator protein controls its responses to different DNA structures.

The checkpoint mediator protein Claspin is indispensable for the ATR-dependent phosphorylation of Chk1 in response to stalled DNA replication forks in Xenopus egg extracts. We show that Claspin also participates in the detection of chromosomal double-stranded DNA breaks (DSBs) in this system. Significantly, removal of Claspin from egg extracts only partially abrogates the activation of Chk1 in response to chromatin with DSBs, whereas depletion of both Claspin and BRCA1 completely abolishes this activation. The function of Claspin in this DSB-triggered pathway depends on phosphorylation of T817 and S819 by ATR. Conversely, neither phosphorylation of Claspin on these sites nor the presence of BRCA1 is necessary for activation of Chk1 in response to stalled replication forks. Thus, site-specific phosphorylation of a checkpoint mediator protein is a crucial determinant in the discrimination between various checkpoint-inducing structures. Furthermore, checkpoint mediator proteins exhibit functional overlap that varies depending on the nature of the checkpoint-triggering DNA signal.

Adaptor Proteins, Signal Transducing↗
PubMed1982

Condensed DNA structures derived from bacteriophage heads.

Bacteriophage lambda particles were rendered osmotically fragile by incubation, spread over hypophase and examined by electron microscopy. When water was used as hypophase, condensed structures were released from the phage heads and treatment of these with cytochrome c or several alternative proteins resulted in the release of free, relaxed DNA. Phage were pretreated with nitrogen mustard, a bifunctional alkylating agent; when the condensed structures from such phage particles were treated with protein, DNA was released in small supercoiled domains. This confirmed a previous finding that bacteriophage DNA has a supercoiled topology and suggests that the winding pattern of DNA in the phage might involve small domains of coiled DNA analogous to nucleosomes. Such a conformation could be consistent with other studies on the arrangement of DNA in phage heads if the domains have parallel axes.

Bacteriophage lambda↗
PubMed2005

Surfactant encapsulated DNA: structure characterization and interaction with dye molecules in organic media.

The recognition of electrostatically-bound DNA-didodecyldimethylammonium (DNA-DDDA) complex by three dye molecules, acridine orange (AO), ethidium bromide (EB) and 5,10,15,20-tetrakis(4-N-methylpyridyl) porphyrin tetra(p-toluenesulfonate) (TMPyP) in organic media was investigated through 1H NMR, UV-vis, and circular dichroism (CD) spectroscopies. When the organic solvent in which DNA-DDDA complex dissolves is changed from ethanol to chloroform, the adsorbed AO undergoes a reversible transformation from a monomer to a highly aggregated state at the interface between DNA and DDDA. EB also adsorbs at the interface between DNA and DDDA when EB interacts with the DNA-DDDA complex in organic media, but its existing state is independent of the used solvents. The third dye, TMPyP cation can intercalate into the G-C region while its anionic p-tosylate counterion remains unbound when it mixes with DNA complex in organic media. The complexes of DDDA with previously recognized DNA by the three dye molecules (DNA-dye), respectively, are also investigated. AO seems having changed its location from the grooves of DNA to the interface between DNA and DDDA after DNA-AO complex was electrostatically encapsulated with DDDA. The aggregation behavior of AO also shows a dependence on the polarity of the organic solvent. EB molecules are believed to intercalate into the base pairs of DNA in aqueous solution. The intercalation mode is still maintained after the encapsulation for DNA-EB in organic solvents, which is different from the situation between DNA-DDDA complex and EB. But in both cases, the existing states of EB are independent of the polarity of the organic solvents. Finally, TMPyP in the complex of DNA-TMPyP and DDDA is also judged to intercalate into the G-C region of DNA while its anionic p-tosylate counterion remains separated from DNA complex, which is similar to its interaction with DNA-DDDA complex in organic media. These data also strongly suggest that the intercalation state of TMPyP is more stable than its adsorption state in grooves when it is recognized with DNA. The present results are significant for the designs of both laser dye and conductive materials.

Animals↗
PubMed1988

Salt dependence of DNA structural stabilities in solution. Theoretical predictions versus experiments.

The predictions of currently available theories for treating DNA-diffuse ionic cloud free energy contributions to conformational stability have been tested against experimental data for salt induced B-Z and B-A transitions. The theories considered are (i) Manning's counterion condensation approach (CC), (ii) the idealized Poisson-Boltzmann approximation (PB), and (iii) the potentials of mean force (PMF) approach proposed by Soumpasis. As far as we can judge from comparison with the set of experimental data currently available, it is found that only the latter theory yields satisfactory quantitative results for the dependence of the B-Z and B-A relative stabilities on monovalent salt concentration. The correct application of the PB and CC theories does not yield very low salt Z-B transitions, in contradiction to earlier assertions. At low salt concentrations the PB theory is qualitatively correct in predicting that the B form is electrostatically more favorable than both the A and Z forms, whereas the CC theory is qualitatively wrong predicting that Z-DNA is more stable than both B and A DNA.

DNA↗