SEARCH · Search PubMed

Results for “Double Bind Interaction”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 379 records · Page 21Linked to original sources

PubMed1979

Binding of exogenous DNA by human lymphocytes and by their isolated plasma membranes.

The binding of labeled bacterial DNA to human tonsil lymphocytes and to plasma membranes isolated from these cells involved macromolecules mainly located at the cell surface, since plasma membrane preparations showed properties in common with those of viable cells. DNA binding to lymphocytes was a dissociable, saturable, time, temperature, pH and concentration dependent process. A double reciprocal plot of the data obtained from DNA saturation curves gave an apparent dissociation constant of about 4 X 10(-10) M. The process of interaction of 3H-DNA with lymphocyte membranes gave a complex Scatchard plot, whose first slope yielded an apparent dissociation constant similar to that obtained for DNA-cell interaction. Binding was shown to be specific for DNA because RNA did not displace the bound DNA. Double stranded DNA was preferentially bound relative to single stranded DNA. Temperatures greater than 55 degrees C abolished the binding capacity. Results of experiments in which pH and salt concentration were varied point to the importance of conformational changes of the nucleic acid in the binding process.

Bacillus cereus↗

PubMed1998

An archaeal DNA binding protein from thermophilic Sulfolobus acidocaldarius forms different types of complexes with DNA.

We have characterized a DNA binding protein (DBNP-B) from the thermoacidophilic archaeon Sulfolobus acidocaldarius with respect to its interaction with single and double stranded DNA. The protein in solution exists predominantly as dimer as indicated by cross linking studies. Binding of DBNP-B to etheno DNA and poly (dA) resulted in fluorescence enhancement and hyperchromicity respectively. Ethidium bromide intercalated into DNA was completely displaced by DBNP-B. DNase I digestion of dsDNA was increased at subsaturating concentration of the protein and was inhibited at higher concentrations. These results and electron microscopy indicate that the protein forms different types of novel complexes with DNA at different protein to DNA ratios.

Archaeal Proteins↗

PubMed1978

Interaction of contractile proteins with DNA.

The interaction of contractile proteins (myosin, actin, tropomyosin and troponin) with DNA was studied in vitro using a nitrocellulose filter binding technique. The data indicate a high affinity of myosin and troponin for DNA, a lesser interaction between DNA and tropomyosin and the absence of binding of actin to DNA. When binding to DNA was detected, the interaction was higher with single-stranded DNA than with RNA or double-stranded DNA, although in some conditions myosin binds equally as well to native as to denatured eukaryotic DNA. Myosin binds better to eukaryotic than to phage native DNA.

Actins↗

PubMed2006

Structural basis for the cooperative assembly of large T antigen on the origin of replication.

Large T antigen (LTag) from simian virus 40 (SV40) is an ATP-driven DNA helicase that specifically recognizes the core of the viral origin of replication (ori), where it oligomerizes as a double hexamer. During this process, binding of the first hexamer stimulates the assembly of a second one. Using electron microscopy, we show that the N-terminal part of LTag that includes the origin-binding domain does not present a stable quaternary structure in single hexamers. This disordered region, however, is well arranged within the LTag double hexamer after specific ori recognition, where it mediates the interactions between hexamers and constructs a separated structural module at their junction. We conclude that full assembly of LTag hexamers occurs only within the dodecamer, and requires the specific hexamer-hexamer interactions established upon binding to the origin of replication. This mechanism provides the structural basis for the cooperative assembly of LTag double hexamer on the cognate viral ori.

Antigens, Polyomavirus Transforming↗

PubMed1989

A murine nephritogenic monoclonal anti-DNA autoantibody binds directly to mouse laminin, the major non-collagenous protein component of the glomerular basement membrane.

The interaction of the murine monoclonal anti-DNA antibody H241 with extracellular glomerular antigens was found to be due to the binding of this antibody to laminin, the major non-collagenous protein constituent of the glomerular basement membrane. This interaction is specific, since it is inhibited by laminin, double-stranded DNA and single-stranded DNA in solution. Furthermore, the binding of H241 to mouse laminin is mediated by conformational properties of the antigen because mild denaturation of laminin strongly decreases the binding capacity of H241, while exposure of laminin to sodium dodecyl sulfate, completely abolishes this interaction. H241 is able to bind to both, human and mouse laminin. These findings are in agreement with the ligand binding specificities of the autoantibodies spontaneously produced, that differ from those generated by artificial immunization. We conclude that the polyreactivity of H241 that confers to it the capacity to bind laminin, may account for its ability to form immune deposits by binding directly to non-DNA glomerular antigens.

Animals↗

PubMed2002

Helicase from hepatitis C virus, energetics of DNA binding.

The ability of a helicase to bind single-stranded nucleic acid is critical for nucleic acid unwinding. The helicase from the hepatitis C virus, NS3 protein, binds to the 3'-DNA or the RNA strand during unwinding. As a step to understand the mechanism of unwinding, DNA binding properties of the helicase domain of NS3 (NS3h) were investigated by fluorimetric binding equilibrium titrations. The global analysis of the binding data by a combinatorial approach was done using MATLAB. NS3h interactions with single-stranded DNA (ssDNA) are 300-1000-fold tighter relative to duplex DNA. The NS3h protein binds to ssDNA less than 15 nt in length with a stoichiometry of one protein per DNA. The minimal ssDNA binding site of NS3h helicase was determined to be 8 nucleotides with the microscopic K(d) of 2-4 nm or an observed free energy of -50 kJ/mol. These NS3h-DNA interactions are highly sensitive to salt, and the K(d) increases 4 times when the NaCl concentration is doubled. Multiple HCV helicase proteins bind to ssDNA >15 nucleotides in length, with an apparent occluded site of 8-11 nucleotides. The DNA binding data indicate that the interactions of multiple NS3h protein molecules with long ssDNA are both noncooperative and sequence-independent. We discuss the DNA binding properties of HCV helicase in relation to other superfamily 1 and 2 helicases. These studies provide the basis to investigate the DNA binding interactions with the unwinding substrate and their modulation by the ATPase activity of HCV helicase.

Adenosine Triphosphatases↗

PubMed2001

The magnitude of [C-H...O] hydrogen bonding in molecular and supramolecular assemblies.

Ab initio calculations at the MP2/6-311++G** level on model systems (N-methylpyridinium complexes of dimethyl ether and dimethyl phosphate anion) provide quantitative measures of the large stabilization energies that arise from [C-H...O] contacts in charged systems. These attractive interactions control (i) the self-assembly of bipyridinium-based catenanes and rotaxanes in solution, (ii) the self-organization of left-handed Z-DNA with alternating [dC-dG] sequences in the solid state, and (iii) the binding of pyridinium derivatives with single- and double-stranded DNA. Slightly attractive interactions occur between the donor ether and phosphate moieties and a neutral pyridine molecule in the gas phase. Electrostatic potential and solvation calculations demonstrate that [C-H...O] interactions which involve a cationic [C-H] donor are dominated by electrostatic terms.

DNA↗

PubMedDate not supplied

[Physico-chemical properties of the RNA of Sendai virus. III. Interaction with proflavin].

The binding isotherms of the Sendai virus single- and double-stranded RNA-proflavine complexes have been studied. The existence of two regions on the binding curves, corresponding to two subtypes of the strong complex (I1 and I2) has been demonstrated. The association constants and the numbers of binding sites for both subtypes were determined as a function of ionic strength. Both of the single- and for the double-stranded RNA the association constant for I1 complex were higher than those for I2 complex under all ionic strengths conditions. For the double-stranded RNA the variation of the ionic strength is more importance in case of the I1 complex formation. The total number of binding sites increases with a decrease of ionic strength. At low ionic strength (10(-4) M NaCl) the number of binding sites for single- and double-stranded RNA is practically the same and is equal to the number of binding sites for DNA at high ionic strength (1 molecule of proflavine per 3 nucleotides pairs). The heat denaturation of the RNA-proflavine complexes under different ionic conditions has been also investigated. The melting curves for double-stranded RNA-proflavine complex had two waves at high and low ionic strengths. For the single-stranded RNA the high temperature wave occured only at the high ionic strength. The dependence of heat denaturation of single-stranded RNA on ionic strength was examined for the evaluation of RNA structure. In these experiments a significant decrease of the width of melting interval under low ionic strength conditions was observed. It may reflect the existance in the RNA molecule of long helical regions. The occurence of such structures is likely to be responsible for an increase in the number of binding sites at low ionic strength and also for the appearance of the second wave on the melting curves of the single-stranded RNA-proflavine complexes at high ionic strength.

Acridines↗

PubMed2003

Spectroscopic and thermodynamic studies on the binding of sanguinarine and berberine to triple and double helical DNA and RNA structures.

A comparative study on the interaction of sanguinarine and berberine with DNA and RNA triplexes and their parent duplexes was performed, by using a combination of spectrophotometric, UV thermal melting, circular dichroic and thermodynamic techniques. Formation of the DNA and RNA triplexes was confirmed from UV-melting and circular dichroic measurements. The interaction process was characterized by increase of thermal melting temperature, perturbation in circular dichroic spectrum and the typical hypochromic and bathochromic effects in the absorption spectrum. Scatchard analysis indicated that both the alkaloids bound to the triplex and duplex structures in a non-cooperative manner and the binding was stronger to triplexes than to parent duplexes. Thermal melting studies further indicated that sanguinarine stabilized the Hoogsteen base paired third strand of both DNA and RNA triplexes more tightly compared to their Watson-Crick strands, while berberine stabilized the third strand only without affecting the Watson-Crick strand. However, sanguinarine stabilized the parent duplexes while no stabilization was observed with berberine under identical conditions. Circular dichroic studies were also consistent with the observation that perturbations of DNA and RNA triplexes were more compared to their parent duplexes in presence of the alkaloids. Thermodynamic data revealed that binding of sanguinarine and berberine to triplexes (T.AxT and U.AxU) and duplexes (A.T and A.U) showed negative enthalpy changes and positive entropy changes but that of sanguinarine to C.GxC(+) triplex and G.C duplex exhibited negative enthalpy and negative entropy changes. Taken together, these results suggest that both sanguinarine and berberine can bind and stabilize the DNA and RNA triplexes more strongly than their respective parent duplexes.

Alkaloids↗

PubMed1988

Sequence-specific interactions between a cellular DNA-binding protein and the simian virus 40 origin of DNA replication.

The core origin of simian virus 40 (SV40) DNA replication is composed of a 64-base-pair sequence encompassing T-antigen-binding site II and adjacent sequences on either side. A 7-base-pair sequence to the early side of T-antigen-binding site II which is conserved among the papovavirus genomes SV40, BK, JC, and SA12 was recently shown to be part of a 10-base-pair sequence required for origin activity (S. Deb, A.L. DeLucia, C.-P. Baur, A. Koff, and P. Tegtmeyer, Mol. Cell. Biol. 6:1663-1670, 1986), but its functional role was not defined. In the present report, we have used gel retention assays to identify a monkey cell factor that interacts specifically with double-stranded DNA carrying this sequence and also binds to single-stranded DNA. DNA-protein complexes formed with extracts from primate cells are more abundant and display electrophoretic mobilities distinct from those formed with rodent cell extracts. The binding activity of the factor on mutant templates is correlated with the replication activity of the origin. The results suggest that the monkey cell factor may be involved in SV40 DNA replication.

Animals↗

PubMed1982

An F-actin- and calmodulin-binding protein from isolated intestinal brush borders has a morphology related to spectrin.

A high molecular weight protein from the brush border of chicken intestinal epithelial cells has been purified. This protein (TW 260/240), a complex of two polypeptides with apparent molecular weights of 260,000 and 240,000, accounts for a significant amount of the terminal web organization. TW 260/240 is an F-actin-binding protein that also interacts with calmodulin. Rotary shadowing reveals long flexible rods of double-stranded morphology tightly connected at each end. TW 260/240 is quite distinct from smooth muscle filamin and macrophage actin-binding protein (APB), but, in spite of its higher contour length (265 nm), seems to be related to erythrocyte spectrin (194 nm for the tetramer). Immunofluorescence microscopy with antibodies against TW 260/240 indicates the existence of a submembranous organization distinctly different from that of stress fibers. We have compared TW 260/240 with fodrin, a brain protein known to occur in submembranous organization but not previously characterized in molecular terms. TW 260/240 and fodrin are clearly distinct molecules but are similar in many aspects. Ultrastructural, biochemical and immunological results indicate three distinct classes of rod-like high molecular weight actin-binding proteins, possibly reflected by the prototypes filamin (ABP), spectrin and TW 260/240 (fodrin). The latter group may be responsible for calmodulin control of submembranous microfilament structures in various nonmuscle cells.

Actins↗

PubMed2001

A mutational analysis of the globotriaosylceramide-binding sites of verotoxin VT1.

Escherichia coli verotoxin, also known as Shiga-like toxin, binds to eukaryotic cell membranes via the glycolipid Gb(3) receptors which present the P(k) trisaccharide Galalpha(1-4)Galbeta(1-4)Glcbeta. Crystallographic studies have identified three P(k) trisaccharide (P(k)-glycoside) binding sites per verotoxin 1B subunit (VT1B) monomer while NMR studies have identified binding of P(k)-glycoside only at site 2. To understand the basis for this difference, we studied binding of wild type VT1B and VT1B mutants, defective at one or more of the three sites, to P(k)-glycoside and pentavalent P(k) trisaccharide (pentaSTARFISH) in solution and Gb(3) presented on liposomal membranes using surface plasmon resonance. Site 2 was the key site in terms of free trisaccharide binding since mutants altered at sites 1 and 3 bound this ligand with wild type affinity. However, effective binding of the pentaSTARFISH molecule also required a functional site 3, suggesting that site 3 promotes pentavalent binding of linked trisaccharides at site 1 and site 2. Optimal binding to membrane-associated Gb(3) involved all three sites. Binding of all single site mutants to liposomal Gb(3) was weaker than wild type VT1B binding. Site 3 mutants behaved as if they had reduced ability to enter into high avidity interactions with Gb(3) in the membrane context. Double mutants at site 1/site 3 and site 2/site 3 were completely inactive in terms of binding to liposomal Gb(3,) even though the site 1/site 3 mutant bound trisaccharide with almost wild type affinity. Thus site 2 alone is not sufficient to confer high avidity binding to membrane-localized Gb(3). Cytotoxic activity paralleled membrane glycolipid binding. Our data show that the interaction of verotoxin with the Gb(3) trisaccharide is highly context dependent and that a membrane environment is required for biologically relevant studies of the interaction.

Animals↗

PubMed1999

Enhanced binding to DNA and topoisomerase I inhibition by an analog of the antitumor antibiotic rebeccamycin containing an amino sugar residue.

Many antitumor agents contain a carbohydrate side chain appended to a DNA-intercalating chromophore. This is the case with anthracyclines such as daunomycin and also with indolocarbazoles including the antibiotic rebeccamycin and its tumor active analog, NB506. In each case, the glycoside residue plays a significant role in the interaction of the drug with the DNA double helix. In this study we show that the DNA-binding affinity and sequence selectivity of a rebeccamycin derivative can be enhanced by replacing the glucose residue with a 2'-aminoglucose moiety. The drug-DNA interactions were studied by thermal denaturation, fluorescence, and footprinting experiments. The thermodynamic parameters indicate that the newly introduced amino group on the glycoside residue significantly enhanced binding to DNA by increasing the contribution of the polyelectrolyte effect to the binding free energy, but does not appear to participate in any specific molecular contacts. The energetic contribution of the amino group of the rebeccamycin analog was found to be weaker than that of the sugar amino group of daunomycin, possibly because the indolocarbazole derivative is only partially charged at neutral pH. Topoisomerase I-mediated DNA cleavage studies reveal that the OH-->NH2 substitution does not affect the capacity of the drug to stabilize enzyme-DNA covalent complexes. Cytotoxicity studies with P388 leukemia cells sensitive or resistant to camptothecin suggest that topoisomerase I represents a privileged intracellular target for the studied compounds. The role of the sugar amino group is discussed. The study provides useful guidelines for the development of a new generation of indolocarbazole-based antitumor agents.

Amino Sugars↗

PubMed1998

Purification and characterization of a protein binding to the SP6 kappa promoter. A potential role for CArG-box binding factor-A in kappa transcription.

A protein interacting with an A-T-rich region that is a positive control element within the SP6 kappa promoter was purified and identified as CArG-box binding factor-A. The purified protein was shown to interact specifically with the coding strand of single-stranded DNA and, with lower affinity, with double-stranded DNA. A mutation that inhibited binding of the protein to the A-T-rich region also aborted the transcriptional stimulatory effect of the region. Two Ets proteins, PU.1 and elf-1, that have previously been shown to bind to an adjacent DNA element were shown to physically interact with CArG-box binding factor-A. An antiserum raised against the protein recognized two different forms indicating either that different splice-forms of CArG-box binding factor-A are expressed, or that the protein is subject to post-translational modification.

Alternative Splicing↗

PubMed2003

Structural determinants for substrate binding and catalysis by the structure-specific endonuclease XPG.

XPG belongs to the Fen1 family of structure-specific nucleases and is responsible for the 3' endonucleolytic incision during mammalian nucleotide excision repair. In addition, it has ill-defined roles in the transcription-coupled repair of oxidative DNA damage and likely also in transcription that are independent of its nuclease activity. We have used DNA binding and footprinting assays with various substrates to gain insight into how XPG interacts with DNA. Ethylation interference footprinting revealed that XPG binds to its substrates through interaction with the phosphate backbone on one face of the helix, mainly to the double-stranded DNA. By comparing DNA binding and cleavage activity using single-/double-stranded DNA junction substrates differing in the length of the single-stranded regions, we have found that the 3' but not the 5' single-stranded arm was necessary for DNA binding and incision activity. Furthermore, we show that although a 5' overhang is not required for XPG activity, an overhang containing double-stranded DNA near the junction inhibits the nuclease but not substrate binding activity. Apparently, junction accessibility or flexibility is important for catalysis but not binding of XPG. These results show that XPG has distinct requirements for binding and cleaving DNA substrates.

Animals↗

PubMed2005

Applying the SPOT peptide synthesis procedure to the study of protein tyrosine phosphatase substrate specificity: probing for the heavenly match in vitro.

This section provides detailed protocols for peptide synthesis on membrane (SPOT) and describes the application of this technology to protein tyrosine phosphatase (PTPs) substrate selectivity studies. Applications include PTP binding and dephosphorylation assays on phosphotyrosine peptides derived from known substrates, such as the insulin receptor (IR) autophosphorylation site, and on peptides from focused or random SPOT peptide libraries, to discover consensus binding motifs. Weak or transient interactions that cannot be revealed by regular SPOT binding can be uncovered using SPOT double synthesis (SPOT-DS), whereby two different peptides are synthesized on the same spot. In SPOT-DS, one peptide is a substrate for the enzyme, whose conversion is indicative of a transient interaction of the enzyme with the other (variable) peptide. Using SPOT-DS, three IR regions that interact with full-length PTP-1B in a non-phosphorylation-dependent manner were revealed. In order to further study multiple interaction sites, we have developed a strategy to synthesize up to four peptides per spot: "SPOT(4)". Finally, several examples are provided that illustrate how the SPOT technology can be used in kinase and protease selectivity studies as well.

Animals↗

PubMed2004

Biological activity and delivery of peptide nucleic acids (PNA)-DNA chimeras for transcription factor decoy (TFD) pharmacotherapy.

Peptide nucleic acids (PNAs) are recently described DNA mimics, in which the sugar-phosphate backbone is replaced by N-(2-aminoethyl)glycine units. These molecules efficiently hybridize with complementary DNA, forming Watson-Crick double helices. In addition, the interest of PNAs and PNA-based analogs is related to the fact that they are resistant to DNases and proteinases. While applications of PNAs as antisense and antigéne molecules in non-viral gene therapy are well documented, their effects as potential transcription factor decoy (TFD) molecules is not demonstrated. PNA/PNA and PNA/DNA duplex are not suitable for TFD. In fact, PNA/PNA duplex does not recognize transcription factors, while, in the case of PNA/DNA hybrids containing nuclear factor binding sites, the interaction with transcription factors is unstable. By sharp contrast, double stranded molecules based on PNA-DNA chimeras exhibit strong TFD activity, display enzymatic stability in serum and cellular extracts and can be delivered to target cells after complexation with liposomes and microspheres. The TFD molecules based on PNA-DNA chimeras can be further engineered by addition of short peptides facilitating cell penetration and nuclear localization. Therefore, these engineered molecules could be of great interest for in vivo experiments on non-viral gene therapy of a variety of diseases, including neoplastic and viral diseases, for which the TFD approach has been already demonstrated as a very useful strategy.

DNA↗

PubMed1995

Double-stranded RNA binding proteins and their substrates.

Double-stranded RNA (dsRNA) binding proteins (dsRBPs) pose unique questions in regard to how proteins interact with RNA. This article presents a general overview of these questions and also introduces specific dsRBPs that are studied by my laboratory.

Adenosine Deaminase↗