Heat-induced diffusion of nucleosomes along DNA is an experimentally well-studied phenomenon, presumably induced by twist defects that propagate through the wrapped DNA portion. The diffusion constant depends dramatically on the local mechanical properties of the DNA and the presence of DNA-binding ligands. This has been quantitatively understood by a stochastic three-state model. Future experi...

A series of bis-naphthalimide derivatives with different diamine linkers were designed and synthesized. All of the synthesized bis-naphthalimide derivatives were characterized by NMR and HRMS spectra. The binding ability between the compounds and CT DNA was evaluated by using UV-Vis titration experiments. The bis-naphthalimide compound with an ethylenediamine linker showed the largest binding c...

A binding study of nickel ions by a new recombinant human Growth Hormone (hGH), produced as an injected drug, has been done at 27˚C in NaCl solution (50 mM) using an isothermal titration calorimetry. There is a set of three identical and non-interacting binding sites for nickel ions. The intrinsic dissociation equilibrium constant and the molar enthalpy of binding are 40 μM and -16...

Brewer et al. (Biophys. J. 85 (2003) 2519-2524) have studied the compaction of dsDNA in a double flow cell by observing the extension of stained DNA tethered in buffer solutions with or without Abf2p. They use a Langmuir adsorption model in which one Abf2p molecule adsorbs on one site on the DNA, and the binding constant, K, is given as the ratio of the experimental rates of adsorption and deso...

Absorbance and fluorescence quenching monitoring of the binding of the anthracyclines adriamycin (ADM) and daunomycin (DNM) to calf thymus DNA, provides reproducible binding data only when moderate drug/DNA molar ratios are used in the assays. Under these conditions, the fraction of DNA-bound drug, in equilibrium with free anthracycline, which can be reliably detected, ranged from 40-60% to 80-...

the effects of allopurinol, acyclovir and theophylline on the activity of adenosine deaminase (ada) were studied in 50 mm sodium phosphate buffer ph 7.5 at 27°c, using a uv– vis spectrophotometer. adenosine deaminase is inhibited by these ligands, via different types of inhibition. allopurinol, as a transition state analog of xanthine oxidase, and acyclovir competitively inhibit the catalytic a...

[Cr(phen)(2)(X(2)dppz)](3+) {X = H, Me, or F} have been synthesised, characterised, and chromatographically resolved into their constituent Delta and Lambda enantiomers. The DNA-binding interactions of each of the racemic complexes were investigated, with the results of linear dichroism, thermal denaturation, and emission quenching studies indicative of intercalative binding to CT-DNA with a si...

Gene regulatory proteins find their target sites on DNA remarkably quickly; the experimental binding rate for lac repressor is orders-of-magnitude higher than predicted by free diffusion alone. It has been proposed that nonspecific binding aids the search by allowing proteins to slide and hop along DNA. We develop a reaction-diffusion theory of protein translocation that accounts for transport ...

Quantitative determination of dissociation constants for DNA-protein complexes will help clarify the molecular mechanisms of transcription, replication and DNA repair. A practical capillary electrophoresis mobility shift assay (CEMSA) for protein-DNA affinities free in solution is presented. The method is fast and simple, precise and general. The speed (<2 min separations) and simplicity derive...

Understanding of cellular processes and underlying molecular events requires knowledge about different aspects of molecular interactions, networks of molecules and pathways in addition to the sequence, structure and function of individual molecules involved. Databases of interacting molecules, pathways and related chemical reaction equations have been developed. The kinetic data for these inter...