Jean Sturm

Interaction between hydroxystilbamidine and DNA: I. Binding isotherms and thermodynamics of the association

Isotherms describing the binding of hydroxystilbamidine to DNA and polydeoxyribonucleotides were obtained by means of sedimentation or dialysis experiments and fluorescence measurements, over a large range of ionic strengths, temperatures and base compositions. Two different sets of binding sites are necessary to explain the shapes of the isotherms. The first one is characterized by a higher binding constant, a topological specificity for the A-T pair, exclusion of four base pairs per bound dye molecule, the involvement of two ion-pairs, an almost purely entropic free energy of binding and a large enhancement of the blue fluorescence (450 nm) when the site corresponds to three adjacent A-T pairs. The latter does not present any specificity nor enhancement of fluorescence and only one ion-pair is formed. From the geometry of the dye and its selective binding to a double stranded structure, the hydroxystilbamidine molecule in the first set of sites is likely to be situated in the small groove astride the two complementary strands and slightly distorting the helical structure. The angle of the dye axis with the helix axis has a value close to 47 degrees. No definite explanation could be given for the specific binding of hydroxystilbamidine but the phenolic hydroxyl group is likely to play a major role. The hydroxystilbamidine molecule can be considered as a useful tool for checking the accessibility of the small groove.

Statistics of confined chains. III: Hamiltonian paths

The entropy of self-avoiding walks embedded in a square lattice has been Monte Carlo estimated inside plane squares of various side sizes R. The length of the walks ranged from one to steps, the maximum allowed length, which corresponds to the so-called Hamiltonian paths. It was found that if is the ratio of the occupied over the total number of available lattice sites inside the square, the number of configurations scales to a good approximation as . The limiting curve has then been estimated from the available data, and expressed as a fourth-degree polynomial in . A table is given for Z(1), that is Hamiltonian paths, comparing values obtained from the theoretical relationship given by Orland et al, from the exact enumeration data of Mayer et al, and from the Monte Carlo estimates of the present work.

DNA deformation in gel electrophoresis

A quantitative study of the rise, magnitude, and decay of birefringence of DNA in agarose gel under an electric pulse E has been performed. It provides us with the molecular weight dependence of the characteristic times which describe the deformation of the chain during the transport and which are the parameters requested for designing electric pulse programs for pulsed field gel electrophoresis capable of achieving separation of DNA fragments of very high molecular weight.