Comparison of different approaches for calculation of polyelectrolyte free energy.

We consider the problem of the mean field (Poisson-Boltzmann) calculation of the electrostatic free energy for a strongly charged polyelectrolyte such as DNA in a salt solution. We compare two approaches to calculate the free energy: (i) direct one starting from the statistical-mechanical expression for the electrostatic free energy and (ii) the polyion charge variation method. In the infinite dilution limit (in respect to polyion) and in excess salt (IDLES) the two approaches are fully equivalent.

Statistical analysis of nucleotide runs in coding and noncoding DNA sequences.

A statistical analysis of the occurrence of particular nucleotide runs in DNA sequences of different species has been carried out. There are considerable differences of run distributions in DNA sequences of procaryotes, invertebrates and vertebrates. There is an abundance of short runs (1-2 nucleotides long) in the coding sequences and there is a deficiency of such runs in the noncoding regions.

A theoretical study of formation of DNA noncanonical structures under negative superhelical stress.

The development of statistical mechanical models of the formation of noncanonical structures in circular DNA and the finding of the energy parameters for these models made it possible to predict the appearance of such structures in a DNA with any given sequence. It does not seem feasible, however, to perform such calculations for DNA sequences of considerable length by allowing for all the possible states. We propose a special algorithm for calculating the thermodynamic characteristics of various conformational rearrangements in DNA that occur under negative supercoilings, allowing for several possible states of each base pair in the chain.

The ionic strength dependence of the cooperativity factor for DNA melting.

The melting temperature for the d(AT)24.d(AT)24 stretch, located inside the DNA helix and terminally, have been determined in a wide range of ionic strength values (0.01 - 1 M Na+).