[Nucleosomes in gene regulation: theoretical approaches].

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangement in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are mentioned. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field.

Melting of cross-linked DNA. III. Calculation of differential melting curves.

In our previous papers I and II (D. Y. Lando et al, J. Biomol. Struct. Dynam. (1997) v. 15, N1, p. 129-140, p. 141-150), two methods were developed for calculation of melting curves of cross-linked DNA. One of them is based on Poland's and another on the Fixman-Freire approach. In the present communication, III, a new theoretical method is developed for computation of differential melting curves of DNAs cross-linked by anticancer drugs and their inactive analogs. As Poland's approach, the method allows study of the influence of the loop entropy factor, delta(n), on melting behavior (n is the length of a loop in base pairs). However the method is much faster and requires computer time that inherent for the most rapid Fixman-Freire calculation approach. In contrast to the computation procedures described before in communications I and II, the method is suitable for computation of differential melting curves in the case of long DNA chains, arbitrary loop entropy factors of melted regions and arbitrary degree of cross-linking including very low values that occur in vivo after administration of antitumor drugs. The method is also appropriate for DNAs without cross-links. The results of calculation demonstrate that even very low degree of cross-linking alters the DNA differential melting curve. Cross-linking also markedly strengthens the influence of particular function delta(n) upon melting behavior.

[Nucleoprotein melting. II. Melting of irreversible DNA-protein complexes]. / Issledovanie plavleniia nukleoproteidov. II. Plavlenie kompleksov DNK--belok v usloviiakh neobratimogo sviazyvaniia.

Three with different complexity models: single-stranded, periodic theeropolymer, two-stranded periodic heteropolymer and complex of DNA with irreversible bound proteins have been considered. It is shown that the individual bands on the differential melting curve appear if the length of protein bound regions exceed 25 base pairs. In this case the melting temperature of free and protein bound regions depends on their reciprocal length in almost linear manner. Moreover, the temperature of the peak corresponding to the protein bound regions is independent on the length of the adjacent free DNA regions if their length exceeds 15 base pairs. If the length of free and protein bound regions exceed 300 base pairs, their melting temperatures becomes almost equal to that of infinitely long polymer with the analogous structure. A simple method for determination of length of the free and the protein bound regions length has been proposed.

[Nucleoprotein melting. I. Theory of helix-coil transition of DNA in the presence of proteins with cooperative character of interaction under conditions of reversible binding]. / Issledovanie plavleniia nukleoproteidov. I. teoriia perekhoda spiral'-klubok DNK v prisutstvii belkov pri obratinom sviazyvanii.

Helix-coil transition of DNA with attached extended ligands able to interact with one another during adsorption on DNA (cooperative or uncooperative binding) has been considered. The general formulae describing dependence of polymer melting curve on concentration of attached ligands have been obtained. It has been shown that cooperativity of interaction with DNA stipulates for two phase profile of the melting curve. The results obtained show that proteins which interact with DNA cooperatively may cause two phase helix-coil transition under conditions of reversible binding.

[Fusion of complexes of DNA and extended ligands]. / Plavlenie kompleksov DNK s protiazhennymi ligandami

The theory of melting of DNA complexes with extended ligands (ties) is considered. Influence of ties interacting electorally with certain DNA regions and influence of extender ties, interacting unelectorally on the helix coil transition parameters is compared. It has been shown that both types of ties cause, coincided qualitatively, but differed quantatively, shifts of melting temperature and change of the melting range width of DNA. Comparison of theory with experiment in the case of DNA complexes with ribonuclease is given.