The double-stranded DNA stability in presence of a flexible polymer

The mixture of the short segments of double-stranded DNA and a flexible polymer are addressed. It is shown that in the condensed phase, rigid DNA molecules exhibit transition between isotropic and orientationally ordered phases. It is shown that orientational ordering stabilizes the secondary structure of double-stranded DNA that could be relevant for the regulation of the gene expression at the condensed state of DNA.     

Theoretical treatment of helix–coil transition of complexes DNA with two different ligands having different binding parameters

The melting transition of DNA–ligand complexes, allowing for two binding mechanisms to different DNA conformations is treated theoretically. The obtained results express the behavior of the experimentally measurable quantities, degree of denaturation, and concentrations of bound ligands on the temperature. The range of binding parameters is obtained, where denaturation curves become multiphasic. The possible application to the nanocomposites crystallization is discussed.     

Stacking and hydrogen bonding: DNA cooperativity at melting

By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition in both polypeptides and polynucleotides. In the framework of the GMPC we show that correctly introduced nearest-neighbor stacking interactions against the background of hydrogen bonding lead to increased stability (melting temperature) and, unexpectedly, to decreased cooperativity (maximal correlation length). The increase in stability is explained as due to an additional stabilizing interaction (stacking) and the surprising decrease in cooperativity is seen as a result of mixing of contributions of hydrogen bonding and stacking.