Stacking heterogeneity: a model for the sequence dependent melting cooperativity of duplex DNA.

A microscopic Potts-like one-dimensional model with many particle interactions [referred as the generalized model of polypeptide chains (GMPCs)] is developed to investigate cooperativity of DNA sequence dependent melting. For modeling sequence, regular homogeneous sequences were arranged in heterogeneous blocks of various lengths. Within the framework of the GMPC the authors show that the inclusion of stacking interaction heterogeneity relative to homogeneous hydrogen bond interactions leads to an unexpected and quite remarkable increase in melting cooperativity for small blocks. In some cases this tendency persists for long blocks having sharp sequence heterogeneity.

The helix-coil transition in heterogeneous double stranded DNA: microcanonical method.

A microscopic Potts-like one-dimensional model with many-particle interactions is developed to construct a statistical mechanical description of the melting of heterogeneous sequence duplex DNA. For this model, referred as the generalized model of polypeptide chains (GMPC), a closed-form expression for the free energy is derived. The characteristic equation of the model enables estimates on the melting temperature and transition interval, consistent with results obtained from more classical approaches. From the characteristic equation of the model, the temperature-dependent statistical weight parameter for helical states is evaluated. This parameter is shown to change throughout the transition from a harmonic form in early regions of the transition to an arithmetic form in later stages. The GMPC is extended to consider the influence of sequence heterogeneity in the melting of duplex DNA.

[Modification of the DNA spatial structure when complexed with cisplatin]. / Modifikatsiia prostranstvennoi struktury DNK v komplekse s tsis-platinoi.

The experimental and theoretical analyses of the conformational transitions of DNA-cis-platinum complexes have been carried out. It is shown that at low concentrations of the ligand, the thermodynamic parameters of the helix-coil transition of the complexes are not the result of the local B-->A transition.