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. (C) 2004 Wiley Periodicals, Inc.