Statistical Mechanics of Biopolymers and Its Application to the Melting Transition of Polynucleotides

Abstract

An extended version of the method of the quasi-grand partition function is presented to take into account intra- and inter-molecular interactions. This method is applied to synthetic polynucleotides, in particular to the melting transition of dAT alternating copolymer in which intra-chain folding plays an important role besides inter-chain folding. The equilibrium between single stranded and double stranded molecules in dilute solution is discussed and it is found that the major part of the alternating copolymers are single stranded when the degree of polymerization is sufficiently large. The maximum slope of the transition curve is calculated to estimate the stacking free energy which is found to be about 5.6 kcal. per mole of base pairs.