Abstract
Taking into account the nearest neighbor frequencies of two kinds of base pairs, helix-coil transition in the thermal denaturation process of DNA molecules is investigated. The partition function of a helical part of the molecule is calculated by using the matrix formulation which leads to the algebraic mean of the partition function for various base-pair sequences. The melting curves, that is the fraction of the number of unbonded base pairs as a function of temperature, are evaluated. Thus we can find rather strong dependence of the melting curve on the nearest neighbor frequencies as well as on the base compositions. Actually, when the base sequence has large nearest neighbor frequencies for the same kind of base pairs, it is shown that the melting occurs by two steps of transitions.
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