Near-neighbor effects in cooperative modified self-consistent phonon approximation melting in DNA.

Abstract

The modified self-consistent phonon approximation approach is a microscopic theory describing DNA thermal fluctuational motion both in the premelting temperature regime and in the helix-coil transition region. In the present paper we show that the near-neighbor effects can be introduced into the theory by a simple extension in the logic of the cooperativity. The present theory can give base-sequence effects on melting as well as premelting behavior in agreement with experiments. These effects arise from the same interatomic interaction model used in our earlier calculations [Biopolymers 33, 351 (1993); 33, 797 (1993)] and the results do not require the explicit introduction of near-neighbor parameters. The work then becomes a no-parameter derivation of near-neighbor effects in DNA.