Premelting thermal fluctuational interbase hydrogen-bond disrupted states of a B-DNA guanine-cytosine base pair: significance for amino and imino proton exchange.

Modified self-consistent phonon theory when applied to the DNA double helix indicates the existence of fairly long-lived states in which single interbase H bonds are disrupted. One can then postulate a number of situations in which particular disrupted H bonds can enhance particular proton exchange. In this paper we postulate a number of such partially open states for a B-conformation GC base pair and calculate the probability of each of these states for a B-conformation poly(dG).poly(dC). We compare these probabilities to those probabilities needed to explain various observed proton exchange rates. We propose that, for a GC base pair in B conformation, there are two amino proton exchangeable states--a cytosine amino proton exchangeable state and a guanine amino proton exchangeable state; both require the disruption of only the corresponding interbase H bond. The imino proton exchange, however, requires the disruption of all three interbase H bonds and this defines a third open state. Our calculated probabilities for a GC base pair in these three states are in fair agreement with available experimental estimates from measurements of amino and imino proton exchange.