Premelting thermal fluctuational interbase hydrogen‐bond disrupted states of a B‐DNA guanine–cytosine base pair: Significance for amino and imino proton exchange

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Abstract
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 inter base H bond. The imino proton exchange, however, requires the disruption of all three inter base 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.