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| - Does the A·T or G·C Base-Pair Possess Enhanced Stability?Quantifying the Effects of CH···O Interactions and SecondaryInteractions on Base-Pair Stability Using a PhenomenologicalAnalysis and ab Initio Calculations
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| - An empirically based relationship between overall complex stability (−ΔG°) and various possiblecomponent interactions is developed to probe the question of whether the A·T/U and G·C base-pairs exhibitenhanced stability relative to similarly hydrogen-bonded complexes. This phenomenological approachsuggests ca. 2−2.5 kcal mol-1 in additional stability for A·T owing to a group interaction containing aCH···O contact. Pairing geometry and the role of the CH···O interaction in the A·T base-pair were alsoprobed using MP2/6-31+G(d,p) calculations and a double mutant cycle. The ab initio studies indicatedthat Hoogsteen geometry is preferred over Watson−Crick geometry in A·T by ca. 1 kcal mol-1. Factorsthat might contribute to the preference for Hoogsteen geometry are a shorter CH···O contact, a favorablealignment of dipoles, and greater distances between secondary repulsive sites. The CH···O interactionwas also investigated in model complexes of adenine with ketene and isocyanic acid. The ab initiocalculations support the result of the phenomenological approach that the A·T base-pair does have enhancedstability relative to hydrogen-bonded complexes with just N−H···N and N−H···O hydrogen bonds.
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