Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine

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Abstract
DNA heptamers containing the mutagenic base analogue 2- aminopurine (AP) have been chemically synthesized and physically characterized. We report on the relative stabilities of base pairs between AP and each of the common DNA bases, as determined from heptamer duplex melts at 275 and 330nm. Base pairs are ranked in order of decreasing stability: AP·T > AP·A> AP·C > AP·G. It is of interest that AP·A is more stable than AP·C even though DNA polymerase strongly favors the formation of AP·C over AP·A base pairs. Comparisons of nelting profiles at 330nm and 275nm indicate that AP·T, AP·A, and AP·C base pairs are annealed in heptamer duplexes and melt 2–3° prior to surrounding base pairs, whereas AP·G appears not to be annealed.