Structural Transitions in A Fluorescent Dna Duplex Decamer

Incorporation of 2-aminopurine (2AP) for adenine in DNA gives an optical probe of local and global DNA conformation, since 2AP does not seriously disturb the B-DNA structure. The temperature dependence of the absorption of the double-stranded d[CTGA[2AP]TTCAG]2 DNA decamer shows that the helix melts in an all-or-none fashion. Absorbance at wavelengths of 260 nm and 330 nm monitor, respectively, the `average' normal base conformation and the 2AP base local conformation. The 2AP base locally melts at a temperature 0.5 degree(s)C or less below the other bases. Temperature dependence of the longest fluorescence decay time of the decamer also shows the melting transition, with the transition curve shifted a few degrees higher. Temperature dependent fluorescence spectral shifts, on the other hand, suggest the environment of the 2AP base changes about 10 degree(s)C below the primary melting temperature. The data suggest a premelting transition purely dynamic in nature--transient 2AP exposure to water increases but the average conformation remains B helical. A summary of conformational information extractable from 2AP fluorescence measurements is presented.