Multistate modeling of the time and temperature dependence of fluorescence from 2-aminopurine in a DNA decamer

Abstract

ABSTRACT The time and temperature dependence of the intrinsic fluorescence of double-stranded d(CTGA[2AP]TTCAG)2 DNA decamer containing a modified adenine base, 2AP, show that the bases exists in at least four distinct, interconverting conformations. The melting transition of the duplex governs the equilibrium of these states. Measurements on a purely single- stranded decamer facilitate the interpretation of data. States are identified as completelyunstacked, maximally stacked, and partially stacked, according to state fluorescencelifetimes and the temperature dependence of lifetimes and populations. The equilibrium ofstate populations in the single-stranded decamer is described accurately by simple enthalpyand entropy differences, where linear ln [population] vs. lIT plots are observed. Similar plots for the double-stranded show nonlinearities. The cooperative melting transition ofthe double-stranded decamer is reflected most strongly in the interconversion of the completely unstacked state with a partially-stacked state.