BASE-SEQUENCE DEPENDENCE OF EMISSION LIFETIMES FOR DNA OLIGOMERS AND DUPLEXES COVALENTLY LABELED WITH PYRENE - RELATIVE ELECTRON-TRANSFER QUENCHING EFFICIENCIES OF A-NUCLEOSIDE, G-NUCLEOSIDE, C-NUCLEOSIDE, AND T-NUCLEOSIDE TOWARD PYRENE

This paper reports both continuous and time-resolved spectroscopic studies of the emission properties of photoexcited pyrene labels covalently attached to uridine nucleosides and oligonucleotides. For all nucleic acid systems, uridine is substituted with pyrene at the 2'-oxygen position, 2'-O-[hexyl-N-(1-pyrenepropylcarbonyl)amino]uridine, U(12)*. Three types of nucleic acid systems are investigated: the 5'-OH (1) and the 5'-ODMT (2) substituted U(12)*-nucleosides; four pentameric oligonucleotides, X(2)U(12)*X(2), where X is 2'-deoxyadenosine (A), 2'-deoxyguanosine (G), 2'-deoxythymidine (T), or 2'-deoxycytidine (C); and four duplexes with 18 base pairs each containing one strand with a central U(12)* label. The central U(12)* label in the duplexes has the following flanking base-sequences, 5'-... AX(2)U(12)*X(2)A ... 3', where X is A, G, T, or C. The 400-nm region emission kinetics for the four U(12)*-labeled pentamers establish the following order of pyrene*-quenching reactivities by flanking DNA bases: A < G < T < C. This ordering of reactivities is generally consistent with expected reactivites based on estimates of the free energies of pyrene* quenching by electron transfer, Delta G degrees(ET), to or from flanking DNA bases. Emission spectra and lifetimes in the 495-mn region for both U(12)*-labeled pentamers and duplexes provide direct evidence for the formation and decay of the pyrene(.+)/U(12)(.-) charge-transfer (CT) product. In general ca. 20% of the amplitude of the CT emission decays in the 1-7 ns time range and 70-80% of its amplitude decays in less than or equal to 0.2 ns. The C2U(12)*C-2 pentamer has uniquely short pi,pi* emission decay with its longest emission-lifetime component lasting only 5.6 ns and its average emission lifetime less than or equal to 0.6 ns. (In contrast the longest pi,pi* emission components for pyrene butanoic acid (PBA) and U(12)*OH (1) in methanol last, respectively, 231 and 37 ns.) Finally, the longest pi,pi* emission lifetimes of U(12)*-labeled DNA duplexes exceed those of the corresponding pentamers. A measure of duplex-induced restricted access of pyrene* to base-paired nucleosides in double-strand (ds) versus single-strand(ss) DNA can be obtained by noting that the average pi,pi* emission lifetimes (for greater than 1 ns components) lengthen 3-fold on going from the T2U(12)*T-2 pentamer to the corresponding ... AT(2)U(12)*T(2)A .... duplex and 9-fold on going from the C2U(12)*C-2 pentamer to the ... AC(2)U(12)*C(2)A ... duplex.