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, ANDT-NUCLEOSIDE TOWARD PYRENE

This paper reports both continuous and time-resolved spectroscopic stu dies of the emission properties of photoexcited pyrene labels covalent ly attached to uridine nucleosides and oligonucleotides. For all nucle ic acid systems, uridine is substituted with pyrene at the 2'-oxygen p osition, -O-[hexyl-N-(1-pyrenepropylcarbonyl)amino]uridine, U(12). Th ree types of nucleic acid systems are investigated: the 5'-OH (1) and the 5'-ODMT (2) substituted U(12)-nucleosides; four pentameric oligon ucleotides, X(2)U(12)X(2), where X is 2'-deoxyadenosine (A), 2'-deoxy guanosine (G), 2'-deoxythymidine (T), or 2'-deoxycytidine (C); and fou r duplexes with 18 base pairs each containing one strand with a centra l U(12) label. The central U(12)* label in the duplexes has the follo wing 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(1 2)-labeled pentamers establish the following order of pyrene*-quenchi ng 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 tra nsfer, Delta G degrees(ET), to or from flanking DNA bases. Emission sp ectra and lifetimes in the 495-mn region for both U(12)-labeled penta mers and duplexes provide direct evidence for the formation and decay of the pyrene(.+)/U(12)(.-) charge-transfer (CT) product. In general c a. 20% of the amplitude of the CT emission decays in the 1-7 ns time r ange and 70-80% of its amplitude decays in less than or equal to 0.2 n s. The C2U(12)C-2 pentamer has uniquely short pi,pi* emission decay w ith its longest emission-lifetime component lasting only 5.6 ns and it s 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.) Fina lly, the longest pi,pi emission lifetimes of U(12)*-labeled DNA duple xes exceed those of the corresponding pentamers. A measure of duplex-i nduced restricted access of pyrene to base-paired nucleosides in doub le-strand (ds) versus single-strand(ss) DNA can be obtained by noting that the average pi,pi emission lifetimes (for greater than 1 ns comp onents) 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 fro m the C2U(12)C-2 pentamer to the ... AC(2)U(12)*C(2)A ... duplex.