Exploration of sequence specific DNA-duplex/pyrene interactions for intercalated and surface-associated pyrene species. Technical progress report

摘要

The use of both short (5-atom) and long (12-atom) covalent linking chains to attach, respectively, a pyrenesulfonate or a pyrenebutyrate moiety to a central region of a DNA duplex allows construction of DNA-duplex/pyrene assemblies of two types. Long linking chains permit pyrene to intercalate within the DNA duplex, while the short chains constrain pyrene to remain in the outer-surface region of the major-groove of the duplex. Electrochemical data suggest that reductive electron-transfer (ET) quenching of photoexcited pyrene (pyrene*) labels will be most exothermic for guanosine than for the other three DNA nucleosides and that oxidative ET quenching of pyrene* will be most exothermic for thymidine than for the other three DNA nucleosides. The study combines two effects, (1) differential DNA/pyrene geometries in covalent assemblies with different length linking chains and (2) differential ET quenching reactivities among the DNA nucleotides to explore sequence specific and duplex/pyrene association specific effects on DNA-base ionization reactions. This report describes progress in synthesizing target pyrene-labeled nucleosides and oligonucleotides, in commissioning our fluorescence lifetime measurement system, and in the photochemical behavior of pyrene-labeled nucleosides, single strands of DNA, and duplexes of DNA.