Photophysical quenching mediated by guanine groups in pyrenyl-N-alkylbutanoamide end-labeled oligonucleotides

Two series of pyrenyl-N-alkylbutanoamide end-labeled oligonucleotides have been prepared as models for photophysical quenching along DNA segments. Pyr enebutanoic acid (P) has been attached through 6-aminohexyl or 3-aminopropy l linkers to the 5' edge of an oligonucleotide composed of 10 deoxyadenosin es (A) and one deoxyguanosine (G) at a defined site along each strand, P-NH -(CH2)(3) (or 6)-5'-A(n)GA(10-n)-3' (n = 2-10). The complementary strand is composed of deoxythymidosines (T) and one deoxycytidosine (C) at the corre sponding positions required for matched base pairing 5'-T10-nCTn-3' (n = 2- 10). This configuration has allowed us to investigate deoxyguanosine-induce d quenching of pyrenebutanoamide fluorescence (through guanine to pyrenebut anoamide electron transfer or nonradiative internal conversion) along oligo nucleotides in either single- or double-stranded forms. The observed quench ing rates in the (CH2)(6)-linked series do not depend monotonically on the distance separating the excited pyrenebutanoamide from the deoxyguanosine q uencher because a less efficient competing quenching by deoxythymidosine on the complementary chain complicates the kinetic analysis. The observed que nching efficiency along a DNA segment is significantly affected by the conf ormation of the appended quencher.