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. Pyrenebutanoic acid (P) has been attached through 6-aminohexyl or 3-aminopropyl linkers to the 5‘ edge of an oligonucleotide composed of 10 deoxyadenosines (A) and one deoxyguanosine (G) at a defined site along each strand, P−NH−(CH 2 ) 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 corresponding positions required for matched base pairing, 5‘-T 10 - n CT n -3‘ ( n = 2−10). This configuration has allowed us to investigate deoxyguanosine-induced quenching of pyrenebutanoamide fluorescence (through guanine to pyrenebutanoamide electron transfer or nonradiative internal conversion) along oligonucleotides in either single- or double-stranded forms. The observed quenching rates in the (CH 2 ) 6 -linked series do not depend monotonically on the distance separating the excited pyrenebutanoamide from the deoxyguanosine quencher because a less efficient competing quenching by deoxythymidosine on the complementary chain complicates the kinetic analysis. The observed quenching efficiency along a DNA segment is significantly affected by the conformation of the appended quencher.