Effects of Base Stacking on Guanine Electron Transfer: Rate Constants for G and GG Sequences of Oligonucleotides from Catalytic Electrochemistry

Abstract

The electron-transfer rate constants for oligonucleotides containing adjacent guanines were determined by digital simulation of cyclic voltammograms of Ru(bpy)32+ in the presence of the oligonucleotides (bpy = 2,2‘-bipyridine). These experiments showed that sequences containing an isolated guanine (included in a 5‘-AGT segment) gave a rate constant of 1.4 × 105 M-1 s-1 (in terms of guanine concentration) while sequences containing a 5‘-GG segment gave an overall rate constant of 7.5 × 105 M-1 s-1. Both rate constants were independent of DNA concentration in the simulations. By assuming that the 3‘-G of the GG doublet exhibits the same rate constant as the isolated guanine, we estimate the ratio of rate constants for the 5‘-G of the GG doublet to the 3‘-G to be kGG/kG = 12 ± 2. This value was independent of DNA concentration and scan rate. Similar experiments using oligonucleotides containing inosine (I) in place of guanosine gave the same rate constant for a 5‘-IG doublet as for isolated guanine (kIG/kG = 1.0 ± 0.2) but gave significant enhancement for the 5‘-GI sequence (kGI/kG = 2.8 ± 0.4). These experiments show that it is in fact the 5‘-G that is enhanced and support the assumption that the 3‘-G of the GG doublet gives the same rate constant as isolated guanine. Stacking of guanines on the 5‘ side of 7-deazaguanine did not produce current enhancements as large as those for the GG segments, strongly supporting the idea that favorable placement of the electronegative N7 atom of the 3‘ base in the doublet is responsible for the increased electron donor reactivity.