A guanine-linked end-effect is a sensitive reporter of charge flow through DNA and RNA double helices

Abstract

The property of charge (electron hole) flow in DNA duplexes has been the subject of intensive study. RNA–DNA heteroduplexes have also been investigated; however, little information exists on the conductive properties of purely RNA duplexes. In investigating the relative conductive properties of a three molecule DNA–DNA duplex design, using piperidine and aniline to break strands at modified bases, we observed that duplexes with guanine-rich termini generated a large oxidative end-effect, which could serve as a highly sensitive reporter of charge flow through the duplexes. The end-effect was found faithfully to report attenuations in charge flow due to certain single-base mismatches within a duplex. Comparative charge flow experiments on DNA–DNA and RNA–RNA duplexes found large end-effects from both, suggesting that the A and B family of double helices conduct charge comparably. The sheer magnitude of the end-effect, and its high sensitivity to helical imperfections, suggest that it may be exploited as a sensitive reporter for DNA mismatches, as well as a versatile device for studying the structure, folding, and dynamics of complexly folded RNAs and DNAs.