title: 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.
authors.affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
authors.forename: Lucien Junior
authors.initials: LJ
authors.lastname: Bergeron
authors.forename: Kaushiki
authors.initials: K
authors.lastname: Sen
authors.forename: Dipankar
authors.initials: D
authors.lastname: Sen
mesh_terms: D000225:Adenine / Q000737:chemistry; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004583:Electrons; D006147:Guanine / Q000737:chemistry*; D008954:Models, Biological; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D006147:Guanine; D012313:RNA; D004247:DNA; D000225:Adenine