Electrochemical Determination of Triple Helices:  Electrocatalytic Oxidation of Guanine in an Intramolecular Triplex

• Published in: Inorganic chemistry 2004-08, Vol.43 (16), p.5080-5085
• Main Authors: Holmberg, Rebecca C, Thorp, H. Holden
• Format: Article
• Language: English
• Subjects: Base Sequence; DNA - chemistry; Electrochemistry; Guanine - chemistry; Models, Molecular; Nucleic Acid Conformation; Oligonucleotides - chemistry; Organometallic Compounds - chemistry; Oxidation-Reduction; Ruthenium - chemistry; Thermodynamics
• ISSN: 0020-1669; 1520-510X
• DOI: 10.1021/ic049895x

Electrocatalytic oxidation of the oligonucleotide 5‘- GAA GAG GTT TTT CCT CTT CTT TTT CTT CTC C (TS) by Ru(bpy)3 2+ was studied by cyclic voltammetry. This oligonucleotide forms either an intramolecular triplex, hairpin, or single strand, depending on the pH (Plum, G. E.; Breslauer, K. J. J. Mol. Biol. 1995, 248, 679−695). In the triplex form, the guanine doublet in TS is buried inside the folded structure, and as such is less susceptible to oxidation by electrogenerated Ru(bpy)3 3+. Digital simulations of the catalytic voltammograms gave a rate constant of 3.5 ± 0.2 × 102 M-1 s-1 for oxidation of the triplex form, while oxidation of the duplex and single-stranded forms occurred with much faster rate constants of (3.5−9.1) × 104 M-1 s-1. Experiments using a truncated form of TS that lacked the third strand of the triplex were consistent with these measurements. The Ru(bpy)3 3+ complex was also generated by photolyzing Ru(bpy)3 2+ in the presence of Fe(CN)6 3-. This reaction produced strand scission following piperidine treatment, which was visualized using high-resolution gel electrophoresis. These experiments showed decreased reactivity for the triplex form, and also gave an unusual reversal of a common selectivity for the 5‘-G of GG doublets generally seen in B-form DNA. This reversal was ascribed to strain caused by the location of the GG doublet adjacent to the hairpin loop.