ELECTROCHEMICAL MEASUREMENT OF THE SOLVENT ACCESSIBILITY OF NUCLEOBASES USING ELECTRON-TRANSFER BETWEEN DNA AND METAL-COMPLEXES

Oxidizing metal complexes mediate the electrochemical oxidation of gua nine nucleotides in polymeric DNA and oligonucleotides. This catalysis results in an enhancement in cyclic voltammograms that yields the rat e constant for oxidation of guanine by the metal complex via digital s imulation. The rate constant for oxidation of guanine in calf thymus D NA by Ru(bpy)(3)(3+) is 9.0 x 10(3) M(-1) s(-1). which has been confir med in separate experiments utilizing pulsed voltammetry and stopped-f low spectrophotometry. The rate constant depends linearly on the drivi ng force with a slope of 1/2, as predicted by Marcus theory. Formation of the double helix precludes direct collision of the metal complex w ith the guanine residue, which imposes a finite distance of solvent th rough which the electron must tunnel. This distance is dependent on th e presence of the oxidized guanine in a mismatch, which decreases the tunneling distance as assessed from electron-transfer theory. The oxid ation rate constants therefore follow the trend G (single strand) > GA > GG > GT > GC. These mismatches are all distinguishable from one ano ther, providing a new basis for probing small changes in the solvent a ccessibility of guanine that may be useful in DNA sequencing or quanti tatively mapping complex nucleic acid structures.