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The electrophoretic gel-based chemical cleavage of the mismatch method gives an incomplete view of the DNA conformational changes induced by a single base mismatch. This spectroscopic study investigates the permanganate oxidation reactions with matched and mismatched DNA under constant and variable temperature conditions. The results, which include the oxidation levels, reaction patterns with isosbestic points, color changes, thermal spectra, spectroscopy derivative, and gel separation and melting temperatures, provide a fundamental background for identification of oligonucleotides containing single base mismatches by chemical means.

Background: The conventional solution-phase Chemical Cleavage of Mismatch (CCM) method is time-consuming, as the protocol requires purification of DNA after each reaction step. This paper describes a new version of CCM to overcome this problem by immobilizing DNA on silica solid supports.