KMnO4 has been well known as a powerful chemical probe for numerous applications in biological fields, particularly for those used in conformational studies of DNA. The KMnO4 assay provides essential information for understanding biochemical processes and detecting aberrant DNA, which is associated with many genetic diseases. Elegant examples are sequencing techniques, foot-printing assays for transcriptional studies, an interference method for hormone receptor binding assays as well as DNA conformational studies of Z-DNA, Z-Z junctions, hairpins, curvatures, short nucleotide base repeats, binding of intercalators and groove binders, etc. Recently, KMnO4 has been successfully applied to detect single base changes and mutations in DNA (chemical cleavage of mismatch method, CCM) as well as other types of base damage (8-oxoguanine and thymine dimers). This paper aims to review the usefulness and limitations of the permanganate oxidation reaction used in various biological studies of DNA.
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