5. Detection of Mutations in DNA and RNA by Chemical Cleavage
By: R. G. H. Cotton2
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This technique was developed to screen for point mutations, but deletions and insertions too small to be recognized by gel
electrophoretic techniques are also detected. Whereas earlier techniques are able to detect point mutations, not all mutations
were detected and/or the technique was not convenient or direct (reviewed in 1). The chemical cleavage of mismatch method (CCM) rapidly and reliably detects all classes of point mutations (2). Reference DNA probe is mixed with excess test DNA or RNA; the mixture is melted, and then cooled to allow reannealing and,
thus, heteroduplex formation with mismatched or unmatched base pairs at the position of the mutation. Probe is modified at
mismatched C and T bases by reaction with hydroxylamine and osmium tetroxide, respectively, and subsequently cleaved by piperidine
treatment. Fragments are sized on gels (of the type needed for sequencing) to locate the point of cleavage and, hence, the
mutation. In the case of point mutations, mismatched G and A bases will not be directly detected, but they are transposed
to mismatched C and T bases, respectively, by use of probe of opposite sense for detection. However, matched bases adjacent
or close to mismatched or unmatched bases become reactive by transmission of the distortion (2,3), and can signal the presence of the mutation and hence allow indirect detection. This allows detection of insertions (3). Unmatched C and T bases are also reactive, allowing detection of deletions.
Affiliation(s): (2) Olive Miller Protein Laboratory, Murdoch Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
Book Title: Protocols in Human Molecular Genetics
Series: Methods in Molecular Biology | Volume: 9 | Pub. Date: Nov-01-1991 | Page Range: 39-49 | DOI: 10.1385/0-89603-205-1:39
Subject: Genetics/Genomics
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