Mismatches between RNA:RNA and RNA:DNA heteroduplexes are cleaved by ribonuclease A.68 Cleavage of labeled fragments is detected by the presence of shorter fragments on denaturing gels. Fragments as large as 1000 base pairs can be analyzed. Larger fragments are separated under denaturing conditions, but incomplete separation makes interpretation difficult.69 Only about 70% of mutations are detected. The need to prepare RNA as a probe and the inherent instability of RNA as a substrate are additional drawbacks of this technique. For these reasons, this method is less suitable for scanning than other methods.
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