Detection of Single Base Substitutions by Ribonuclease Cleavage at Mismatches in RNA:DNA Duplexes

TLDR

Single base substitutions can be detected and localized by ribonuclease cleavage of mismatches in RNA:DNA heteroduplexes. A 32P‑labeled RNA probe complementary to wild‑type DNA is annealed to test DNA containing a single base substitution, the mismatch is cleaved by ribonuclease A, and the cleavage site is identified by gel electrophoresis of the product sizes. Analysis of all mismatch types and sequence contexts shows that more than 50 % of single base substitutions are detectable, and the method successfully localizes mutations in genomic DNA from β‑thalassemia patients.

Abstract

Single base substitutions can be detected and localized by a simple and rapid method that involves ribonuclease cleavage of single base mismatches in RNA:DNA heteroduplexes. A 32 P-labeled RNA probe complementary to wild-type DNA is synthesized in vitro and annealed to a test DNA containing a single base substitution. The resulting single base mismatch is cleaved by ribonuclease A, and the location of the mismatch is then determined by analyzing the sizes of the cleavage products by gel electrophoresis. Analysis of every type of mismatch in many different sequence contexts indicates that more than 50 percent of all single base substitutions can be detected. The feasibility of this method for localizing base substitutions directly in genomic DNA samples is demonstrated by the detection of single base mutations in DNA obtained from individuals with β-thalassemia, a genetic disorder in β-globin gene expression.