RNase cleavage-based methods for mutation/SNP detection, past and present

Hum Mutat. 2001 Sep;18(3):190-204. doi: 10.1002/humu.1175.


Mutation detection based on ribonuclease cleavage of basepair mismatches in single-stranded RNA probes hybridized to DNA targets was first described over 15 years ago. The original methods relied on RNase A for mismatch cleavage; however, this enzyme fails to cleave many mismatches and has other drawbacks. More recently, a new method for RNase-cleavage-based mutation scanning has been developed, which takes advantage of the ability of RNase 1 and RNase T1 to cleave mismatches in duplex RNA targets, when these enzymes are used in conjunction with nucleic acid intercalating dyes. The method, called NIRCA, is relatively low-cost in terms of materials and equipment required. It is being used to detect mutations and SNPs in a wide variety of genes involved in human genetic disease and cancer, as well as in disease-related viral and bacterial genes. This review describes historical and recently developed RNase cleavage-based methods for mutation/SNP scanning.

Publication types

  • Review

MeSH terms

  • DNA / genetics
  • DNA / metabolism
  • DNA Mutational Analysis / methods*
  • Humans
  • Mutation / genetics*
  • Nucleic Acid Heteroduplexes / genetics
  • Nucleic Acid Heteroduplexes / metabolism
  • Polymorphism, Single Nucleotide / genetics*
  • RNA / genetics
  • RNA / metabolism
  • Ribonuclease T1 / metabolism
  • Ribonuclease, Pancreatic / metabolism
  • Ribonucleases / metabolism*


  • Nucleic Acid Heteroduplexes
  • RNA
  • DNA
  • Ribonucleases
  • Ribonuclease T1
  • Ribonuclease, Pancreatic