Restriction site insertion-PCR (RSI-PCR) for rapid discrimination and typing of closely related microbial strains

Daniele Daffonchio*, Sara Borin, Arianna Consolandi, Claudia Sorlini

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


Taking advantage of point mutations between DNA sequences of closely related microbial strains, PCR primers modified with respect to the target sequence at positions 2-5 near the 3' end were designed to obtain a fragment harbouring an artificial restriction site specific for a given strain. The modified forward primer coupled with a specific reverse primer allows for the amplification of DNA fragments which can be digested with the specific endonuclease only in those strains where the restriction site is inserted by the DNA polymerase. The effectiveness of the method, named restriction site insertion-PCR (RSI-PCR), was tested on isolates of the 'Bacillus cereus group' for the rapid typing and discrimination of these closely related strains. Copyright (C) 1999 Federation of European Microbiological Societies.

Original languageEnglish (US)
Pages (from-to)77-83
Number of pages7
JournalFEMS Microbiology Letters
Issue number1
StatePublished - Nov 1 1999
Externally publishedYes

Bibliographical note

Funding Information:
The study was performed in the ambit of the ELECTRO Project ‘Electrochemical treatment of fresh animal manure for reducing environment and health risk’, financed by the European Community (E.C. contract no. FAIR5-PL97-3506). We thank Prof. M. Mock and Dr. G. Patra, who kindly gave us the total DNA of B. anthracis, Prof. S. Scherer and Dr. R. Mayr for providing us the strains of B. weihenstephanensis and Prof. L.K. Nakamura for the B. pseudomycoides strains.


  • 3' End primer modification
  • Bacillus cereus group
  • Point mutation
  • Restriction analysis
  • Restriction site insertion-PCR
  • Strain identification

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology
  • Genetics


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