In Silico PCR Analysis

  • Bing YuEmail author
  • Changbin Zhang
Part of the Methods in Molecular Biology book series (MIMB, volume 760)


In silico PCR analysis is a useful and efficient complementary method to ensure primer specificity for an extensive range of PCR applications from gene discovery, molecular diagnosis, and pathogen detection to forensic DNA typing. In silico PCR, SNPCheck, and Primer-BLAST are commonly used web-based in silico PCR tools. Their applications are discussed here in stepwise detail along with several examples, which aim to make it easier for the intended users to apply the tools. This virtual PCR method can assist in the selection of newly designed primers, identify potential mismatches in the primer binding sites due to known SNPs, and avoid the amplification of unwanted amplicons so that potential problems can be prevented before any “wet bench” experiment.

Key words

Polymerase chain reaction primer binding site single nucleotide polymorphism (SNP) specific amplification 


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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of Molecular and Clinical GeneticsRoyal Prince Alfred HospitalCamperdownAustralia
  2. 2.Sydney Medical School (Central)The University of SydneyCamperdownAustralia
  3. 3.Prenatal Diagnostic CenterGuangdong Women and Children HospitalGuangzhouChina

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