Primer Design

Design of Oligonucleotide PCR Primers and Hybridization Probes
  • Henrik ChristensenEmail author
  • John Elmerdahl Olsen
Part of the Learning Materials in Biosciences book series (LMB)


An overview of the application of oligonucleotide design is given in relation to applications involving exploratory investigations and diagnostics. The criteria for selection of oligonucleotides including lengths of PCR primers and products, lengths of oligonucleotide hybridization probes, and the principles for sequence comparison are introduced as well as rules for sequence-based prediction of amplification as well as prediction of Tm. Computer programs are suggested accounting for the different applications mainly related to PCR such as degenerate primers, multiplex PCR, nested PCRs and SNPs, and hybridization such as microarrays and in situ hybridization. The activity demonstrates the design of oligonucleotides for PCR amplification of single DNA sequences and primerBLAST for the design of diagnostic PCR primers.


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Further Readings

  1. Introduction to practical work with PCR as well to the historical background is found in Sambrook and Russell (2001).Google Scholar
  2. Sambrook and Russell. 2001. Molecular Cloning. A laboratory manual. CSHL Pres.Google Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Department of Veterinary Animal SciencesUniversity of CopenhagenCopenhagenDenmark

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