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Selecting Specific PCR Primers with MFEprimer

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PCR Primer Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1275))

Abstract

Selecting specific primers is crucial for polymerase chain reaction (PCR). Nonspecific primers will bind to unintended genes and result in nonspecific amplicons. MFEprimer is a program for checking the specificity of PCR primers against the background DNA. In this chapter, we introduce: (1) the factors that affect the specificity of primers; (2) the principle of MFEprimer and its settings; (3) how to use the MFEprimer to examine the specificity of primers.

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Acknowledgement

This work was supported by the National Basic Research Project (973 program) (2012CB518200), the General Program (31371345, 30900862, 30973107, 81070741, 81172770) of the Natural Science Foundation of China, the State Key Laboratory of Proteomics of China (SKLP-O201104, SKLP-K201004, SKLP-O201002), and the Special Key Programs for Science and Technology of China (2012ZX09102301-016).

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Authors and Affiliations

  1. Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Cognitive and Mental Health Research Center of PLA, Beijing, 100850, China

    Wubin Qu & Chenggang Zhang

Authors
  1. Wubin Qu
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  2. Chenggang Zhang
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Corresponding author

Correspondence to Chenggang Zhang .

Editor information

Editors and Affiliations

  1. Department of Biology, California State University, Northridge, Los Angeles, California, USA

    Chhandak Basu

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Qu, W., Zhang, C. (2015). Selecting Specific PCR Primers with MFEprimer. In: Basu, C. (eds) PCR Primer Design. Methods in Molecular Biology, vol 1275. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2365-6_15

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  • DOI: https://doi.org/10.1007/978-1-4939-2365-6_15

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2364-9

  • Online ISBN: 978-1-4939-2365-6

  • eBook Packages: Springer Protocols

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