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Single nucleotide polymorphism detection by polymerase chain reaction-restriction fragment length polymorphism

Nature Protocols volume 2, pages 2857–2864 (2007)Cite this article

Abstract

Accurate analysis of DNA sequence variation in not only humans and animals but also other organisms has played a significant role in expanding our knowledge about genetic variety and diversity in a number of different biological areas. The search for an understanding of the causes of genetic variants and mutations has resulted in the development of a simple laboratory technique, known as the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, for the detection of single nucleotide polymorphisms (SNPs). PCR-RFLP allows rapid detection of point mutations after the genomic sequences are amplified by PCR. The mutation is discriminated by digestion with specific restriction endonucleases and is identified by gel electrophoresis after staining with ethidium bromide (EtBr). This convenient and simple method is inexpensive and accurate for SNP genotyping and especially useful in small basic research studies of complex genetic diseases. The whole protocol takes only a day to carry out.

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Figure 1: PCR-RFLP typing of HLA-DRB132.
Figure 2: ABO genotyping by PCR-RFLP34.
Figure 3: The mismatch PCR-RFLP method for the detection of Y393N in exon 9 of the BCKDHA gene38.

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Authors and Affiliations

  1. Department of Legal Medicine, Shinshu University School of Medicine, Nagano, 390-8621, Japan

    Masao Ota & Hirofumi Fukushima

  2. Centre for Comparative Genomics, School of Information Technology, Murdoch University, Murdoch, 6150, Western Australia, Australia

    Jerzy K Kulski

  3. Department of Molecular Life Science, Division of Molecular Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa, 259-1143, Japan

    Jerzy K Kulski & Hidetoshi Inoko

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  1. Masao Ota
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Correspondence to Masao Ota.

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Ota, M., Fukushima, H., Kulski, J. et al. Single nucleotide polymorphism detection by polymerase chain reaction-restriction fragment length polymorphism. Nat Protoc 2, 2857–2864 (2007). https://doi.org/10.1038/nprot.2007.407

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