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Molecular Toxicology Protocols pp 365–380Cite as

Gel-Based Nonradioactive Single-Strand Conformational Polymorphism and Mutation Detection: Limitations and Solutions

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1105))

Abstract

Single-strand conformation polymorphism (SSCP) for screening mutations/single-nucleotide polymorphisms (SNPs) is a simple, cost-effective technique, saving an expensive exercise of sequencing each and every polymerase chain reaction product and assisting in choosing only the amplicons of interest with expected mutations. The principle of detection of small changes in DNA sequences is based on changes in single-strand DNA conformations. The changes in electrophoretic mobility that SSCP detects are sequence dependent. The limitations faced in SSCP range from routine polyacrylamide gel electrophoresis (PAGE) problems to the problems of resolving mutant DNA bands. Both these problems can be solved by controlling PAGE conditions and by varying physical and environmental conditions such as pH, temperature, voltage, gel type and percentage, addition of additives or denaturants, and others. Despite much upgrading of the technology for mutation detection, SSCP remains the method of choice to analyze mutations and SNPs in order to understand genomic variations, both spontaneous and induced, and the genetic basis of diseases.

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Authors and Affiliations

  1. Human Genetics Section, School of Life Sciences, National Centre of Applied Human Genetics, Jawaharlal Nehru University, New Meharuli Road, New Delhi, 110067, India

    Vibhuti Gupta, Reetakshi Arora, Sailesh Gochhait, Narendra K. Bairwa & Rameshwar N. K. Bamezai

Authors
  1. Vibhuti Gupta
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  2. Reetakshi Arora
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  3. Sailesh Gochhait
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  4. Narendra K. Bairwa
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  5. Rameshwar N. K. Bamezai
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Corresponding author

Correspondence to Rameshwar N. K. Bamezai .

Editor information

Editors and Affiliations

  1. Occupational Health, University of Pittsburgh Dept. Environmental &, Pittsburgh, Pennsylvania, USA

    Phouthone Keohavong

  2. Dept. of Pharmaceutical Sciences, Nova Southeastern University College of Pharmacy, Fort Lauderdale, Florida, USA

    Stephen G. Grant

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© 2014 Humana Press

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Gupta, V., Arora, R., Gochhait, S., Bairwa, N.K., Bamezai, R.N.K. (2014). Gel-Based Nonradioactive Single-Strand Conformational Polymorphism and Mutation Detection: Limitations and Solutions. In: Keohavong, P., Grant, S. (eds) Molecular Toxicology Protocols. Methods in Molecular Biology, vol 1105. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-739-6_28

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  • DOI: https://doi.org/10.1007/978-1-62703-739-6_28

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-738-9

  • Online ISBN: 978-1-62703-739-6

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