Single-strand conformation polymorphism

Single-strand conformation polymorphism (SSCP), or single-strand chain polymorphism, is defined as conformational difference of single-stranded nucleotide sequences of identical length as induced by differences in the sequences under certain experimental conditions. This property allows sequences to be distinguished by means of gel electrophoresis, which separates fragments according to their different conformations.[1]

Physical background

A single nucleotide change in a particular sequence, as seen in a double-stranded DNA, cannot be distinguished by electrophoresis, because the physical properties of the double strands are almost identical for both alleles. After denaturation, single-stranded DNA undergoes a 3-dimensional folding and may assume a unique conformational state based on its DNA sequence. The difference in shape between two single-stranded DNA strands with different sequences can cause them to migrate differently on an electrophoresis gel, even though the number of nucleotides is the same, which is, in fact, an application of SSCP.

Applications in molecular biology

SSCP used to be a way to discover new DNA polymorphisms apart from DNA sequencing, but is now being supplanted by sequencing techniques on account of efficiency and accuracy.[2] These days, SSCP is most applicable as a diagnostic tool in molecular biology. It can be used in genotyping to detect homozygous individuals of different allelic states, as well as heterozygous individuals that should each demonstrate distinct patterns in an electrophoresis experiment.[3] SSCP is also widely used in virology to detect variations in different strains of a virus, the idea being that a particular virus particle present in both strains will have undergone changes due to mutation, and that these changes will cause the two particles to assume different conformations and, thus, be differentiable on an SSCP gel.[4]

References

  1. ↑ Masato Orita, Hiroyuki Iwahana, Hiroshi Knazawa, Kenshi Hayashi and Takato Sekiya Detection of the polymorphisms of human DNA by gelelectrophoresis as single-strand conformation polymorphisms. Proc. Natd.Acad. Sci. USA 86, 2766-2770, 1989.
  2. ↑ Tahira, T.; Kukita, Y.; Higasa, K.; Okazaki, Y.; Yoshinaga, A.; Hayashi, K. (2009). "Estimation of SNP allele frequencies by SSCP analysis of pooled DNA.". Methods Mol Biol 578: 193–207. doi:10.1007/978-1-60327-411-1_12. PMID 19768595.
  3. ↑ Michiei Oto, Satoshi Miyake and Yasuhito Yuasa. Optimization of Nonradioisotopic Single Strand Conformation Polymorphism Analysis with a Conventional Minislab Gel Electrophoresis Apparatus. Analytical Biochemistry, 213, 19-22, 1993.
  4. ↑ Karen Sumire Kubo, R. M. Stuart, J. Freitas-Astúa1, R. Antonioli-Luizon, E. C. Locali-Fabris, H. D. Coletta-Filho1, M. A. Machado and E. W. Kitajima. Evaluation of the genetic variability of orchid fleck virus by single-strand conformational polymorphism analysis and nucleotide sequencing of a fragment from the nucleocapsid gene. Archives of Virology, Official Journal of the Virology Division of the International Union of Microbiological Societies, 21 May 2009.


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