Single strand conformation polymorphism

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[edit] Definition

Single strand conformation polymorphism (SSCP) 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 to distinguish the sequences by means of gel electrophoresis, which separates the different conformations.

[edit] Physical background

A single nucleotide change in a particular sequence, as seen in a double stranded DNA cannot be distinguished by electrophoresis, since the physical properties of the double strands are almost identical for both alleles. Contrariwise, after denaturation, single strands undergo a 3-dimensional folding and may assume different conformational state according to DNA sequence. Depending on this folded structure that the molecules have assumed, they may travel faster or slower on a gel, even though the number of nucleotides is the same. This implies the limitation of SSCP, since conformational states are subject to many experimental conditions and sequence differences may or may not be detected.

[edit] 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 reasons. Also, SSCP can be used in genotyping to detect homozygous individuals of different allelic states, as well as heterozygous individuals which should demonstrate distinct patterns in an electrophoresis experiment each.

http://en.wikipedia.org/w/index.php?title=Single_strand_conformation_polymorphism (Retrieved 5 March 2007)