The accurate analysis of genetic variation has major implications in many areas of biomedical research, including the identification of
infectious agents (such as parasites), the diagnosis of infections, and the detection of unknown or known disease-causing mutations.
Mutation scanning methods, including PCR-coupled single-strand conformation polymorphism (SSCP), have significant advantages
over many other nucleic acid techniques for the accurate analysis of allelic and mutational sequence variation. The present protocol
describes the SSCP method of analysis, including all steps from the small-scale isolation of genomic DNA and PCR amplification of
target sequences, through to the gel-based separation of amplicons and scanning for mutations by SSCP (either by the analysis of
radiolabeled amplicons in mutation detection enhancement (MDE) gels or by non-isotopic SSCP using precast GMA gels). The
subsequent sequence analysis of polymorphic bands isolated from gels is also detailed. The SSCP protocol can readily detect point
mutations for amplicon sizes of up to 450–500 bp, and usually takes 1–2 days to carry out. This user-friendly, low-cost, potentially
high-throughput platform has demonstrated the utility to study a wide range of pathogens and diseases, and has the potential to be
applied to any gene of any organism.
The accurate analysis of genetic variation has major implications in many areas of biomedical research, including the identification ofinfectious agents (such as parasites), the diagnosis of infections, and the detection of unknown or known disease-causing mutations.Mutation scanning methods, including PCR-coupled single-strand conformation polymorphism (SSCP), have significant advantagesover many other nucleic acid techniques for the accurate analysis of allelic and mutational sequence variation. The present protocoldescribes the SSCP method of analysis, including all steps from the small-scale isolation of genomic DNA and PCR amplification oftarget sequences, through to the gel-based separation of amplicons and scanning for mutations by SSCP (either by the analysis ofradiolabeled amplicons in mutation detection enhancement (MDE) gels or by non-isotopic SSCP using precast GMA gels). Thesubsequent sequence analysis of polymorphic bands isolated from gels is also detailed. The SSCP protocol can readily detect pointmutations for amplicon sizes of up to 450–500 bp, and usually takes 1–2 days to carry out. This user-friendly, low-cost, potentiallyhigh-throughput platform has demonstrated the utility to study a wide range of pathogens and diseases, and has the potential to beapplied to any gene of any organism.
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