Single-strand conformation polymorphism (SSCP) is a popular method used to study the genetic heterogeneity and population variability of Citrus tristeza virus (CTV) isolates. It is a simple, low-cost, and highly specific method for mutation detection of specific genes, mostly of the CTV major coat protein gene (p25). The technique is based on a comparison on polyacrylamide gel of electrophoretic profiles of single-stranded (ss) DNA sequences in terms of their spatial conformation. SSCP involves cDNA synthesis and amplification of the target gene, denaturation of single strands, and electrophoresis in non-denaturing conditions. The ssDNAs can be afterward visualized by staining the polyacrylamide gel. Alternatively, using fluorescently labeled primers, the procedure can be performed in automated sequencers equipped with an appropriate capillary (CE-SSCP), which increases the potential of high-throughput analysis, precision, and the reproducibility of results. CE-SSCP can be also directly applied to the virus particles obtained by elution from ELISA plates or tissue-print membranes.
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