Derived Cleaved Amplified Polymorphic Sequences (dCAPS)

FROM NCBI

Introduction

The Derived Cleaved Amplified Polymorphic Sequences (dCAPS) assay is a modification of CAPS (or alternatively, PCR-RFLP) technique for detection of Single Nucleotide Polymorphisms (SNPs). In dCAPS assay a mismatches in PCR primer are used to create restriction endonuclease (RE)-sensitive polymorphism based on the target mutation. This technique is useful for genotyping known mutations and genetic mapping of isolated DNAs.

Similar to the CAPS technique, this method is simple, relatively inexpensive, and uses the ubiquitous technologies of PCR, restriction digestion and standard agarose gel electrophoresis

How It Works


The dCAPS technique introduces or destroys a restriction enzyme recognition sites by using primers that containing one or more micmatches to the template DNA. The PCR product modified in this manner is then subjected to restriction enzyme digestion and the presence or absence of the SNP is determined by the resulting restriction pattern.

Applications of dCAPS primers


To create a restriciton site that is dependent on the presence or absence of the SNP allele in question
To introduce a specific restriction site for each of two alleles being analyzed, to positively identify homozygotes for a particular allele without the possibbility of mis-scoring due to partial restriciton enzyme digestion
To disrupt an additional restriction site situated in close proximity to the CAPS polymorphism to be analyzed

REF：
Neff MM, Neff JD, Chory J, Pepper AE. dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J. 1998 May;14(3):387-92. PMID: 9628033


http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/TechDCAPS.shtml