COBRA is a great, flexible, and easy method to quantitatively analyze CpG dinucleotides within DNA, at specific gene loci in small amount of DNA. It is a great method to use, as it can quantitatively assess CpG islands. Sodium bisulfite treatment of DNA is the initial step, followed by PCR. Subsequently, restriction digestion of the DNA is carried out. Methylation levels in the original DNA sample are revealed by the differing amounts of digested and undigested PCR products quantitatively. Overall, a great method, especially for paraffin sections, and clinical studies due to its ease and quantitative aspects.
Z. Xiong et al. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res (1997) 24: 5058-5059.