How can I confirm new-found SNP when probably no restriction enzyme exists for my target site?
You could see your SNP on High resolution polyacrilamide gel (MDE) cut your bands, put on water H2Odd 10 min, take 1 or 2 ul to reamplified your fragments, clone, and sequence.
Why not just Sanger sequence the region of interest? Perform Big Dye reaction in triplicate and pool the samples prior to sequencing for high accuracy.
You can make a specific qPCR or ddPCR assay (with MGB or LNA probe, or something similar) which is specific for only one of the variants. You can also do more sophisticated things, like this: http://bioscience.sequenom.com/biomarker-validation.
Just PCR amplify the region of interest, gel purify the PCR product and Sanger sequence it. To increase the reliability of your analysis you can sequence with both forward and reverse primers. Ideally your PCR product should be approx. 300-400 bp long with the SNP right in the middle of the amplicon. Don't forget that in presence of heterozygous SNPs you have to manually inspect the sequencing chromatogram in order to identify the presence of the double peak.
Avoid gel purification if possible (single band) and go straight to PCR clean up before sequencing.
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