Using Restriction Enzymes to Identify SNPs

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June 28, 2016

Due to exciting future Citizen Salmon events we’ve been a bit slow on the Bioinformatics front. We are currently focused on the concept of using restriction enzymes to identify what alleles a sample may have for a specific SNP. Remember that SNPs are single nucleotide polymorphisms, and can present themselves as single base replacements (‘T’ or ‘G’) or as deletions. Restriction enzymes allow us to cut DNA at particular sites:

 

NEB provides a large range of restriction enzymes with different recognition sites. https://www.neb.com/tools-and-resources/usage-guidelines/nebuffer-performance-chart-with-restriction-enzymes

 

To practice this concept we’ll soon be running the PTC Tasting Lab. PTC is a chemical that tastes sour to some people while others may taste nothing. This is a common trait typically talked about in high school because it strongly follows Mendelian inheritance. It is also useful for us because much of the variation in bitterness perception is caused by three single nucleotide polymorphisms found on the TAS2R38 gene.

In this lab, we will isolate our DNA, run PCR on TAS2R38, and perform a DNA restriction digest using Fnu4HI. This restriction enzyme’s recognition site is

Fnu4H-I-cutsite_1

(N representing any of the 4 bases). One of the TAS2R38 SNPs reads GCTGC (taster) or GTTGC (non-taster), resulting in a cut for one allele but not the other.

For a further look, click here for a great explanation of the lab we’ll be running.