Principles of the GOOD Assay

As the third step of the GOOD assay is a primer extension with a specifically tailored set of a-S-dNTPs and a-S-ddNTPs, dNTPs of the PCR have to be removed. This is done enzymatically by degradation of the dNTPs in the second step by shrimp alkaline phosphatase (SAP). 

A primer extension reaction is used to generate allele-specific products. A primer is chosen upstream of the SNP that is to be genotyped. Primers can be placed on either strand of the PCR product. They are synthesised with functionalities that will result in the final products being H-1 or -1 in net charge. Primers with chemical modifications are shown in figure 3. 

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Figure 4. Principle of the GOOD assay. CT synibolises the charge-tag, N" a DNA base and N a quartemary ammonium.

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