A quantitative and specific method for measuring transcript levels of highly homologous genes.

Because of their high nucleotide sequence homology, the specific detection of mRNA transcripts of individual members of a gene family presents certain problems. Here we apply and defend the single nucleotide primer extension (SNuPE) as a simple, specific, and highly quantitative assay for this purpose. The method distinguishes regions of the brain sodium channel gene family that vary by as little as a single nucleotide. The technique has been modified to include an intersample normalizer, and adaptation of the SNuPE assay to other gene families of interest to neuroscientists should be easy to achieve.