Improved Allelic Differentiation Using Sequence‐Specific Oligonucleotide Hybridization Incorporating an Additional Base‐Analogue Mismatch

Abstract

Sequence‐specific oligonucleotide hybridization (SSOH, ‘dot‐blotting’) is a widely employed method of typing single nucleotide polymorphisms (SNPs), but it is often compromised by lack of allelic differentiation. We describe a novel improvement to SSOH that incorporates an additional mismatch into the oligonucleotide probe using the universal base analogue 3‐nitropyrrole. This method greatly increases allelic differentiation compared to standard SSOH where oligonucleotides contain only SNP‐defining base changes. Moreover, stringency of the hybridisation is predictably maintained over a wide range of temperatures, which can be calculated empirically, thus facilitating the genotyping of multiple SNPs using similar conditions. This improved method increases the usefulness of hybridisation‐based methods of rapid genotyping of SNPs and may have implications for array methodologies.

Keywords:

• Sequence‐specific oligonucleotide hybridization
• Dot‐blotting
• Universal base analogue
• Base mismatch

Acknowledgments

We thank Val Cooper (University of Oxford, UK) and Peter Dean (Cambio Ltd., Cambridge, UK) for assistance with oligonucleotide preparation. Grant sponsors: Medical Research Council UK (DB and DK) and Telethon Italy 368/b (MD).