ABSTRACT
This chapter discusses in some detail methods for detection of single nucleotide polymorphisms. Hybridization modifiers such as minor-groove binders and locked nucleic acids have been incorporated into a variety of genotyping platforms. These modifications increase the stability of deoxyribonucleic acid duplexes, thereby enabling the use of shorter oligonucleotides in analyses which in turn leads to greater differences in allele-specific hybridization reactions. Mass spectrometry (MS) can be used to measure small differences in molecular weights of allele-specific reaction products. The MS technique termed matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been successfully implemented in a number of single nucleotide polymorphisms detection schemes. The oligonucleotide ligation assay has been further developed in the padlock probe assay. Allele-specific and locus-specific probes are designed so that they are connected at their distal ends to form a single probe that becomes circularized upon ligation.
