Development of a universal probe for electronic microarray and its application in characterization of the...

Electronic microarray technology is an exceptionally accurate and effective technique for detecting and defining single nucleotide polymorphisms (SNPs) in DNA sequences. Target oligonucleotides are electronically addressed to a gel matrix containing streptavidin to which biotinylated polymerase chain reaction (PCR) amplicons are bound. Typically, a fluorescent-labeled reporter oligonucleotide specific for each locus of interest is hybridized and reported. We detail the development of a universal reporter system to replace the standard method that is used to detect many different sequences accurately. The universal reporter eliminates the need to synthesize specific labeled reporters for each SNP sequence thereby dramatically reducing the cost and time required for assay development. The feasibility of this approach was demonstrated by successfully analyzing eight SNPs distributed within a highly variable 1-kb region of the polC gene from six isolates of Staphylococcus aureus.