DNA Chip Microarray, Overlapping Sequences, Specific Solitary Nucleotides, Involves Tiling Strategy, Biotinylated PCR Product, Suitable Detection System

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DNA chip/microarray.

An array of oligonucleotides of known overlapping sequences, which differ at specific solitary nucleotides (at the site of SNP) can also be used for detection of SNPs.

The technique is also described as sequencing by hybridization (SBH) and involves tiling strategy.

Four oligonucleotides will differ at the SNP position and only one will be fully homologous.

When such an array is hybridized with biotinylated PCR product, the perfect match will allow binding and mismatched products will be washed away.

The perfect match can be detected through a suitable detection system.

As many as 300,000 oligonucleotides can be available on a 1.3 x 1.3 cm² slide, permitting many SNPs to be analysed in parallel.

This technique is not suitable for genotyping many individuals at one or few SNP sites, as needed for

MAS, but is suitable for detecting new SNPs (consult Chapter for SBH using microarrays).

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