Allele-specific oligonucleotide

An allele-specific oligonucleotide (ASO) is a short piece of synthetic DNA complementary to the sequence of a variable target DNA. It acts as a probe for the presence of the target in a Southern blot assay or, more commonly, in the simpler dot blot assay. It is a common tool used in genetic testing, forensics, and molecular biology research.

An ASO is typically an oligonucleotide of 15–21 nucleotide bases in length. It is designed (and used) in a way that makes it specific for only one version, or allele, of the DNA being tested.^[1] The length of the ASO, which strand it is chosen from, and the conditions by which it is bound to (and washed from) the target DNA all play a role in its specificity. These probes can usually be designed to detect a difference of as little as 1 base in the target's genetic sequence, a basic ability in the assay of single-nucleotide polymorphisms (SNPs), important in genotype analysis and the Human Genome Project. To be detected after it has bound to its target, the ASO must be labeled with a radioactive, enzymatic, or fluorescent tag. The Illumina Methylation Assay technology takes advantage of ASO to detect one base pair difference (cytosine versus thymine) to measure methylation at a specific CpG site.