FIG. 1.

Schematic depiction of the reaction steps involved in the padlock probe assay. This example shows a pair of probes that discriminate the two alleles at an adenosine/guanosine polymorphism. (a) When a padlock probe hybridizes to complementary target DNA, the probe's two ends are brought into juxtaposition. Ligation of adjacent ends produces a circular DNA molecule. (b) In contrast, padlock probes that do not match the target DNA are not circularized and hence are removed through subsequent exonucleation. (c) Circular padlock probes can be PCR amplified by using one universal primer and one of two allele-specific primers that are labeled with different fluorescent dyes. (d) Amplification products are identified through hybridization to probes on a microarray that are complementary to the padlock probes' locus tags.