Specific annealing of 3' hairpin OCP to its genomic target followed by ligation. The hairpin structure can increase OCP discrimination during ligation by providing a two state equilibrium for the OCP, where OCP is either in the hairpin form or annealed to target. A mismatch between target and OCP favors the intra-molecular hairpin formation. A match between the OCP and the target provides an extended region of complementarity that is sufficient to maintain stable binding of the 3' end of the OCP to the target, allowing ligase to circularize the OCP. This balance contributes to accurate and sensitive allele discrimination.
Alsmadi et al. BMC Genomics 2003 4:21 doi:10.1186/1471-2164-4-21