Schematic outline of molecular inversion probe (MIP) assay.

The MIP consists of two binding domains at its 3′ and 5′ ends which are designed complementary to target sequences in DNA. The MIPs also contained two universal primer binding domains (P1 and P2) in its DNA backbone. (A) Hybridization: B1 and B2 bind to specific sequences on the target DNA creating a 48 base single stranded gap between the binding domains of the MIP. (B) Gap filling: A DNA polymerase that lacks exonuclease and strand displacement activities synthesizes DNA from 3′ end of the MIP to 5′ end until the single stranded gap is filled. (C) Ligation: A DNA ligase ligates the 3′ end of the newly synthesized DNA strand with the 5′ end of the MIP creating a circular DNA. (D) Digestion: exonucleases I and III digest the linear MIPs and the DNA target in the reaction mixture leaving the circularized MIPs for amplification. (E) Polymerase chain reaction (PCR): A pair of universal primers (P1 and P2) amplifies the circularised MIP using the universal primer binding domains to generate PCR amplicons.