Interaction-Dependent PCR (IDPCR) (CAT#: STEM-MB-0208-WXH)

IDPCR is based on the melting temperature (Tm) difference between duplex DNA formed intramolecularly versus intermolecularly, a difference that exploited to couple covalent bond formation with PCR amplification. We hypothesized that binding of a target to its ligand would increase the effective molarity of single-stranded DNA (ssDNA) oligonucleotides linked to the target and ligand, promoting duplex formation between complementary regions on each strand that are otherwise too short to hybridize. The resulting hairpin could serve as a starting point for primer extension. Crucially, only the newly extended hairpin contains in a single DNA strand two primer (or primer-binding) sequences that enable subsequent PCR amplification. IDPCR therefore results in the selective amplification of those DNA sequences previously attached to, and therefore encoding, ligand−target pairs. In contrast to traditional target-based selections, which rely on the physical separation of active molecules from inactive ones, IDPCR selectively amplifies DNA encoding active library members.

Detection of intermolecular interaction.

General procedure:
1. Denaturation
2. Annealing
3. Extension