Sensitive and selective nucleic acid capture with shielded covalent probes

Abstract

Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible and not all desired targets are bound). These limitations stem from reliance on base pairing to both reject off-targets and retain desired targets. To address this selectivity/affinity tradeoff, shielded covalent probes achieve selectivity via conformation change and durable capture via covalent crosslinking of a photoactive nucleoside analog. In vitro assays show that mismatches are efficiently rejected and desired targets are durably captured. For probes designed to reject two-nucleotide mismatches, desired targets are captured nearly quant. Single-nucleotide mismatches are discriminated near the thermodn. limit. The probes operate isothermally and crosslinking activation is rapid with low-cost light sources. If desired, crosslinks can be reversed to release the target after capture. We envision a wide array of applications.