Shiva P Adhikari

Major: Chemistry

Faculty Advisor: Patrick Hrdlicka

Project Title:

Optimizing Invader probes for enhanced sequence-unrestricted recognition of double-stranded DNA targets

Abstract

Sequence-specific recognition of double-stranded (ds) DNA at physiological conditions has a wide range of applications in diagnostic and therapeutic fields. Our laboratory has designed so-called Invader probes, which are short DNA duplexes featuring +1 interstrand arrangements of O2'-intercalator-functionalized RNA monomers as the central design feature that activates Invader probes for specific sequence-unrestricted dsDNA recognition. The design relies on large stability differences between probe duplexes and recognition complexes to drive dsDNA recognition. Invader probes exhibit avidity in binding to dsDNA via invasion modes, offer the promise of favorable binding affinity and specificity, and straightforward design. In the present study, we set out to optimize the dsDNA-recognition properties of Invader probes through introduction of nicks  (i.e., nicked Invader probes, NIPs). Appropriately designed nicked Invader probes display significantly more efficient recognition of model mixed-sequence dsDNA targets than conventional Invader probes at physiological conditions.