Simulation-guided tunable DNA probe design for mismatch tolerant hybridization.

ABSTRACT: The ability to both sensitively and specifically assess the sequence composition of a nucleic acid strand is an ever-growing field. Designing a detection scheme that can perform this function when the sequence of the target being detected deviates significantly from the canonical sequence however is difficult in part because probe/primer design is based on established Watson-Crick base-pairing rules. We present here a robust and tunable toehold-based exchange probe that can detect a sequence with a variable number of SNPs of unknown identity by inserting a series of controlled, sequential mismatches into the protector seal of the toehold probe, in an effort to make the protector seal "sloppy". We show that the mismatch-tolerant system follows predicted behavior closely even with targets co

SUBMITTER: Bugga P 

PROVIDER: S-EPMC11340886 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature