Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches.

摘要: Naturally occurring chemoreceptors almost invariably employ structure-switching mechanisms, an observation that has inspired the use of biomolecular switches in a wide range artificial technologies areas diagnostics, imaging, and synthetic biology. In one mechanism for generating such behavior, clamp-based switching, binding occurs via clamplike embrace two recognition elements onto single target molecule. addition to coupling with large conformational change, this offers second advantage: it improves both affinity specificity simultaneously. To explore physics we have dissected here thermodynamics clamp-switch recognizes DNA sequence through Watson-Crick base pairing triplex-forming Hoogsteen interactions. When compared equivalent linear probe (which relies solely on interactions), extra interactions increase probe's its by ∼0.29 ± 0.02 kcal/mol/base. The likewise provide additional check increases discrimination efficiency toward single-base mismatch 1.2 0.2 kcal/mol. This, turn, leads 10-fold improvement width "specificity window" relative probe. Given these attributes, clamp-switches should be utility not only sensing applications but also, specific field nanotechnology, calling better control over building nanostructures nanomachines.