Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches.
Naturally occurring chemoreceptors almost invariably employ structure-switching mechanisms, an observation that has inspired the use of biomolecular switches in a wide range of artificial technologies in the areas of diagnostics, imaging, and synthetic biology. In one mechanism for generating such behavior, clamp-based switching, binding occurs via the clamplike embrace of two recognition elements onto a single target molecule. In addition to coupling recognition with a large conformational change, this mechanism offers a second advantage: it improves both affinity and specificity simultaneously. To explore the physics of such switches we have dissected here the thermodynamics of a clamp-switch that recognizes a target DNA sequence through both Watson-Crick base pairing and triplex-forming Hoogsteen interactions. When compared to the equivalent linear DNA probe (which relies solely on Watson-Crick interactions), the extra Hoogsteen interactions in the DNA clamp-switch increase the probe's affinity for its target by ∼0.29 ± 0.02 kcal/mol/base. The Hoogsteen interactions of the clamp-switch likewise provide an additional specificity check that increases the discrimination efficiency toward a single-base mismatch by 1.2 ± 0.2 kcal/mol. This, in turn, leads to a 10-fold improvement in the width of the "specificity window" of this probe relative to that of the equivalent linear probe. Given these attributes, clamp-switches should be of utility not only for sensing applications but also, in the specific field of DNA nanotechnology, for applications calling for a better control over the building of nanostructures and nanomachines.
Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata , Via della Ricerca Scientifica, 00133, Rome, Italy.
Andrea
A
Idili
Kevin W
KW
Plaxco
Alexis
A
Vallée-Bélisle
Francesco
F
Ricci
D020029:Base Pairing; D001483:Base Sequence; D015374:Biosensing Techniques; D001709:Biotechnology; D004247:DNA / Q000737:chemistry*; D005818:Genetic Engineering / Q000379:methods; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008024:Ligands; D008969:Molecular Sequence Data; D053761:Nanocomposites / Q000737:chemistry; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation; D013696:Temperature; D013816:Thermodynamics
D008024:Ligands; D004247:DNA