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

Area of Science:

• Biophysics
• Molecular Biology
• Nanotechnology

Background:

• Naturally occurring chemoreceptors utilize structure-switching mechanisms, inspiring artificial biomolecular switches for diagnostics, imaging, and synthetic biology.
• Clamp-based switching involves two recognition elements embracing a target molecule, coupling recognition with conformational change and improving affinity and specificity.

Purpose of the Study:

• To investigate the thermodynamics of a clamp-switch designed to recognize DNA through both Watson-Crick and Hoogsteen interactions.
• To quantify the thermodynamic contributions of Hoogsteen interactions to DNA probe affinity and specificity.

Main Methods:

• Thermodynamic analysis of a DNA clamp-switch.
• Comparison of the clamp-switch with an equivalent linear DNA probe relying solely on Watson-Crick interactions.

Main Results:

• The DNA clamp-switch's Hoogsteen interactions increased target DNA affinity by approximately 0.29 ± 0.02 kcal/mol/base compared to a linear probe.
• Hoogsteen interactions enhanced specificity, increasing discrimination against single-base mismatches by 1.2 ± 0.2 kcal/mol.
• The clamp-switch demonstrated a 10-fold improvement in the specificity window width.

Conclusions:

• Clamp-switches offer significant improvements in binding affinity and specificity due to combined Watson-Crick and Hoogsteen interactions.
• These enhanced properties make clamp-switches valuable for sensing applications and for precise control in DNA nanotechnology for nanostructure and nanomachines construction.