QCM-based rupture force measurement as a tool to study DNA dehybridization and duplex stability

Area of Science:

• Biophysics
• Molecular Biology
• Materials Science

Background:

• Assessing the mechanical stability of double-stranded DNA (dsDNA) is crucial for understanding DNA-protein interactions and DNA-based technologies.
• Traditional methods for measuring DNA unwinding forces can be complex and may require specialized equipment.
• Developing novel, sensitive techniques for direct force measurement is essential for advancing molecular mechanics studies.

Purpose of the Study:

• To develop and validate a novel method for directly measuring the unwinding force of dsDNA.
• To determine the rupture force of dsDNA using a quartz crystal microbalance (QCM) technique.
• To investigate the influence of DNA sequence and structure on its mechanical stability.

Main Methods:

• Utilized a quartz crystal microbalance (QCM) to measure the unwinding force of dsDNA.
• Controlled dsDNA unwinding by varying the amplitude of QCM surface oscillations in a liquid medium.
• Employed oligonucleotide duplexes with mismatches at various positions to pinpoint unwinding initiation sites.

Main Results:

• The QCM method reliably measured rupture forces as low as 5-10 pN.
• Viscous forces induced by QCM oscillations at 14 MHz caused dsDNA helix unwinding.
• Unwinding initiated at the free end of the dsDNA molecule, consistent across different mismatch positions.
• The measured helix unwinding force for 20 base pair dsDNA was 30-40 pN, aligning with atomic force microscopy (AFM) data.

Conclusions:

• Quartz crystal microbalance (QCM) offers a sensitive and direct approach for measuring dsDNA unwinding forces.
• The technique provides accurate quantification of DNA mechanical stability and rupture forces.
• Findings contribute to a deeper understanding of DNA structural dynamics and mechanical properties at the molecular level.