Determining intrachain diffusion coefficients for biopolymer dynamics from single-molecule force spectroscopy...

Area of Science:

• Biophysics
• Polymer Physics
• Molecular Dynamics

Background:

• The conformational diffusion coefficient (D) governs biopolymer structural dynamics timescales.
• Force spectroscopy is increasingly used to measure D in proteins and nucleic acids.
• Interpreting force spectroscopy data for D remains challenging due to instrumental effects.

Purpose of the Study:

• To investigate the impact of force probe instrumental effects on D measurements.
• To compare D values obtained from rates versus transition path time analysis.
• To develop methods for deconvoluting instrumental compliance effects.

Main Methods:

• Optical tweezers force spectroscopy applied to DNA hairpin folding.
• Analysis of single-molecule trajectories using rate and transition path time methods.
• Brownian dynamics simulations to model force probe compliance and bead size effects.

Main Results:

• Apparent D values derived from rates were significantly lower than those from transition time analysis.
• Instrumental force probe compliance was identified as the cause of underestimated D.
• Deconvolution of compliance effects successfully recovered the intrinsic D value.

Conclusions:

• Force probe mechanical properties critically influence measured D values in biopolymer dynamics.
• Transition path time analysis offers a more robust method for D determination.
• Accurate D measurements require accounting for and deconvoluting instrumental artifacts.