Nanomechanical resonance captures pre-melting transition in DNA unravelling

Abstract

A double-stranded DNA unravels thermally through intermediate denatured bubble segments. Intrinsically, fluctuations ensue at the bubble boundaries from non-equilibrium (NE) energy exchanges with the environment. However, such details gets obscured by large population kinetics at the macroscale, associating equilibrium pathway to the unravelling landscape. In this work, we capture evidence of fluctuation energetics with picoliter samples in a microfluidic cantilever. We exploit nanomechanical resonance to measure the NE energy exchanges through dissipation, revealing a crucial pre-melting transition at T~42C . This signifies that unravelling possibly proceeds via intermediate collapsed-bubble conformations releasing energy, sufficient to unbind bubble ends, assisting further unbinding. Fluctuation theorem explains the observations opening further avenues to investigate fluctuation kinetics in other biological phenomena that also proceed through similar NE energetics.

arXiv commentManuscript and Supplementary Information

References in corpus (11)

• A nonequilibrium equality for free energy differences
• The Entropy Production Fluctuation Theorem and the Nonequilibrium Work Relation for Free Energy Differences
• Entropy production along a stochastic trajectory and an integral fluctuation theorem
• Frequency fluctuations in silicon nanoresonators
• Kolmogorov-Sinai entropy-rate vs. physical entropy
• Roles of stiffness and excluded volume in DNA denaturation
• Theory of Bubble Nucleation and Cooperativity in DNA Melting
• A two-state kinetic model for the unfolding of single molecules by mechanical force
• Statistical mechanics of base stacking and pairing in DNA melting
• Equilibration of energy in slow-fast systems
• A nanostructured surface increases friction exponentially at the solid-gas interface