Double helix unpacking reveals DNA physics

Accurately reconstructing how the parts of a complex molecule are held together and only knowing how the molecule deforms and falls apart – that was the challenge taken on by a research team led by SISSA’s Cristian Micheletti and recently published at Physical assessment letters. In particular, the scientists studied how a DNA double helix unzips when moved at high speed through a nanopore, reconstructing basic thermodynamic properties of DNA based on the single speed of the process.

The translocation of polymers through nanopores has long been studied as a fundamental theoretical problem and also for its various practical ramifications, e.g. for genome sequencing. We recall that the latter involves driving a DNA filament through a pore so narrow that only one of the double helix strands can pass, leaving the other strand behind. As a result, the translocated DNA double helix will necessarily split and relax, an effect known as unwrapping.

The research team, which also includes Antonio Suma of the University of Bari, first author, and Vincenzo Carnevale of Temple University, used a cluster of computers to simulate the process with different drivers tracking the DNA extraction rate, a type of data that has rarely been studied, despite being readily accessible in experiments.

Using previously developed theoretical and mathematical models, researchers were able to work “backward,” using the velocity information to accurately reconstruct the thermodynamics of the formation and breakage of the double-helical structure.

“Previous theories,” the researchers explain, “relied on detailed knowledge of the thermodynamics of a molecular system that was then used to predict the response to more or less invasive external stresses. This alone is a major challenge in itself. We looked at the reverse problem: we relied on DNA’s response to aggressive stresses, such as the forced unzipping of the double helix, to restore the details of thermodynamics.”

“Due to the invasive and rapid nature of the unpacking process, the project seemed doomed to failure, which is probably why it had never been attempted before. However, we also knew that the right theoretical and mathematical models, if any, could give us a promising solution to the problem. After analyzing the extensive set of data collected, we were delighted to discover that this was exactly the case; we were pleased to have had the right intuition.”

The technique used in the study is general, so the researchers expect to be able to extend it beyond DNA to other molecular systems that are still relatively unexplored. An example of this are the so-called molecular motors, protein aggregates that use energy to make cyclic transformations, just like the motors in our daily lives.

“Until now,” researchers point out, “studies on molecular motors have begun by formulating hypotheses about their thermodynamics and then comparing predictions with experimental data. They have used equilibrium experiments to restore thermodynamics, with clear conceptual and practical benefits.”