Double-helix unwrapping reveals DNA physics

Reconstructing exactly how the parts of a complex molecule are held together and knowing just how the molecule distorts and breaks up – this was the challenge taken on by a research team led by SISSA’s Cristian Micheletti and recently published on Physical review letters. In particular, the researchers studied how a DNA double helix opens when it is translocated at high speed through a nanopore, reconstructing fundamental DNA thermodynamic properties from the single speed of the process.

Translocation of polymers through nanopores has long been studied as a fundamental theoretical problem, as well as for its several practical consequences, for example for genome sequencing. We recall that the latter involves driving a DNA filament through a pore so narrow that only one of the double-helical strands can pass, while the other strand remains behind. As a result, the translocated DNA double helix will necessarily split and relax, an effect known as unzipping.

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 of different driving forces that kept track of DNA’s unwrapping rate, a type of data that has rarely been studied despite that it is directly available in experiments.

Using previously developed theoretical and mathematical models, scientists were able to work “backwards”, using the information about the rate to accurately reconstruct the thermodynamics of the formation and breaking of the double helix structure.

“Previous theories”, the researchers explain, “start from detailed knowledge of the thermodynamics of a molecular system which 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 took as a starting point DNA’s response to aggressive stresses, such as forced uncoiling of the double helix, to recover the details of thermodynamics.”

“Because of the invasive and rapid nature of the unpacking process, the project seemed doomed to failure, which is probably why it had never been tried before. But we also knew that the right theoretical and mathematical models, if applicable, could offer us a promising solution to the problem. After analyzing the extensive set of collected data, we were very excited to discover that this was exactly the case; we were happy that we had the right intuition.”

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

“Until now”, researchers emphasize, “studies on molecular engines have started by formulating hypotheses about their thermodynamics and then comparing predictions with experimental data. The new method that we have validated should allow taking the reverse route, namely using data from non-equilibrium experiments to restore thermodynamics, with clear conceptual and practical advantages.”