DNA Double Helix Splits Due to Invasive Nature of Unzipping Process

Scientists had a hard time reconstructing how complex molecular parts are being held together. However, that was before SISSA's Cristian Micheletti and his team studied how the DNA double helix unzips when translocated at high velocity through a nanopore.

DNA Double Helix's Unzipping

DNA has a double helix structure because it consists of two spiral chains of deoxyribonucleic acid. Its shape is reminiscent of a spiral staircase.

It has been well established that the translocation of polymers through nanopores is a key theoretical issue with numerous practical applications, such as genome sequencing. According to the researchers, a DNA filament is forced through a pore that is so small that only one double-helical strand may pass, leaving the other strand behind. The resultant unzipping effect is the inevitable splitting and unwinding of the translocated DNA double helix, Phys.org reported.

First author Antonio Suma from the University of Bari and Vincenzo Carnevale from Temple University are also members of the research team. They used a cluster of computers to simulate the process with various driving forces monitoring the DNA's unzipping speed, a type of data that has not received much attention despite being readily available in experiments.

Researchers were able to "work backward," using the information on the speed to precisely reconstruct the thermodynamics of the development and rupture of the double-helix structure, using previously published theoretical and mathematical models.

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Inverse Problem Approach

According to the researchers, previous theories started from detailed knowledge of a molecular system's thermodynamics and were then used to predict the response to more or less invasive external stresses. This alone is a major challenge in itself.

They looked at the inverse problem by starting from the DNA's response to aggressive stresses, like the forced unzipping of the double helix, to recover the details of the thermodynamics.

They understood that the correct theoretical and mathematical models, if applicable, may provide a promising answer to the problem. However, the project seemed doomed to fail due to the invasive and quick nature of the unzipping process, and that was presumably why it had never been tried before.

But after evaluating the extensive data collection, they were thrilled to know they were right with their expectations. The method used in the study is general, so the researchers anticipate being able to apply it to molecular systems other than DNA that are still largely unexplored, such as so-called molecular motors, protein aggregates that use energy to undergo cyclic transformations, much like the engines in our daily lives.

Initially, when studying molecular motors, researchers would formulate a hypothesis on thermodynamics and compare their prediction with the experimental data. However, a recent study proved that they could go the other way or the inverse route by using data from out-of-equilibrium experiments to recover the thermodynamics, with clear conceptual and practical advantages.

The study is published in Physical Review Letters.