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Molecular simulations provide new insights into the dynamics of supercoiled DNA

DNA (deoxyribonucleic acid), the molecular "blueprint" carrying the genetic instructions that influence the growth, development, reproduction and predispositions of individual humans, can undergo different types of mechanical stress inside cells. For instance, it can be twisted or stretched, impacting its overall structure and dynamics.

Researchers at the University of York recently explored how DNA behaves under torsion and tension using molecular dynamics simulations. These atomic-scale simulations yielded interesting new findings, which were in a paper in Â鶹ÒùÔºical Review Letters.

"I have always been interested in studying how DNA behaves inside the cell," Dr. Agnes Noy, senior author of the paper, told Â鶹ÒùÔº. "We are used to thinking of DNA as a relaxed 'perfect' double helix, but the reality is far from that. Inside cells, DNA is under/overtwisted, resulting in the formation of 'supercoiled' loops, resembling what can happen to long cords or garden hoses in our homes."

In contrast with relaxed DNA, supercoiled DNA has been difficult to observe closely in experimental settings due to its dynamic nature. In one of their previous studies, the researchers overcame this challenge using a combination of microscopy and atomic resolution simulations.

"As these two methodologies agreed so well on the global shapes found for the DNA, simulations proved to be an effective boost to microscopy resolution," explained Dr. Noy. "We could see for the first time that undertwisted DNA presents defects on the double helix structure in the form of bubbles (which is when the two DNA strands separate). However, the trick there was the use of tiny DNA circles as a model."

Building on their previous findings, Dr. Noy and her colleagues set out to investigate what happens in linear or longer DNA strands, such as the molecules constituting genomes in living organisms. To do this, they developed novel approaches that could be used to model supercoiled DNA without the need to be circular.

"Our objective was to simulate the main experiments on supercoiling linear DNA where the ends of the molecule are subjected to a controllable amount of torsion and tension," explained Dr. Noy.

"While these experiments have given us a good understanding of how DNA responds to mechanical forces (DNA is also pulled in cells), they can't show us the different structures that DNA can take. Several models tried to paint a picture of it, but none has attempted to characterize DNA at atomic resolution under such conditions."

The researchers performed molecular dynamics simulations based on classical mechanics equations to determine the motion of individual atoms in DNA. To simulate the desired experimental setup, they also placed restraints on the DNA ends.

"By making sure our simulations reproduced the experimental DNA extension (or end-to-end distances), we mapped the different conditions where DNA presented supercoiled loops or bubbles," said Dr. Noy. "We discovered that DNA forms bubbles more easily than expected, triggered only by changes in its twist and without the need of being pulled, contrary to previous assumptions.

"This is particularly applicable to AT-rich sequences, as the base pair resulting from adenine (A) and thymine (T) is less stable than the one formed by cytosine (C) and guanine (G). Bubbles form when the two DNA strands are separated and are necessary to read the genetic information."

Since researchers uncovered the existence of a double helix in DNA, they determined that the molecular elements carrying genetic information (i.e., the nucleobases A, T, C and G) are stored inside this structure and are thus difficult to access. Before this discovery, scientists believed that observed 'bubbles' were formed due to specialized proteins that mechanically destabilize the DNA.

"Our findings mean that the genetic information is easier to read than was previously thought and that sequence codifies which are the most accessible parts," explained Dr. Noy. "This will improve scientists' understanding of how genetic programs unfold, which will help in disease detection and treatment as well as in the synthesis of compounds via synthetic biology."

The recent study by this research team sheds new light on how torsional stress affects the structure of linear and longer DNA strands. In her next studies, Dr. Noy plans to further examine sites in genomes where genetic information is read first, as these generally serve as 'signal points' for the start of a gene.

"These short sequences are known as a gene's 'promoters' and are critical because they control whether the DNA sequence for a specific gene is read and translated into its actual function," added Dr. Noy.

"The formation of bubbles in 'promoters' is carefully regulated, allowing organisms to determine when a feature is presented. I am planning to investigate this regulation so we can better understand which processes control the opening of a DNA bubble in key sites and consequently gene expression."