Breaking Down Supercoiled DNA: New Insights from Molecular Simulations

Scientists at the University of York have tackled the intricate behavior of DNA under mechanical stress, leveraging advanced molecular dynamics simulations. Their findings, published in Physical Review Letters, reveal how DNA forms “supercoiled” loops and “bubbles” in response to torsion and tension.

The Hidden Complexity of DNA

“Understanding DNA behavior inside cells is crucial,” said Dr. Agnes Noy, lead author of the study. “DNA is often visualized as a perfect double helix, but in reality, it’s far more dynamic. Inside cells, DNA is frequently under or overtightened, leading to supercoiled structures similar to knotted cords or garden hoses.”

Simulations versus Microscopy: A Complementary Approach

The study combined molecular simulations with microscopic techniques. “Using both methods, we obtained consistent results on global DNA shapes,” Dr. Noy explained. “Simulations enhanced our understanding, especially regarding ‘bubbles’—temporary separations where the DNA double helix splits apart—previously observed under specialized protein influence.”

Visualizing DNA at the Atomic Level

The researchers simulated molecular dynamics at the atomic scale, applying controlled torsion and tension to model the DNA segment ends. “By restraining the DNA at both ends, we could observe how structural changes occur,”Dr. Noy added.

The Role of AT-Rich Sequences

Bubbles primarily occur in AT-rich regions due to the less stable adenine-thymine (AT) base pair compared to cytosine-guanine (CG) pairs. “These bubbles are essential for genetic information reading,” Dr. Noy noted. They form naturally under torsional stress without specialized proteins opening the DNA strands.

Implications for Gene Expression

The study brings fresh insights into how torsional stress influences DNA structure and function. Dr. Noy plans to explore specific genomic regions known as promoters. “Promoters act as starting points for gene expression,” she said. “Studying bubble formation here could illuminate how gene activity is controlled under different conditions.”

The Future of DNA Research

This research represents a significant advancement in understanding DNA dynamics. By refining our knowledge of supercoiling and bubble formation, scientists can better comprehend gene regulation and potential diagnostic and therapeutic targets. Further studies may uncover new mechanisms controlling DNA behavior in various biological processes.

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