Separation of the two DNA strands occurs in millionths of a second, making it extremely difficult to study experimentally and forcing researchers to rely on computational simulations. After four years of fine-tuning an effective physical model and using the Mare Nostrum supercomputer, scientists at the Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Supercomputing Center (BSC) have managed to produce the first realistic simulation of DNA opening at high resolution. The research group led by Modesto Orozco, head of the Molecular Modeling and Bioinformatics Group at IRB Barcelona and director of the BSC Life Sciences Department, and Alberto Pérez, Juan de la Cierva researcher at the BSC, currently at the University of California, San Francisco (USA), has published its findings in the prestigious journal Angewandte Chemie.
The researchers have studied a small DNA fragment, of 12 base pairs (the human genome has about 3,000 million base pairs), and have obtained 10 million structural snapshots that show how DNA unfolds. In this process, they have revealed the two main ways the natural folded structure moves to an unfolded state. "This project is part of one of the lab’s greater aims: to understand the changes that DNA structure undergoes in biological processes that occur within the cell, such as the expression and repression of genes or DNA replication and transcription," explains Modesto Orozco
DNA holds the genetic information of living organisms and its double-helix structure was discovered more than 50 years ago by Watson and Crick. DNA and the proteins that modify it are the most important therapeutic targets in several pathologies, particularly in cancer. The work carried out at the IRB Barcelona and the BSC provides a detailed view of the mechanism through which one of the most crucial processes in DNA occurs, and opens up new prospects regarding the connection between physical properties, functionality and pharmacological effects. The final aim is for new breakthroughs to make DNA a universal pharmacological target.
Reference articles:?
Real-time Atomistic Description of DNA Unfolding, Alberto Pérez and Modesto Orozco. ?
Angewandte Chemie 2010 (doi: 10.1002/ange.201000593). ?
Angewandte Chemie - International Edition 2010 (doi: 10.1002/anie.201000593).
See video of a DNA fragment unfolding.