DNA opening occurs when the molecular "rungs" of the famous double-helix ladder break apart. This crucial step is at the heart of many life processes, including those that allow cells to divide and repair DNA.
Using a computational method known as "coarse-grained" simulations, researchers based at RIKEN in Japan have successfully animated one of the major steps in DNA unravelling, called "unzipping."
"Our models represent DNA as strings of tiny spheres connected by springs, and the water around them as a dense continuum," says Masaki Susa of the RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program.
The research team used a supercomputer to simulate the motion of one billion DNA base pairs (or "rungs" of the DNA ladder). They found that these tiny beads jiggle around in a manner strikingly consistent with experimental measurements of DNA flexibility and elasticity, providing confidence that their method is capturing the essence of DNA's physical behavior.
"Our computations reveal in detail how thermal motion allows DNA to open up. As individual base pairs break, they expose single-stranded 'sticky' DNA ready to bind with other molecules—a fundamental step in DNA processing," says team leader Hiroshi Orland.
The unzipped segment then flutters in the watery environment, waving around like a flag. "This fluttering is essential to understanding the dynamics of DNA, as it is how DNA interacts with proteins and other molecules around it," says Susa.
"Coarse-grained" simulations are relatively fast, and the team are now using this technique to study even larger pieces of DNA and simulate the complete opening and closing of these double-stranded molecules.
The research appears in the journal Nucleic Acids Research.
