According to researchers at Virginia Tech, DNA is a lot more flexible than previously thought.
Click to download the structural fluctuations of the Nucleosomal DNA movie (ZIP 61 MB)
Virginia Tech researchers used novel methodology and the university’s System X supercomputer to carry out what is probably the first simulation that explores full range of motions of a DNA strand of 147 base pairs, the length that is required to form the fundamental unit of DNA packing in the living cells — the nucleosome. Contrary to a long-held belief that DNA is hard to bend, the simulation shows in crisp atomic detail that DNA is considerably more flexible than commonly thought.
Every cell in your body has identical DNA. The DNA in your muscle cells is the same as the DNA in your hair cells, but these cells obviously perform very differently. According to Alexey Onufriev, assistant professor of computer sciences and physics at Virginia Tech this occurs because, roughly speaking, the DNA in different cell types is packed differently and the complexes it forms with the surrounding proteins are in different positions, so only the relevant part of the code can be read at a time.
Previously held views that it takes a lot of energy to bend the DNA double-helix are now being challenged by this discovery.
Using 128 of System X’s 1,100 processors, the research resulted in a System X movie revealing DNA wiggling like a worm, showing greater flexibility than expected from the traditional view. The DNA packing in the nucleosome is also found to be surprisingly loose. “The implication is that it may not cost much energy to bend the DNA even to bend sharply,” said Onufriev.
Simulations like these will help medical animators visualize cellular events as they occur closer to real-time and visualize how individual molecules and proteins interact in their surrounding cellular environment.
“Experiment cannot always probe atomic detail of living molecules because they are too small and often move too fast,” said Onufriev. “But we can combine computational power with good algorithms to simulate these motions at high (atom-scale) resolution. It is an exciting time to do molecular modeling,” he said. “The computing power and the methodology have come to the point that we can begin to fully probe biology on timescales very relevant to living things such as DNA packing.”