First molecular simulation of a long DNA strand shows unexpected flexibility

It turns out that sequencing the human genome determining the order of DNA building blocks -- has not completely cracked the code of how DNA directs various cellular processes. In addition to the sequence of the base pairs, the instructions are in the packaging how DNA is folded within a cell.

Virginia Tech researchers used novel methodology and the universitys 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.

The research is published in the December issue of the Biophysical Journal, in the article A Computational Study of Nucleosomal DNA Flexibility, by Jory Zmuda Ruscio of Leesburg, Va., a Ph.D. student in the Genetics, Bioinformatics and Computational Biology Program at Virginia Tech, and Alexey Onufriev of Blacksburg, assistant professor of computer sciences and physics at Virginia Tech. They have been invited to do a platform presentation at the 51st Biophysical Society Annual Meeting in Baltimore in March.

There is about 12 feet of DNA in a human cell but it is packaged into nucleosomes lengths of 147 base pairs each wrapped around eight special proteins. A nucleosome looks kind of like the lumpy beginning of a rubber-band ball. Or maybe more like a lumpy worm coil. Uncoiled, the worm wiggles, flexes, and even kinks, according to a simulation performed on System X.

As we know from watching forensic detective shows on TV, the DNA in all of an individuals cells is identical. The DNA in fingernail cells is exactly the same as in muscle. Yet the cells are different. This is because, roughly speaking, the DNA in different cell types is packed differently

Contact: Susan Trulove
Virginia Tech

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