Computer program to predict where DNA molecules will pop open when twisted

Biologists are used to thinking about DNA sequences as a string of letters (A, C, G, T) that happens to be arranged in an elegant double helix. But DNA also has mechanical properties that affect how genes are turned on or off, say researchers at the UC Davis Genome Center.

Graduate student Chengpeng Bi and associate director of bioinformatics Craig Benham have developed a computer program to predict where DNA molecules will pop open when twisted. The program could help explain how genes are turned on or off under various conditions.

DNA in living cells is stressed and mostly undertwisted -- twisted in the opposite direction to the run of the double helix. That makes it easier for the two strands of the helix to open up so that DNA can be copied or read, said Benham. When DNA opens up, it releases stress from elsewhere and makes it possible for other sites to open or close, he said.

"Everybody sees what everyone else is doing, " he said.

The twisting stresses on DNA are influenced by environmental conditions such as a shortage of food, Benham said. That could affect how a bacterial cell responds to its environment.

The enzymes that unwind DNA so that genes can be copied also make use of this twisting effect. They push waves of "overtwist" ahead of them up the DNA, and leave undertwist in their wake.

The work is published in the May issue of the journal Bioinformatics. The prediction tool, called WebSIDD, is available online.

Additional information: WebSIDD prediction tool


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