Chemical biology news from across RSC Publishing.
Genetic code does the twist
06 June 2008
Revealing how DNA strands curl up is the first step to understanding how structure affects how these big biological molecules behave, says a team of US scientists.
Free energy landscapes for nucleic acid folding show the most likely pathway for hairpin formation
The group, at Caltech in Pasadena, has developed a computational model to discover how DNA and RNA strands fold into hairpins - loops that form when the strand bends back on itself. Ahmed Zewail and colleagues say that pinning down this process shows their model could be used to understand how larger DNA molecules behave.
'Hairpins are a very important structural feature of DNA,' says Zewail, 'and they are a manageable size to test our ideas on how long, macromolecular DNA strands fold.'
Hairpin creation is typically thought of as a two-state process - the strand is either unfolded or folded. But Zewail's recent experiments, using changes in UV absorbance to follow a hairpin refolding after being subjected to a laser induced temperature jump, suggest the process occurs in a series of steps. Now Zewail has developed a computational kinetic intermediate structure model to examine the energy landscape as DNA refolds, showing intermediate states - energy valleys - as the hairpins zip up.
- Philip Bevilacqua
Philip Bevilacqua, who studies RNA folding at Pennsylvania State University, University Park, US, says the model will be a useful tool. 'It corroborates data already out there and it should make useful predictions to guide future experiments. It will be well used because it's simple to apply.'
James Mitchell Crow
Link to journal article
Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes
Milo M. Lin, Lars Meinhold, Dmitry Shorokhov and Ahmed H. Zewail, Phys. Chem. Chem. Phys., 2008, 10, 4227
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