Structural diversity of supercoiled DNA

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown.

Now an international team led by researchers at Baylor College of Medicine have used electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. These results revealed that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, the research team uncovered striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, they also detected exposed bases in positively supercoiled DNA.

minivectors

(a) Docking of 336bp traces into the cryo-ET densities of open circles. Traces (purple lines) were generated by docking circular strings of length 336bp into the density maps. Each trace was then used to isolate the minicircles (grey surfaces) from the cryo-ET density maps. (b) Docking of 336bp traces into the cryo-ET tomograms of writhed minicircles following the same protocol as for the open circles. (c) Docking of double-length (672bp) traces into the cryo-ET tomograms following the same protocol as for 336bp.

Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. This integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

Reference

Irobalieva RN, Fogg JM, Catanese DJ, Sutthibutpong T, Chen M, Barker AK, Ludtke SJ, Harris SA, Schmid MF, Chiu W, Zechiedrich L. (2015) Structural Diversity of supercoiled DNA. Nature Comm [Epub ahead of print]. [article]