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Conformational dynamics of DNA with atomic-scale resolution

August 2017. The conformational motions of DNA are essential for its biological function. DNA often stretches and bends to bind proteins resutling in rather complex dynamics. Experiments have largely been interpreted in terms of geometric models, which captured the essential behaviour of DNA, but did not provide an atomic-scale view of the dynamics.

By combining molecular dynamics simulations with pulsed electron–electron double resonance (PELDOR) experiments a team of Frankfurt scientists have succeeded in obtaining a very resolution view of the conformational motions of DNA. PELDOR experiments of nucleic acids with rigid spin labels provide highly accurate distance and orientation information. The molecular dynamics simulations closely reproduced the PELDOR time traces, and demonstrated that bending, in addition to twist-stretch motions, underpin the sub-microsecond dynamics of DNA. PELDOR experiments correctly ranked DNA force fields and resolved subtle differences in the conformational ensembles of nucleic acids, on the order of 1–2 Å. Long-range distance and angle measurements with rigid spin labels provide critical input for the refinement of computer models and the elucidation of the structure and dynamics of complex biomolecules. More ...

 

Contact
Gerhard Hummer
Max Planck Institute of Biophysics
Frankfurt am Main
Germany
gerhard.hummer@biophys.mpg.de

 

Publication
Stelzl LS, Erlenbach N, Heinz M, Prisner TF, Hummer G (2017) Resolving the conformational dynamics of DNA with ­­­Ångstrom resolution by pulsed electron-electron double resonance and molecular dynamics. J Am Chem Soc: published online 4 August 2017. http://dx.doi.org/10.1021/jacs.7b05363

 

Cluster of Excellence Macromolecular Complexes, Frankfurt am Main