Determination of helix orientations in a flexible DNA by multi-frequency EPR spectroscopy

Physical Chemistry Chemical Physics : PCCP
C M GrytzT F Prisner

Abstract

Distance measurements are performed between a pair of spin labels attached to nucleic acids using Pulsed Electron-Electron Double Resonance (PELDOR, also called DEER) spectroscopy which is a complementary tool to other structure determination methods in structural biology. The rigid spin label Ç, when incorporated pairwise into two helical parts of a nucleic acid molecule, allows the determination of both the mutual orientation and the distance between those labels, since Ç moves rigidly with the helix to which it is attached. We have developed a two-step protocol to investigate the conformational flexibility of flexible nucleic acid molecules by multi-frequency PELDOR. In the first step, a library with a broad collection of conformers, which are in agreement with topological constraints, NMR restraints and distances derived from PELDOR, was created. In the second step, a weighted structural ensemble of these conformers was chosen, such that it fits the multi-frequency PELDOR time traces of all doubly Ç-labelled samples simultaneously. This ensemble reflects the global structure and the conformational flexibility of the two-way DNA junction. We demonstrate this approach on a flexible bent DNA molecule, consisting of two short h...Continue Reading

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Citations

Feb 17, 2018·Chemistry : a European Journal·Nilesh R Kamble, Snorri Th Sigurdsson
Dec 1, 2017·Physical Chemistry Chemical Physics : PCCP·Anna G MatveevaAlexander G Maryasov
Jun 9, 2018·Chembiochem : a European Journal of Chemical Biology·Parker J NicholsBeat Vögeli
Jul 18, 2018·Beilstein Journal of Organic Chemistry·Timo WeinrichMichael W Göbel
Aug 20, 2021·The Journal of Organic Chemistry·Anna-Lena Johanna Segler, Snorri Th Sigurdsson
Feb 28, 2020·The Journal of Organic Chemistry·Haraldur Y Juliusson, Snorri Th Sigurdsson
Dec 14, 2021·Biophysical Journal·Burkhard EndewardXianyang Fang
Jan 28, 2022·Chemical Reviews·Qing MiaoMarcellus Ubbink

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Methods Mentioned

BETA
NMR
FRET
by

Software Mentioned

PELDOR
Specman4EPR
CYANA

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