High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Issue 2 (28th November 2019)

• Record Type: Journal Article
• Authors: Heinz, Marcel; Erlenbach, Nicole; Stelzl, Lukas S; Thierolf, Grace; Kamble, Nilesh R; Sigurdsson, Snorri Th; Prisner, Thomas F; Hummer, Gerhard
• Is Part Of: Nucleic acids research. Volume 48:Issue 2(2020)
• Page Start: 924
• Page End: 933
• Publication Date: 2019-11-28
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkz1096
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Pulsed electron paramagnetic resonance (EPR) experiments, among them most prominently pulsed electron-electron double resonance experiments (PELDOR/DEER), resolve the conformational dynamics of nucleic acids with high resolution. The wide application of these powerful experiments is limited by the synthetic complexity of some of the best-performing spin labels. The recently developed $\bf\acute{G}$ (G-spin) label, an isoindoline-nitroxide derivative of guanine, can be incorporated non-covalently into DNA and RNA duplexes via Watson-Crick base pairing in an abasic site. We used PELDOR and molecular dynamics (MD) simulations to characterize $\bf\acute{G}$, obtaining excellent agreement between experiments and time traces calculated from MD simulations of RNA and DNA double helices with explicitly modeled $\bf\acute{G}$ bound in two abasic sites. The MD simulations reveal stable hydrogen bonds between the spin labels and the paired cytosines. The abasic sites do not significantly perturb the helical structure. $\bf\acute{G}$ remains rigidly bound to helical RNA and DNA. The distance distributions between the two bound $\bf\acute{G}$ labels are not substantially broadened by spin-label motions in the abasic site and agree well between experiment and MD. $\bf\acute{G}$ and similar non-covalently attached spin labels promise high-quality distance and orientation information, also of complexes of nucleic acids and proteins.