Compaction of RNA duplexes in the cell

  • The structure and flexibility of RNA depends sensitively on the microenvironment. Using pulsed electron-electron double-resonance (PELDOR)/double electron-electron resonance (DEER) spectroscopy combined with advanced labeling techniques, we show that the structure of double-stranded RNA (dsRNA) changes upon internalization into Xenopus lævis oocytes. Compared to dilute solution, the dsRNA A-helix is more compact in cells. We recapitulate this compaction in a densely crowded protein solution. Atomic-resolution molecular dynamics simulations of dsRNA semi-quantitatively capture the compaction, and identify non-specific electrostatic interactions between proteins and dsRNA as a possible driver of this effect.
Author:Alberto Collauto, Sören von BülowORCiD, Dnyaneshwar B. Gophane, Subham Saha, Lukas S. StelzlORCiD, Gerhard HummerORCiD, Snorri T. Sigurdsson, Thomas F. PrisnerORCiD
Parent Title (German):Angewandte Chemie
Place of publication:Weinheim
Document Type:Article
Date of Publication (online):2020/08/17
Date of first Publication:2020/08/17
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2022/03/09
Tag:EPR spectroscopy; PELDOR/DEER spectroscopy; RNA structures; molecular dynamics; site-directed spin labeling
Page Number:5
First Page:23025
Last Page:23029
We acknowledge financial support from the German Research Foundation (CRC902: Molecular Principles of RNA Based Regulation). A.C. thanks Heike Biehl and Anja Becker (MPI of Biophysics) for the training with the microinjection procedure and for having provided the oocytes. S.Th.S. acknowledges financial support by the Icelandic Research Fund (141062051). S.v.B, L.S.S. and G.H. acknowledge support by the Max Planck Society and by the Human Frontier Science Program RGP0026/2017. Open access funding enabled and organized by Projekt DEAL.
Biochemie, Chemie und Pharmazie
Wissenschaftliche Zentren und koordinierte Programme / Zentrum für Biomolekulare Magnetische Resonanz (BMRZ)
Angeschlossene und kooperierende Institutionen / MPI für Biophysik
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Licence (German):License LogoCreative Commons - Namensnennung 4.0