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Compaction of RNA Duplexes in the Cell

preprint
submitted on 24.04.2020 and posted on 27.04.2020 by Alberto Collauto, Sören von Bülow, Dnyaneshwar B. Gophane, Subham Saha, Lukas S. Stelzl, Gerhard Hummer, Snorri Th. Sigurdsson, Thomas F. Prisner
The structure and flexibility of RNA depend sensitively on the microenvironment. Using pulsed electron-electron double-resonance (PELDOR) 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 capture semi-quantitatively the compaction, and identify non-specific electrostatic interactions between proteins and dsRNA as a possible driver of this effect.

Funding

German Research Foundation (CRC902: Molecular Principles of RNA Based Regulation)

Icelandic Research Fund (141062051)

Human Frontier Science Program (RGP0026/2017)

History

Email Address of Submitting Author

collauto@chemie.uni-frankfurt.de

Institution

Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt

Country

Germany

ORCID For Submitting Author

0000-0003-1966-9532

Declaration of Conflict of Interest

We declare no conflict of interest.

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