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Compaction of RNA Duplexes in the Cell **
Author(s) -
Collauto Alberto,
Bülow Sören,
Gophane Dnyaneshwar B.,
Saha Subham,
Stelzl Lukas S.,
Hummer Gerhard,
Sigurdsson Snorri T.,
Prisner Thomas F.
Publication year - 2020
Publication title -
angewandte chemie
Language(s) - English
Resource type - Journals
eISSN - 1521-3757
pISSN - 0044-8249
DOI - 10.1002/ange.202009800
Subject(s) - rna silencing , rna , biophysics , chemistry , electron paramagnetic resonance , helix (gastropod) , xenopus , nucleic acid structure , resonance (particle physics) , crystallography , nanotechnology , physics , materials science , biochemistry , nuclear magnetic resonance , biology , rna interference , atomic physics , gene , ecology , snail
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.