Abstract
AbstractThe 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.
Highlights
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 changes upon internalization into Xenopus lævis oocytes
Nuclear magnetic resonance (NMR) spectroscopy is a valuable technique to investigate in a non-invasive way the local structure, dynamics and interactions of nucleic acids inside cells.[7,8,9,10,11,12]
Summary
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. 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.
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