TY  - JOUR
A1  - Erlenbach, Nicole
A1  - Grünewald, Christian
A1  - Krstic, Bisera
A1  - Heckel, Alexander
A1  - Prisner, Thomas F.
T1  - "End-to-End" stacking of small dsRNA
T2  - RNA
N2  - PELDOR (pulse electron-electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the ‘end-to-end’ stacking of small double stranded (ds)RNAs. For this study, the dsRNA molecules were only singly labelled with the spin label TPA to avoid multi-spin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π-π-interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From this data the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we could demonstrate by PELDOR experiments quantitatively.
KW  - EPR
KW  - PELDOR/DEER
KW  - dsRNA
KW  - stacking
Y1  - 2018
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/51266
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-512662
SN  - 1469-9001
SN  - 1355-8382
N1  - This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
VL  - 25
IS  - 2
SP  - 239
EP  - 246
PB  - Laboratory Press ; HighWire Press
CY  - Cold Spring Harbor, NY ; Stanford, Calif.
ER  -