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Proceedings Paper

A macromolecular crowding study of RNA folding and activity: polymer pore size matters! (Conference Presentation)
Author(s): Richard Börner; Erica Fiorini; Bishnu Paudel; David Rueda; Roland K. O. Sigel
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Paper Abstract

Catalytic RNAs, like the group IIB intron ribozyme of S. cerevesiae, require a high magnesium(II) concentration to show folding and function in vitro [1]. In contrast, in vivo conditions are characterized by a highly crowded cellular environment and much lower ion concentration. Molecular crowding agents are a widespread tool to mimic cellular crowding [2]. However, particular physical/chemical properties explaining the crowders influence are mostly not understood. In this study, we gain new insights on how polymer properties like viscosity, pore size etc. influence the activity and folding of a large RNA. We combined bulk activity assays and single-molecule Förster Resonance Energy Transfer experiments, screening the PEG volume fraction (%) and molecular weight (MW). Our results revealed that upon the influence of crowding agents, a compaction of the underlying structure depends on the PEG % and the presence of different PEG MW and % unveiled an optimal pore size in terms of catalytic activity. In summary, an increasing density of the crowding environment shifts the RNA towards the most compact state, but the ribozyme is only active if the crowders network matches its size [4]. We interpret the most compact state as necessary, but not sufficient, to keep the ribozyme active. Financial support from the European Research Council (MIRNA N° 259092, to RKOS), the Swiss National Fund (SNF), and the Forschungskredit Grant of the University of Zürich (FK-14-096 and 15-092 to RB) are gratefully acknowledged. [1] Swisher J.F., Su L.J., Brenowitz M., Anderson V.E., Pyle A.M., J. Mol. Bio., 315, 297-310 (2002). [2] Kilburn D., Roh J.H., Guo L., Briber R.M., Woodson S.A., JACS, 132, 8690-6 (2010). [3] Steiner M., Karunatilaka K.S., Sigel R.K.O., Rueda D., Proc. Natl. Acad. Sci. U.S.A.,105, 13853-8 (2008). [4] aBörner R, Fiorini E, Sigel R.K.O., Chimia, 69, 207-212 (2015).; bFiorini E., Paudel B., Börner R., Rueda D., Sigel R.K.O., submitted. [5] König S.L.B., Hadzic M., Fiorini E., Börner R., Kowerko D., Blanckenhorn W.U., Sigel R.K.O., PLoS ONE, 8, e84157 (2013).

Paper Details

Date Published: 27 April 2016
PDF: 1 pages
Proc. SPIE 9719, Biophysics, Biology, and Biophotonics: the Crossroads, 971909 (27 April 2016); doi: 10.1117/12.2209290
Show Author Affiliations
Richard Börner, Univ. Zürich (Switzerland)
Erica Fiorini, Univ. Zürich (Switzerland)
Bishnu Paudel, MRC Clinical Sciences Ctr. (United Kingdom)
David Rueda, MRC Clinical Sciences Ctr. (United Kingdom)
Roland K. O. Sigel, Univ. Zürich (Switzerland)

Published in SPIE Proceedings Vol. 9719:
Biophysics, Biology, and Biophotonics: the Crossroads
Adam Wax; Vadim Backman, Editor(s)

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