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Title: Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot
Authors: Roca, Jorjethe
Hori, Naoto
Baral, Saroj
Velmurugu, Yogambigai
Narayanan, Ranjani
Narayanan, Prasanth
Thirumalai, D.
Ansari, Anjum
Keywords: Laser Temperature-jump Spectroscopy
RNA Folding
Issue Date: 2018
Source: Roca, J., Hori, N., Baral, S., Velmurugu, Y., Narayanan, R., Narayanan, P., . . . Ansari, A. (2018). Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot. Proceedings of the National Academy of Sciences, 115(31), E7313-E7322. doi:10.1073/pnas.1717582115
Series/Report no.: Proceedings of the National Academy of Sciences
Abstract: The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability, and dynamics. Therefore, it is important to elucidate the general principles governing their thermodynamics/folding mechanisms. Here, we combine laser temperature-jump experiments and coarse-grained simulations to determine the folding/unfolding pathways of VPK, a variant of the mouse mammary tumor virus (MMTV) PK involved in ribosomal frameshifting. Fluorescent nucleotide analogs (2-aminopurine and pyrrolocytidine) placed at different stem/loop positions in the PK serve as local probes allowing us to monitor the order of assembly of VPK that has two constituent hairpins with different intrinsic stabilities. We show that at 50 mM KCl, the dominant folding pathway populates only the more stable hairpin intermediate; as the salt concentration is increased, a parallel folding pathway emerges involving the less stable hairpin as an alternate intermediate. Notably, the flux between the pathways is modulated by the ionic strength. Our findings support the principle that the order of PK structure formation is determined by the relative stabilities of the hairpins, which can be altered by sequence variations or salt concentrations. The experimental results of salt effects on the partitioning between the two folding pathways are in remarkable agreement with simulations that were performed with no adjustable parameters. Our study not only unambiguously demonstrates that VPK folds by parallel pathways but also showcases the power of combining experiments and simulations for a more enriched description of RNA self-assembly.
ISSN: 0027-8424
Rights: © 2018 The Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).
Fulltext Permission: open
Fulltext Availability: With Fulltext
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