Revealing the distinct folding phases of an RNA three-helix junction

Nucleic Acids Research
Alex PlumridgeLois Pollack

Abstract

Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy b...Continue Reading

Citations

Jan 24, 2019·Bioscience Reports·Almudena Ponce-SalvatierraJanusz M Bujnicki
Nov 10, 2020·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Johannes Graf, Markus Kretz
Sep 12, 2020·The Journal of Biological Chemistry·Josue San Emeterio, Lois Pollack
Nov 17, 2020·Frontiers in Genetics·Bing LiZhichao Miao
Feb 23, 2020·Analytica Chimica Acta·Diego A HuykeJuan G Santiago
Jul 25, 2019·Biophysical Journal·Samuel BowermanJeff Wereszczynski
Apr 25, 2021·Science Advances·Weiwei HeSerdal Kirmizialtin
Dec 6, 2019·Journal of the American Chemical Society·Alex PlumridgeLois Pollack
Nov 23, 2018·Journal of the American Chemical Society·Clark Templeton, Ron Elber
Sep 18, 2020·Journal of Chemical Theory and Computation·Antarip HalderGovardhan Reddy
Oct 23, 2019·The Journal of Physical Chemistry. B·Yen-Lin Chen, Lois Pollack
Sep 11, 2021·Journal of Chemical Theory and Computation·Liuba MazzantiSamuela Pasquali
Jul 3, 2021·Journal of Synchrotron Radiation·Diego A HuykeJuan G Santiago

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Methods Mentioned

BETA
protein folding
X-ray
PCR
size exclusion chromatography
NMR

Software Mentioned

MATLAB
SAXS
GAJOE
CRYSOL
SASBDB

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