scholarly journals Enthalpy-Driven RNA Folding: Single-Molecule Thermodynamics of Tetraloop−Receptor Tertiary Interaction†

Biochemistry ◽  
2009 ◽  
Vol 48 (11) ◽  
pp. 2550-2558 ◽  
Author(s):  
Julie L. Fiore ◽  
Benedikt Kraemer ◽  
Felix Koberling ◽  
Rainer Edmann ◽  
David J. Nesbitt
Keyword(s):  
Single Molecule ◽  
Rna Folding ◽  
Tertiary Interaction

scholarly journals 40 Probing single molecule RNA folding using temperature and force

2013 ◽  
Vol 31 (sup1) ◽  
pp. 24-25
Author(s):  
William Stephenson ◽  
Rachel Santiago ◽  
Sean Keller ◽  
Scott Tenenbaum ◽  
Michael Zuker ◽  
...  
Keyword(s):  
Single Molecule ◽  
Rna Folding

Real-time monitoring of cotranscriptional riboswitch folding and switching

2019 ◽  
Author(s):  
Boyang Hua ◽  
Christopher P. Jones ◽  
Jaba Mitra ◽  
Peter J. Murray ◽  
Rebecca Rosenthal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Real Time ◽  
Single Molecule ◽  
Rna Folding ◽  
Its Sequence ◽  
Transcriptional Terminator ◽  
Fate Control ◽  
New Methods ◽  
Nascent Chain

SummaryRiboswitches function through cotranscriptional conformation switching governed by cognate ligand concentration, RNA folding and transcription elongation kinetics. To investigate how these parameters influence riboswitch folding, we developed a novel vectorial folding assay (VF) in which the superhelicase Rep-X sequentially liberates the RNA strand from a heteroduplex in a 5’-to-3’ direction, mimicking the nascent chain emergence during transcription. The RNA polymerase (RNAP)-free VF recapitulates the kinetically controlled cotranscriptional folding of a ZTP riboswitch, whose activation is favored by slower transcription, strategic pausing, or a weakened transcriptional terminator. New methods to observe positions and local rates of individual helicases show an average Rep-X unwinding rate similar to bacterial RNAP elongation (~60 nt/s). Real-time single-molecule monitoring captured folding riboswitches in multiple states, including an intermediate responsible for delayed terminator formation. These methods allow observation of individual folding RNAs as they occupy distinct folding channels within the landscape that controls gene expression and showed that riboswitch fate control is encoded in its sequence and is readily interpreted by a directionally moving protein even in the absence of an RNA polymerase.

scholarly journals Cooperative Tertiary Interaction Network Guides RNA Folding

Cell ◽  
2012 ◽  
Vol 149 (2) ◽  
pp. 348-357 ◽  
Author(s):  
Reza Behrouzi ◽  
Joon Ho Roh ◽  
Duncan Kilburn ◽  
R.M. Briber ◽  
Sarah A. Woodson
Keyword(s):  
Rna Folding ◽  
Interaction Network ◽  
Tertiary Interaction

Single-Molecule FRET Studies of RNA Folding: A Diels–Alderase Ribozyme with Photolabile Nucleotide Modifications

2013 ◽  
Vol 117 (42) ◽  
pp. 12800-12806 ◽  
Author(s):  
Andrei Yu. Kobitski ◽  
Stefan Schäfer ◽  
Alexander Nierth ◽  
Marco Singer ◽  
Andres Jäschke ◽  
...  
Keyword(s):  
Single Molecule ◽  
Rna Folding ◽  
Single Molecule Fret

scholarly journals Frictional effects on RNA folding: Speed limit and Kramers turnover

2018 ◽  
Author(s):  
Naoto Hori ◽  
Natalia A. Denesyuk ◽  
D. Thirumalai
Keyword(s):  
Single Molecule ◽  
Rna Folding ◽  
Theoretical Estimate ◽  
Speed Limit ◽  
Free Energy Barrier ◽  
Folding Rate ◽  
Solvent Viscosity ◽  
Folding Rates ◽  
Friction Regime ◽  
Frictional Effects

AbstractWe investigated frictional effects on the folding rates of a human Telomerase hairpin (hTR HP) and H-type pseudoknot from the Beet Western Yellow Virus (BWYV PK) using simulations of the Three Interaction Site (TIS) model for RNA. The heat capacity from TIS model simulations, calculated using temperature replica exchange simulations, reproduces nearly quantitatively the available experimental data for the hTR HP. The corresponding results for BWYV PK serve as predictions. We calculated the folding rates (kFs) from more than 100 folding trajectories for each value of the solvent viscosity (η) at a fixed salt concentration of 200 mM. Using the theoretical estimate ( where N is number of nucleotides) for folding free energy barrier, kF data for both the RNAs are quantitatively fit using one dimensional Kramers’ theory with two parameters specifying the curvatures in the unfolded basin and the barrier top. In the high-friction regime (η ≳ 10−5 Pa·s), for both HP and PK, kFs decrease as 1/η whereas in the low friction regime kFs increase as η increases, leading to a maximum folding rate at a moderate viscosity (~ 10−6 Pa·s), which is the Kramers turnover. From the fits, we find that the speed limit to RNA folding at water viscosity is between (1 − 4)μs, which is in accord with our previous theoretical prediction as well as results from several single molecule experiments. Both the RNA constructs fold by parallel pathways. Surprisingly, we find that the flux through the pathways could be altered by changing solvent viscosity, a prediction that is more easily testable in RNA than proteins.

scholarly journals Co-transcriptional quantification of RNA synthesis, RNA folding and RNA-protein interactions by "Systems NMR" approach.

2019 ◽  
Author(s):  
Yaroslav Nikolaev ◽  
Nina Ripin ◽  
Martin Soste ◽  
Paola Picotti ◽  
Dagmar Iber ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Interactions ◽  
Rna Binding ◽  
Rna Folding ◽  
Single Sample ◽  
Rna Transcription ◽  
Biochemical Assays ◽  
Experimental Approaches ◽  
Reaction Constants ◽  
Time Systems

Abstract The protocol describes how to setup and analyse observation of a co-transcriptional RNA folding network by Systems NMR approach. While most experimental approaches can monitor only a single molecule class or reaction type at a time, Systems NMR permits single-sample dynamic quantification of entire “heterotypic” networks – involving different reaction and molecule types. It thus provides a deeper systems-level understanding of biological network dynamics by combining the dynamic resolution of biochemical assays and the multiplexing ability of “omics”. This particular protocol describes the reconstruction of an 8-reaction co-transcriptional network - with simultaneous monitoring of RNA, metabolite, and proteins in a single sample at the same time. From reactions side, the protocol simultaneously quantifies RNA transcription, RNA folding and RNA-protein interactions (observed both from RNA and from protein side) and few other auxiliary reactions. In addition to fundamental analyses of reaction constants under different conditions, the current applications of this particular reconstruction are: (1) map RNA-binding interfaces on proteins without having to purify/order the RNA; (2) monitor co-transcriptional RNA folding perturbations by proteins and small molecules; (3) monitor RNA-transcription-driven protein phase-separation with the possibility to observe multiple proteins at once, each with residue-level resolution. Not counting the protein and RNA template preparation times, the NMR measurement and data analysis parts take about 1 day each. This protocol accompanies Nikolaev et al, Nature Methods, 2019 (doi:XXX). The most up-to-date version of the protocol (including example code and data) is available at: github.com/systemsnmr/ivtnmr

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