Pathway modulation, circular permutation and rapid RNA folding under kinetic control 1 1Edited by D. E. Draper

Pan, Tao; Fang, Xufei; Sosnick, Tobin R.

doi:10.1006/jmbi.1998.2516

Cited by 77 publications

(64 citation statements)

References 27 publications

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“…Large catalytic RNAs such as the group I intron from Tetrahymena thermophila and the RNase P RNA from Bacillus subtilis fold at vastly different rates under different conditions upon addition of Mg 2+ and have been shown to fold via multiple parallel pathways, in which different molecules follow different routes with different rates and intermediates, to a common final folded structure [4,5]. These observations support the common view that RNAs traverse rugged energy landscapes as they fold [6,7].…”

Section: Discussionsupporting

confidence: 57%

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Chu

Herschlag

2008

Current Opinion in Structural Biology

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SummaryThe rapid development of our understanding of the diverse biological roles fulfilled by non-coding RNA has motivated interest in the basic macromolecular behavior, structure, and function of RNA. We focus on two areas in the behavior of complex RNAs. First, we present advances in the understanding of how RNA folding is accomplished in vivo by presenting a mechanism for the action of DEAD-box proteins. Members of this family are intimately associated with almost all cellular processes involving RNA, mediating RNA structural rearrangements and chaperoning their folding. Next, we focus on advances in understanding and characterizing the basic biophysical forces that govern the folding of complex RNAs. Ultimately we expect that a confluence and synergy between these approaches will lead to profound understanding of RNA and its biology.The explosion in our knowledge about noncoding RNA (ncRNA) -RNA that is not translated into protein -has expanded interest in RNA beyond the traditional RNA community. Diverse ncRNAs include the recently-discovered riboswitches, whose novel gene-regulation function is induced by the binding of small metabolites [1]; most of the so-called "Human Accelerated Regions" (HAR) of the human genome, whose recent evolution may be linked to the emergence of the human brain [2]; and many ncRNAs of unknown function [3]. These discoveries underscore the need to understand the fundamental macromolecular behavior of RNA, its structure and dynamics, and how these RNAs are handled and exploited in biology.Study of catalytic RNAs, which allow detection of correct folding via activity measurements, has established basic thermodynamic and kinetic properties of RNA folding. Large catalytic RNAs such as the group I intron from Tetrahymena thermophila and the RNase P RNA from Bacillus subtilis fold at vastly different rates under different conditions upon addition of Mg 2+ and have been shown to fold via multiple parallel pathways, in which different molecules follow different routes with different rates and intermediates, to a common final folded structure [4,5]. These observations support the common view that RNAs traverse rugged energy landscapes as they fold [6,7]. However, little is known about the true shape of these

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Section: Discussionsupporting

confidence: 57%

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Chu

Herschlag

2008

Current Opinion in Structural Biology

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“…The occurrence of multiple conformers of the Atu RNA indicates, as seen for other RNAs, that much of the molecular population is kinetically trapped, preventing proper folding (Pan and Sosnick 1997;Pan et al 1999;Buck et al 2005b). Since ionic strength influences folding of some RNase P RNAs and high ionic strength is required for catalytic activity of RNase P RNA (Guerrier-Takada et al 1983;Siegel et al 1996), we surmised that the concentration of monovalent salt during in vitro transcription could influence the cotranscriptional folding of RNase P RNA.…”

Section: Preparation Of Rna Samples To Minimize Refolding Artifactsmentioning

confidence: 91%

Solution structure of RNase P RNA

Kazantsev¹,

Rambo²,

Karimpour³

et al. 2011

RNA

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The ribonucleoprotein enzyme ribonuclease P (RNase P) processes tRNAs by cleavage of precursor-tRNAs. RNase P is a ribozyme: The RNA component catalyzes tRNA maturation in vitro without proteins. Remarkable features of RNase P include multiple turnovers in vivo and ability to process diverse substrates. Structures of the bacterial RNase P, including full-length RNAs and a ternary complex with substrate, have been determined by X-ray crystallography. However, crystal structures of free RNA are significantly different from the ternary complex, and the solution structure of the RNA is unknown. Here, we report solution structures of three phylogenetically distinct bacterial RNase P RNAs from Escherichia coli, Agrobacterium tumefaciens, and Bacillus stearothermophilus, determined using small angle X-ray scattering (SAXS) and selective 29-hydroxyl acylation analyzed by primer extension (SHAPE) analysis. A combination of homology modeling, normal mode analysis, and molecular dynamics was used to refine the structural models against the empirical data of these RNAs in solution under the high ionic strength required for catalytic activity.

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“…This approach measures the rate constant for folding in the presence of bound rSA 5 , because the substrate is completely bound by the ribozyme simply by base-pairing under these conditions with a rate constant much faster than that for folding (Herschlag & Cech, 1990). A technique that uses ribozyme activity to measure folding in the absence of bound substrate by adding substrate at various times after initiating folding with Mg 2 has also been developed (Zarrinkar & Williamson, 1994; see also Pan & Sosnick, 1997;Pan et al, 1999). The two methods yielded identical values of k fold for the wild-type ribozyme at 37 C (Figure 3(a) and data not shown), con®rm-ing previous results (Zarrinkar & Williamson, 1994) and suggesting that bound rSA 5 does not affect the overall rate of folding.…”

Section: Multiple Turnover Kineticsmentioning

confidence: 99%