Influence of Hydrostatic Pressure and Cosolutes on RNA Tertiary Structure

Downey, Christopher D.; Crisman, Ryan L.; Randolph, Theodore W.; Pardi, Arthur

doi:10.1021/ja072179k

Cited by 26 publications

(26 citation statements)

References 19 publications

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“…Accordingly it can be concluded that, essentially, the influence of alcohol on DNA, which modifies the DNA ability to bound with the pyrene, is an indirect interaction, due not so much to a direct alcohol-DNA interaction as to a change in the hydration of DNA caused by modification of water structure produced by the alcohol. This idea is consistent with that of Downey according to which there are two kinds of non-ionic molecules that interact with DNA in a different way [18]: ''it has been shown that various cosolutes stabilize a DNA G-quadruplex relative to a random coil [19]. These effects arise because cosolutes perturb the interactions between the surface of a biomolecule and water.…”

Section: Alcoholssupporting

confidence: 87%

Quantification of salts and cosolvents–DNA interactions in terms of free energies: A study using the pyren-1-carboxyaldehyde as fluorescent probe

et al. 2008

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Section: Alcoholssupporting

confidence: 87%

Quantification of salts and cosolvents–DNA interactions in terms of free energies: A study using the pyren-1-carboxyaldehyde as fluorescent probe

et al. 2008

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“…Sucrose and glycerol had little effect on docking, suggesting that they have similar affinity for the RNA, likely due to the presence of the vicinal hydroxyl groups. It has also been observed that increased hydrostatic pressure destabilizes T(GAAA)-R(11 nt) formation, to which a number of interactions with the solvent may also contribute (Downey et al 2007). …”

Section: Free Versus Bound Structure Of the Gaaa Tetraloop And 11 Nt mentioning

confidence: 99%

An RNA folding motif: GNRA tetraloop–receptor interactions

Fiore

Nesbitt

2013

Quart. Rev. Biophys.

105

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Nearly two decades after Westhof and Michel first proposed that RNA tetraloops may interact with distal helices, tetraloop–receptor interactions have been recognized as ubiquitous elements of RNA tertiary structure. The unique architecture of GNRA tetraloops (N=any nucleotide, R=purine) enables interaction with a variety of receptors, e.g., helical minor grooves and asymmetric internal loops. The most common example of the latter is the GAAA tetraloop–11 nt tetraloop receptor motif. Biophysical characterization of this motif provided evidence for the modularity of RNA structure, with applications spanning improved crystallization methods to RNA tectonics. In this review, we identify and compare types of GNRA tetraloop–receptor interactions. Then we explore the abundance of structural, kinetic, and thermodynamic information on the frequently occurring and most widely studied GAAA tetraloop–11 nt receptor motif. Studies of this interaction have revealed powerful paradigms for structural assembly of RNA, as well as providing new insights into the roles of cations, transition states and protein chaperones in RNA folding pathways. However, further research will clearly be necessary to characterize other tetraloop–receptor and long-range tertiary binding interactions in detail – an important milestone in the quantitative prediction of free energy landscapes for RNA folding.

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“…Sometimes FRET can demonstrate the lack of significant conformational dynamics of a ribozyme, for example of the glmS ribozyme upon cofactor binding [18]. Often a specific tertiary interaction of a larger ribozyme can be studied in isolation, which led, for example, to the FRET-based characterization of docking and undocking of the GAAA tetraloop and receptor as induced by metal ions and increased hydrostatic pressure, respectively [28,29].…”

Section: Rna Catalysismentioning

confidence: 99%

RNA dynamics: it is about time

Al‐Hashimi

Walter

2008

Current Opinion in Structural Biology

299

295

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SummaryMany recently discovered RNA functions rely on highly complex multi-step conformational transitions that occur in response to an array of cellular signals. These dynamics accompany and guide, for example, RNA co-transcriptional folding, ligand sensing and signaling, site-specific catalysis in ribozymes, and the hierarchically ordered assembly of ribonucleoproteins. RNA dynamics are encoded by both the inherent properties of RNA structure, spanning many motional modes with a large range of amplitudes and timescales, and external trigger factors, ranging from proteins, nucleic acids, metal ions, metabolites, and vitamins to temperature and even directional RNA biosynthesis itself. Here, we review recent advances in our understanding of RNA dynamics as highlighted by biophysical tools.

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Influence of Hydrostatic Pressure and Cosolutes on RNA Tertiary Structure

Cited by 26 publications

References 19 publications

Quantification of salts and cosolvents–DNA interactions in terms of free energies: A study using the pyren-1-carboxyaldehyde as fluorescent probe

Quantification of salts and cosolvents–DNA interactions in terms of free energies: A study using the pyren-1-carboxyaldehyde as fluorescent probe

An RNA folding motif: GNRA tetraloop–receptor interactions

RNA dynamics: it is about time

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