RNA dynamics: it is about time

Al‐Hashimi, Hashim M.; Walter, Nils G.

doi:10.1016/j.sbi.2008.04.004

Cited by 292 publications

(299 citation statements)

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“…It ranges from 200 nucleotides per second (nt/sec) in phages, to 20-80 nt/sec in bacteria and 10-20 nt/ sec for human polymerase II (Pan and Sosnick 2006). On the other hand, RNA folding is known to occur on a wide range of time scales; some RNAs fold in 10-100 msec (Al-Hashimi and Walter 2008), whereas kinetically trapped conformations can persist for minutes or hours (Sosnick and Pan 2003;Thirumalai and Hyeon 2005;Al-Hashimi and Walter 2008). Experiments in the early 1980s have shown that RNA structure formation can happen during transcription (Boyle et al 1980;Kramer and Mills 1981), i.e., cotranscriptionally, and that folding in vivo can happen on the same timescale as RNA synthesis (Brehm and Cech 1983).…”

Section: Transcription Transcription Speed and Variations Thereofmentioning

confidence: 99%

On the importance of cotranscriptional RNA structure formation

Lai

Proctor

Meyer

2013

RNA

148

132

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The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.

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Section: Transcription Transcription Speed and Variations Thereofmentioning

confidence: 99%

On the importance of cotranscriptional RNA structure formation

Lai

Proctor

Meyer

2013

RNA

148

132

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“…Techniques including NMR and EPR relaxation have been developed to incisively probe motions in the ensemble on different time scales, ranging from picoseconds to milliseconds (3,4). Nonetheless, such dynamic information represents an average of the dynamics of the molecules across the conformational ensemble.…”

Section: Helix-junction-helix | Saxsmentioning

confidence: 99%

From a structural average to the conformational ensemble of a DNA bulge

Shi¹,

Beauchamp

Harbury

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Direct experimental measurements of conformational ensembles are critical for understanding macromolecular function, but traditional biophysical methods do not directly report the solution ensemble of a macromolecule. Small-angle X-ray scattering interferometry has the potential to overcome this limitation by providing the instantaneous distance distribution between pairs of gold-nanocrystal probes conjugated to a macromolecule in solution. Our X-ray interferometry experiments reveal an increasing bend angle of DNA duplexes with bulges of one, three, and five adenosine residues, consistent with previous FRET measurements, and further reveal an increasingly broad conformational ensemble with increasing bulge length. The distance distributions for the AAA bulge duplex (3A-DNA) with six different Au-Au pairs provide strong evidence against a simple elastic model in which fluctuations occur about a single conformational state. Instead, the measured distance distributions suggest a 3A-DNA ensemble with multiple conformational states predominantly across a region of conformational space with bend angles between 24 and 85 degrees and characteristic bend directions and helical twists and displacements. Additional X-ray interferometry experiments revealed perturbations to the ensemble from changes in ionic conditions and the bulge sequence, effects that can be understood in terms of electrostatic and stacking contributions to the ensemble and that demonstrate the sensitivity of X-ray interferometry. Combining X-ray interferometry ensemble data with molecular dynamics simulations gave atomic-level models of representative conformational states and of the molecular interactions that may shape the ensemble, and fluorescence measurements with 2-aminopurinesubstituted 3A-DNA provided initial tests of these atomistic models. More generally, X-ray interferometry will provide powerful benchmarks for testing and developing computational methods. helix-junction-helix | SAXSA grand challenge in biology is to understand the complex free-energy landscape of macromolecules and to decipher the resulting conformational ensembles. To perform their biological functions, macromolecules must adopt a multiplicity of conformations. Balancing and controlling different conformational states is central to biological processes including protein folding, allostery and signaling, and the stepwise assembly and function of macromolecular machines. To understand these complex molecules requires characterization of their free-energy landscapes-i.e., their equilibrium conformational ensembles. Precise measurements of conformational ensembles could allow quantitative modeling of the folding and function of biological macromolecules, would provide valuable experimental data to test current computational models and assumptions, and might facilitate the rational design of specifically acting inhibitors (1, 2).Techniques including NMR and EPR relaxation have been developed to incisively probe motions in the ensemble on different time scales, ranging from pic...

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“…These concepts all invoke conformational flexibility (sampling) in both enzyme and substrate, derived from their structural dynamics, or the sum of all thermally activated global and local motions. While quite well established for protein enzymes (Fersht 1999;Hammes-Schiffer and Benkovic 2006), the potentially intricate linkage between function and structural dynamics is still much more tenuous for RNA (Al-Hashimi and Walter 2008).…”

Section: Introductionmentioning

confidence: 99%

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

McDowell¹,

Jun²,

Walter³

2010

RNA

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Enzymes generally are thought to derive their functional activity from conformational motions. The limited chemical variation in RNA suggests that such structural dynamics may play a particularly important role in RNA function. Minimal hammerhead ribozymes are known to cleave efficiently only in~10-fold higher than physiologic concentrations of Mg 2+ ions. Extended versions containing native loop-loop interactions, however, show greatly enhanced catalytic activity at physiologically relevant Mg 2+ concentrations, for reasons that are still ill-understood. Here, we use Mg 2+ titrations, activity assays, ensemble, and single molecule fluorescence resonance energy transfer (FRET) approaches, combined with molecular dynamics (MD) simulations, to ask what influence the spatially distant tertiary loop-loop interactions of an extended hammerhead ribozyme have on its structural dynamics. By comparing hammerhead variants with wild-type, partially disrupted, and fully disrupted loop-loop interaction sequences we find that the tertiary interactions lead to a dynamic motional sampling that increasingly populates catalytically active conformations. At the global level the wild-type tertiary interactions lead to more frequent, if transient, encounters of the loop-carrying stems, whereas at the local level they lead to an enrichment in favorable in-line attack angles at the cleavage site. These results invoke a linkage between RNA structural dynamics and function and suggest that loop-loop interactions in extended hammerhead ribozymes-and Mg 2+ ions that bind to minimal ribozymes-may generally allow more frequent access to a catalytically relevant conformation(s), rather than simply locking the ribozyme into a single active state.

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RNA dynamics: it is about time

Cited by 292 publications

References 50 publications

On the importance of cotranscriptional RNA structure formation

On the importance of cotranscriptional RNA structure formation

From a structural average to the conformational ensemble of a DNA bulge

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations

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