Kinetics of an RNA conformational switch.

LeCuyer, Karen A.; Crothers, Donald M.

doi:10.1073/pnas.91.8.3373

Cited by 90 publications

(54 citation statements)

References 18 publications

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“…Riboswitches can provide exact temporal control as in the hok/sok system of plasmid R1 which triggers programmed cell death [53,51]. Riboswitches also play a role in the spliced leader of trypanosomes and nematodes [43]. Artificial RNA switches have been designed as well, see e.g.…”

Section: Discussionmentioning

confidence: 99%

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model

Hackermüller¹,

Meisner²,

Auer³

et al. 2005

Gene

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RNA-ligand binding often depends crucially on the local RNA secondary structure at the binding site. We develop here a model that quantitatively predicts the effect of RNA secondary structure on effective RNA-ligand binding activities based on equilibrium thermodynamics and the explicit computations of partition functions for the RNA structures. A statistical test for the impact of a particular structural feature on the binding affinities follows directly from this approach. The formalism is extended to describing the effects of hybridizing small "modifier RNAs" to a target RNA molecule outside its ligand binding site. We illustrate the applicability of our approach by quantitatively describing the interaction of the mRNA stabilizing protein HuR with AU-rich elements [Meisner et al. (2004), Chem. Biochem. in press]. We discuss our model and recent experimental findings demonstrating the effectivity of modifier RNAs in vitro in the context of the current research activities in the field of non-coding RNAs. We speculate that modifier RNAs might also exist in nature; if so, they present an additional regulatory layer for fine-tuning gene expression that could evolve rapidly, leaving no obvious traces in the genomic DNA sequences.

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Section: Discussionmentioning

confidence: 99%

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model

Hackermüller¹,

Meisner²,

Auer³

et al. 2005

Gene

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“…T7 transcription of the 385-nt ribozyme requires about 2 sec (Golomb and Chamberlin 1974), and the formation of local secondary structure about 10-100 µsec LeCuyer and Crothers 1994;Ansari et al 2001;Wallace et al 2001). Thus, synthesis of the ribozyme and initial folding steps are complete within the shortest time of our assay.…”

Section: Cotranscriptional Folding Of the L-21 Ribozymementioning

confidence: 99%

Effect of transcription on folding of the Tetrahymena ribozyme

Heilman-Miller

Woodson²

2003

RNA

102

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Sequential formation of RNA interactions during transcription can bias the folding pathway and ultimately determine the functional state of a transcript. The kinetics of cotranscriptional folding of the Tetrahymena L-21 ribozyme was compared with refolding of full-length transcripts under the same conditions. Sequential folding after transcription by phage T7 or Escherichia coli polymerase is only twice as fast as refolding, and the yield of native RNA is the same. By contrast, a greater fraction of circularly permuted variants folded correctly at early times during transcription than during refolding. Hybridization of complementary oligonucleotides suggests that cotranscriptional folding enables a permuted RNA beginning at G303 to escape nonnative interactions in P3 and P9. We propose that base pairing of upstream sequences during transcription elongation favors branched secondary structures that increase the probability of forming the native ribozyme structure.

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“…Taken together these observations suggest that the structural rearrangements that lead the molecule from misfolded structures to the native state occur through pathways made up of multiple small unfolding/refolding steps and not through a path that requires the complete unfolding of the RNA. A similar mechanism has been proposed for the conformational switch of a ribozyme (31).…”

mentioning

confidence: 93%

Real-time control of the energy landscape by force directs the folding of RNA molecules

Bustamante²,

Tinoco³

2007

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

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The rugged folding-energy landscapes of RNAs often display many competing minima. How do RNAs discriminate among competing conformations in their search for the native state? By using optical tweezers, we show that the folding-energy landscape can be manipulated to control the fate of an RNA: individual RNA molecules can be induced into either native or misfolding pathways by modulating the relaxation rate of applied force and even be redirected during the folding process to switch from misfolding to native folding pathways. Controlling folding pathways at the single-molecule level provides a way to survey the manifold of folding trajectories and intermediates, a capability that previously was available only to theoretical studies. mechanical force ͉ misfolding ͉ optical tweezers ͉ RNA folding ͉ single molecule T he folding of a macromolecule can be thought of as a biased diffusion over an energy surface that describes the thermodynamic and kinetic constraints of possible intramolecular interactions. RNAs differ from proteins in the nature, strength, specificity, and degeneracy of the interactions that stabilize their native structures. Whereas proteins are made of 20 amino acids, it takes only 4 nucleotides to build RNAs. This simpler composition, endowed with robust base-pairing rules, greatly increases the promiscuity of interactions between any given nucleotide and the rest of the RNA structure. These RNA-protein differences are reflected in the topography of the energy surface over which the molecules diffuse in their search for the native structure: the energy surfaces of RNAs are significantly more rugged than those of proteins, containing many competing local minima (1-4). Even relatively small RNAs, such as tRNA (4-6), tend to fold into stable alternate secondary structures with energies only a few kilocalories (1 kcal ϭ 4.18 kJ on first use) per mole apart (4). Once trapped kinetically in a secondary structure with suboptimal folding energy, it is difficult for an RNA molecule to reach its native structure (1).The promiscuous nature of secondary interactions in RNA begs answers for three questions: How do RNAs find their native structure? How do they avoid the kinetic traps on their rugged folding-energy landscape? And, how can RNAs switch between alternate structures in response to changes in the cellular environment, as happens, for example, during transcription attenuation in bacteria (7)? To address these questions, we need to follow the folding trajectories of RNA molecules as they diffuse over their energy landscape in search of stable conformations. Because of the structural polymorphism and manifold pathways of RNA, singlemolecule approaches (8-12) are particularly useful for answering these questions by identifying folding intermediates and distinguishing native pathways from those that misfold.Here we use optical tweezers to unfold and control the refolding of single RNA molecules by force (11, 13). Two micrometer-sized beads are attached to the ends of an RNA molecule and are manipulated by ...

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Kinetics of an RNA conformational switch.

Cited by 90 publications

References 18 publications

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model

The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model

Effect of transcription on folding of the Tetrahymena ribozyme

Real-time control of the energy landscape by force directs the folding of RNA molecules

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