RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

Richardson, Jane S.; Schneider, Bohdan; Murray, Laura W.; Kapral, Gary J.; Immormino, R.M.; Headd, Jeffrey J.; Richardson, David C.; Ham, Daniela; Hershkovits, Eli; Williams, Loren Dean; Keating, Kevin S.; Pyle, Anna Marie; Micallef, David; Westbrook, John D.; Berman, Helen M.

doi:10.1261/rna.657708

Cited by 241 publications

(449 citation statements)

References 52 publications

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“…The conformation of the R364 side chain differs for each class. All sugar puckers are in the C3Ј-endo conformation, and classification of the RNA structural suite is unchanged (33,34).…”

Section: Resultsmentioning

confidence: 99%

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

Wang

Opperman

Wickens

et al. 2009

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

110

150

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Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4 -6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.crystal structure ͉ RNA ͉ translational regulation ͉ fem-3 binding factor ͉ base flipping

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“…The conformation of the R364 side chain differs for each class. All sugar puckers are in the C3Ј-endo conformation, and classification of the RNA structural suite is unchanged (33,34).…”

Section: Resultsmentioning

confidence: 99%

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

Wang

Opperman

Wickens

et al. 2009

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

110

150

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“…Although less frequent, the C2Ј-endo conformation is highly overrepresented in catalytic active sites and in critical tertiary structures (12, 13). At the static structure level, the C2Ј-endo conformation induces greater helical twist in an A-form helix (14, 15) and spans a much longer 5Ј-to-3Ј distance (12,16). At the level of local motion, some C2Ј-endo nucleotides exhibit extraordinarily slow conformational dynamics with half-lives on the 10-100-s timescale (17).…”

mentioning

confidence: 99%

“…Most nucleotides in an RNA molecule exist in the C3Ј-endo conformation. Although less frequent, the C2Ј-endo conformation is highly overrepresented in catalytic active sites and in critical tertiary structures (12,13). At the static structure level, the C2Ј-endo conformation induces greater helical twist in an A-form helix (14,15) and spans a much longer 5Ј-to-3Ј distance (12,16).…”

mentioning

confidence: 99%

C2′-endo nucleotides as molecular timers suggested by the folding of an RNA domain

Mortimer

Weeks

2009

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

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A striking and widespread observation is that higher-order folding for many RNAs is very slow, often requiring minutes. In some cases, slow folding reflects the need to disrupt stable, but incorrect, interactions. However, a molecular explanation for slow folding in most RNAs is unknown. The specificity domain of the Bacillus subtilis RNase P ribozyme undergoes a rate-limiting folding step on the minute time-scale. This RNA also contains a C2 -endo nucleotide at A130 that exhibits extremely slow local conformational dynamics. This nucleotide is evolutionarily conserved and essential for tRNA recognition by RNase P. Here we show that deleting this single nucleotide accelerates folding by an order of magnitude even though this mutation does not change the global fold of the RNA. These results demonstrate that formation of a single stacking interaction at a C2 -endo nucleotide comprises the rate-determining step for folding an entire 154 nucleotide RNA. C2 -endo nucleotides exhibit slow local dynamics in structures spanning isolated helices to complex tertiary interactions. Because the motif is both simple and ubiquitous, C2 -endo nucleotides may function as molecular timers in many RNA folding and ligand recognition reactions.RNA folding ͉ RNA SHAPE chemistry T o function properly inside the cell, RNA molecules undergo complex folding transitions to form specific, biologically active, three-dimensional structures (1). These essential structures involve both local base pairing and also complex higherorder tertiary interactions. A persistent and incompletely explained observation is that many RNAs fold very slowly, on timescales requiring minutes or longer. RNAs that fold slowly span all sizes including small riboswitch and catalytic RNAs, medium-sized catalytic introns, and the large RNAs in ribosomes (2-6).Slow folding has important consequences both because correct folding ultimately governs the rate at which an RNA can perform its biological function and because bottlenecks in assembly potentially require cellular mechanisms to overcome slow folding. In some cases, slow folding results from formation of stable, non-native, and kinetically trapped states (7,8). Such misfolding is remedied, in part, by cellular chaperone activities (9-11). In many cases, the molecular basis for slow folding is unknown.The intricate three-dimensional structures formed by RNA molecules ultimately reflect the underlying contributions of individual nucleotides. Most nucleotides in an RNA molecule exist in the C3Ј-endo conformation. Although less frequent, the C2Ј-endo conformation is highly overrepresented in catalytic active sites and in critical tertiary structures (12, 13). At the static structure level, the C2Ј-endo conformation induces greater helical twist in an A-form helix (14, 15) and spans a much longer 5Ј-to-3Ј distance (12,16). At the level of local motion, some C2Ј-endo nucleotides exhibit extraordinarily slow conformational dynamics with half-lives on the 10-100-s timescale (17).Here we show that the slow conformational ...

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“…Although C2′-endo nucleotides are relatively rare, they are highly overrepresented in important RNA tertiary interactions and in catalytic active sites. 4 Local structure at tandem G•A mismatches depends on the local sequence context. 5 Guanosine nucleotides in G•A pairs adopt the C2′-endo conformation in the sequences (UGAA) 2 5a and (GGAU) 2 , 5b the C3′-endo conformation typical of standard A-form helix geometry in (CGAG) 2 , 5c and a mixture of C2′-endo/C3′-endo conformations in (UGAG) 2 .…”

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confidence: 99%

Slow Conformational Dynamics at C2′-endo Nucleotides in RNA

et al. 2008

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Local and global dynamics in folded RNAs occur over broad timescales spanning picoseconds to minutes. 1 Slow motions likely play predominant roles in governing RNA folding and ribonucleoprotein assembly reactions. However, slow local motions are extremely difficult to detect, especially for large RNAs with complex structures.The local environment and degree of flexibility can be evaluated at nucleotide resolution for RNAs of any size using selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry. 2 RNA nucleotides exist in equilibrium between constrained (closed) and flexible (open) states. The 2′-OH group in flexible nucleotides preferentially adopts an open, reactive, conformation that facilitates reaction with electrophilic reagents to form a 2′-O-adduct (Figure 1). SHAPE experiments work well using electrophiles based on the isatoic anhydride (IA) scaffold. 2a,3 Positions that form 2′-O-adducts are detected by primer extension. 2 IA derivatives both react with the RNA 2′-OH group and also undergo concurrent degradation by hydrolysis (Figure 1). 2′-OH reactivity is thus conveniently monitored by allowing a reaction to proceed until the reagent has been consumed, either by hydrolysis or reaction with RNA. At this end point, the fraction adduct at any nucleotide (f) is (1) Where (2) and the rate of hydrolysis has been shown to be proportional to the rate of adduct formation, 2b,3 k adduct /k hydrolysis = β. These relationships lead to two limits. In limit 1, k open + k close ≫ k adduct [reagent] Correspondence to: Kevin M. Weeks, weeks@unc.edu. Supporting Information Available: Methods and four figures. This material is available free of charge via the Internet at http:// pubs.acs.org. HHS Public AccessIt should therefore be possible to monitor local nucleotide dynamics in RNA under conditions where limit 2 applies by varying the reactivity (or k hydrolysis ) of the hydroxylselective electrophile. IA has a hydrolysis half-life (t 1/2 ) of 430 s at 37 °C. Electronwithdrawing substituents at the cyclic amine (R 1 ) or in the benzene ring (R 2 ) enhance reagent reactivity. Compared to IA, N-methyl isatoic anhydride (NMIA), 4-nitroisatioc anhydride (4NIA), and 1-methyl 7-nitroisatoic anhydride (1M7) 3 have progressively shorter hydrolysis half-lives (table, Figure 1).To investigate if distinct local nucleotide dynamics can be captured by varying the SHAPE electrophile, we focused on an important variation in RNA structure: the C2′-endo conformation. Although C2′-endo nucleotides are relatively rare, they are highly overrepresented in important RNA tertiary interactions and in catalytic active sites. 4 Local structure at tandem G•A mismatches depends on the local sequence context. 5 Guanosine nucleotides in G•A pairs adopt the C2′-endo conformation in the sequences (UGAA) 2 5a and (GGAU) 2 , 5b the C3′-endo conformation typical of standard A-form helix geometry in (CGAG) 2 , 5c and a mixture of C2′-endo/C3′-endo conformations in (UGAG) 2 . 5b We constructed a simple hairpin RNA (termed...

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RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

Cited by 241 publications

References 52 publications

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

C2′-endo nucleotides as molecular timers suggested by the folding of an RNA domain

Slow Conformational Dynamics at C2′-endo Nucleotides in RNA

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