The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics

Tubbs, Jason D.; Condon, David E.; Kennedy, Scott D.; Hauser, Melanie; Bevilacqua, Philip C.; Turner, Douglas H.

doi:10.1021/bi3010347

Cited by 75 publications

(177 citation statements)

References 85 publications

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“…Together with CD and UV/Vis melting experiments, these data indicated that the ssRNA is in equilibrium between an ordered A-form-like helical conformation and a highly disordered partially melted state. Similar observations have since been made on polycytosine ssRNA sequences using NMR, UV melting, and MD simulations, showing that ssRNA order is not limited to polyadenine sequences (Tubbs et al 2013).…”

Section: Introductionsupporting

confidence: 76%

Structural dynamics of a single-stranded RNA–helix junction using NMR

Eichhorn

Al‐Hashimi

2014

RNA

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Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3 ′ end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, 13 C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A 6 -tract and forms an acute pivot point for substantial motions within the tail, which increase toward the terminal end. Despite substantial internal motions, the ssRNA tail adopts, on average, an A-form helical conformation that is coaxial with the helix. Our results reveal a surprising degree of structural and dynamic complexity at the ssRNA-helix junction, which involves a fine balance between order and disorder that may facilitate efficient pseudoknot formation on ligand recognition.

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Section: Introductionsupporting

confidence: 76%

Structural dynamics of a single-stranded RNA–helix junction using NMR

Eichhorn

Al‐Hashimi

2014

RNA

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“…Interestingly, while we observe reactivity within the template, nucleotides 44-46 (CCC) consistently did not show reactivity above background levels, suggesting they may be stacked or involved in tertiary interactions. Polycytidylic acid alone can form a helix stabilized by base stacking or hydrogen bonding between adjacent bases (Arnott et al 1976;Freier et al 1981;Broido and Kearns 1982;Tubbs et al 2013). The CCC residues within the template could be adopting a similar structure, resulting in low NMIA reactivity.…”

Section: Resultsmentioning

confidence: 99%

Refined secondary-structure models of the core of yeast and human telomerase RNAs directed by SHAPE

Niederer

Zappulla

2014

RNA

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Telomerase catalyzes the addition of nucleotides to the ends of chromosomes to complete genomic DNA replication in eukaryotes and is implicated in multiple diseases, including most cancers. The core enzyme is composed of a reverse transcriptase and an RNA subunit, which provides the template for DNA synthesis. Despite extensive divergence at the sequence level, telomerase RNAs share several structural features within the catalytic core, suggesting a conserved enzyme mechanism. We have investigated the structure of the core of the human and yeast telomerase RNAs using SHAPE, which interrogates flexibility of each nucleotide. We present improved secondary-structure models, refined by addition of five base triples within the yeast pseudoknot and an alternate pairing within the human-specific element J2a.1 in the human pseudoknot, both of which have implications for thermodynamic stability. We also identified a potentially structured CCC region within the template that may facilitate substrate binding and enzyme mechanism. Overall, the SHAPE findings reveal multiple similarities between the Saccharomyces cerevisiae and Homo sapiens telomerase RNA cores.

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“…Cytidine protonation would also change stacking interactions. A cytidine tetramer shows A-form stacking interactions by NMR (Tubbs et al 2013). If the cytidines were protonated, then different stacking interactions would likely form.…”

Section: Proposed Model For Predicting the Free Energies Of Asymmetrimentioning

confidence: 99%

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops

Phan

Mailey

Saeki

et al. 2017

RNA

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Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites.

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The Nuclear Magnetic Resonance of CCCC RNA Reveals a Right-Handed Helix, and Revised Parameters for AMBER Force Field Torsions Improve Structural Predictions from Molecular Dynamics

Cited by 75 publications

References 85 publications

Structural dynamics of a single-stranded RNA–helix junction using NMR

Structural dynamics of a single-stranded RNA–helix junction using NMR

Refined secondary-structure models of the core of yeast and human telomerase RNAs directed by SHAPE

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops

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