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RNA Structure01:19

RNA Structure

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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Improving NMR Structures of RNA.

Guillermo A Bermejo1, G Marius Clore2, Charles D Schwieters1

  • 1Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA.

Structure (London, England : 1993)
|April 13, 2016
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Summary

A new RNA force field, RNA-ff1, enhances nuclear magnetic resonance (NMR) structure calculations. It reduces steric clashes and improves conformational accuracy, bridging the quality gap between NMR and X-ray structures.

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational chemistry

Background:

  • Solution nuclear magnetic resonance (NMR) structures of RNA often present more steric clashes and conformational ambiguities compared to X-ray crystallography structures.
  • Existing computational methods may not fully capture the nuances of RNA structure, leading to discrepancies between experimental and calculated models.

Purpose of the Study:

  • To develop and validate a new force field, RNA-ff1, for improved RNA structure calculations using Xplor-NIH.
  • To address the limitations of current force fields in accurately representing RNA structures derived from NMR data.

Main Methods:

  • Development of the RNA-ff1 force field tailored for Xplor-NIH structure calculations.
  • Application of RNA-ff1 to seven published NMR datasets of RNA.
  • Validation using MolProbity criteria and residual dipolar coupling (RDC) cross-validation.

Main Results:

  • RNA-ff1 demonstrated improved covalent geometry and reduced steric clashes compared to previous methods and original experimental structures.
  • Structures calculated with RNA-ff1 exhibited better backbone conformation and more favorable base stacking in helical regions.
  • Residual dipolar coupling cross-validation supported enhanced structural accuracy for RNA-ff1 derived models.

Conclusions:

  • The RNA-ff1 force field significantly improves the quality of RNA structures determined by NMR, reducing clashes and conformational ambiguities.
  • RNA-ff1 shows promise in narrowing the quality gap between NMR and X-ray structures of RNA.
  • This advancement facilitates more accurate structural modeling and analysis of RNA molecules.