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Related Concept Videos

RNA Structure01:23

RNA Structure

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RNA Structure01:23

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Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. 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.
Different Types of RNA Have the Same Basic Structure
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RNA Structure01:19

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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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Nucleic Acid Structure01:25

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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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Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

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Physics-based RNA structure prediction.

Xiaojun Xu1, Shi-Jie Chen1

  • 1Department of Physics, University of Missouri, Columbia, MO 65211 USA ; Department of Biochemistry, University of Missouri, Columbia, MO 65211 USA ; Informatics Institute, University of Missouri, Columbia, MO 65211 USA.

Biophysics Reports
|March 5, 2016
PubMed
Summary
This summary is machine-generated.

Predicting complex RNA tertiary structures is challenging. This study introduces the Vfold model, using statistical mechanics and coarse-grained modeling for accurate RNA 3D structure prediction and function correlation.

Keywords:
2D structure prediction3D structure predictionRNATertiary motifVfold

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • RNA secondary structure prediction is established, but predicting long-range tertiary folds remains a significant challenge.
  • RNA 3D structure prediction is hindered by incomplete knowledge of tertiary contacts and their thermodynamic parameters.

Purpose of the Study:

  • To present an overview of computational models for RNA secondary and tertiary structure prediction.
  • To focus on the Vfold model, a statistical mechanical approach for RNA 3D structure prediction.
  • To emphasize the underlying physics, including non-canonical interactions and their link to RNA function.

Main Methods:

  • Low-resolution structural modeling using statistical mechanical calculations to estimate conformational entropies.
  • Coarse-grained modeling to generate initial 3D tertiary folds.
  • All-atom molecular dynamics refinement for building final 3D structures.

Main Results:

  • The Vfold model provides a physics-based approach to RNA tertiary structure prediction.
  • Coarse-grained models enable estimation of conformational entropies for tertiary folds.
  • The methodology allows for refinement into all-atom 3D structures.

Conclusions:

  • The Vfold model offers a promising approach to overcome limitations in RNA 3D structure prediction.
  • Understanding tertiary contacts and thermodynamic parameters is crucial for accurate modeling.
  • The model's insights into non-canonical interactions correlate with RNA functions.