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Related Concept Videos

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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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.
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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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RNA Stability01:53

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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Modeling complex RNA tertiary folds with Rosetta.

Clarence Yu Cheng1, Fang-Chieh Chou1, Rhiju Das2

  • 1Department of Biochemistry, Stanford University, Stanford, California, USA.

Methods in Enzymology
|March 2, 2015
PubMed
Summary
This summary is machine-generated.

This study presents a practical guide to modeling RNA tertiary structures using the Fragment Assembly of RNA with Full-Atom Refinement (FARFAR) method. It details how to integrate experimental data for accurate computational predictions, advancing RNA structure research.

Keywords:
Blind predictionChemical mappingFragment assemblyRNA tertiary structureStructure mapping

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Accurate RNA tertiary structure modeling is crucial for understanding biological functions and enabling molecular design.
  • Advances in computational prediction have been accelerated by initiatives like RNA-Puzzles.
  • Rosetta software enables RNA modeling in the 100-300 nucleotide range at subhelical resolution.

Purpose of the Study:

  • To provide a practical guide to the current workflow for modeling RNA 3D structures.
  • To demonstrate the application of Fragment Assembly of RNA with Full-Atom Refinement (FARFAR) for RNA modeling.
  • To illustrate strategies for integrating experimental data into computational modeling.

Main Methods:

  • Utilizing the Fragment Assembly of RNA with Full-Atom Refinement (FARFAR) method within the Rosetta software.
  • Employing hybrid techniques that combine computational modeling with experimental data.
  • Leveraging multidimensional chemical mapping experiments to guide conformational sampling and selection.

Main Results:

  • The described workflow enables consistent subhelical resolution modeling of RNAs (100-300 nucleotides).
  • FARFAR optimizes RNA conformations using a physically realistic energy function.
  • Integration of experimental data refines computational models for improved accuracy.

Conclusions:

  • The FARFAR method, enhanced by experimental data, represents a state-of-the-art approach for RNA tertiary structure modeling.
  • This workflow facilitates accurate prediction and potential design of RNA molecules.
  • The practical guide aids researchers in applying these advanced computational techniques.