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Related Concept Videos

RNA Structure01:23

RNA Structure

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
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:19

RNA Structure

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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

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
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
Nucleic Acid Structure01:25

Nucleic Acid Structure

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.
DNA Structure
DNA has a double-helix structure. The...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview

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Related Experiment Video

Updated: Jun 25, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular

Costin M Gherghe1, Christopher W Leonard, Feng Ding

  • 1Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.

Journal of the American Chemical Society
|February 6, 2009
PubMed
Summary

This study introduces a novel computational method combined with RNA structure probing experiments to accurately model complex RNA tertiary structures. This approach refines RNA structures efficiently without prior assumptions, aiding in the study of flexible and functionally important RNAs.

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Analyzing and Building Nucleic Acid Structures with 3DNA
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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Related Experiment Videos

Last Updated: Jun 25, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Biochemistry
  • Computational Biology
  • Structural Biology

Background:

  • Analyzing higher-order RNA structures, particularly flexible domains and folding intermediates, is challenging.
  • Existing methods struggle with RNAs requiring conformational flexibility for function.
  • Accurate RNA tertiary structure modeling is crucial for understanding RNA function.

Purpose of the Study:

  • To develop a concise and accurate approach for modeling RNA tertiary structure.
  • To overcome limitations of conventional structural methods for flexible RNAs.
  • To enable structure determination without prior assumptions about RNA folding.

Main Methods:

  • Utilizing facile RNA structure probing experiments, including SHAPE chemistry for secondary structure.
  • Employing sequence-directed cleavage agents to generate inter-residue distance information.
  • Interpreting experimental data with a fast, coarse-grained discrete molecular dynamics algorithm.
  • Representing each RNA nucleotide with pseudoatoms (phosphate, ribose, nucleobase).

Main Results:

  • Successfully refined base-paired positions in yeast tRNA(Asp) to 4 Å root-mean-square deviation (rmsd).
  • Achieved high-resolution structural refinement without pre-existing structural information.
  • Demonstrated a computational algorithm optimized for resolution and speed without user intervention.

Conclusions:

  • This blended experimental and computational approach offers a powerful new tool for RNA structure modeling.
  • The method has the potential to yield native-like models for diverse, functionally important RNAs.
  • It addresses the need for new approaches to study RNAs intractable by conventional structural biology techniques.