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Related Concept Videos

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...
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...
Nucleic Acids02:43

Nucleic Acids

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.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Nucleic acids02:43

Nucleic acids

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.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...

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Updated: May 31, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Correlating SHAPE signatures with three-dimensional RNA structures.

Eckart Bindewald1, Michaela Wendeler, Michal Legiewicz

  • 1Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA.

RNA (New York, N.Y.)
|July 15, 2011
PubMed
Summary
This summary is machine-generated.

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reveals RNA secondary structures. SHAPE signals primarily reflect Watson-Crick base-pairing, offering a refined method for RNA structure analysis.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a key technique for RNA secondary structure analysis.
  • SHAPE signals generally correlate low with base-paired regions and high with single-stranded regions.
  • The relationship between SHAPE reactivity and non-canonical base-pairing or stacking interactions remains incompletely understood.

Purpose of the Study:

  • To investigate the correlation between SHAPE signals and diverse RNA structural properties.
  • To analyze SHAPE reactivity in relation to specific base-pairing, stacking, and backbone interactions.
  • To develop improved models for predicting RNA base-pairing using SHAPE data.

Main Methods:

  • Performed SHAPE experiments on multiple RNA molecules with known 3D structures.
  • Correlated SHAPE reactivity values with detailed structural features of individual nucleotides.
  • Developed and evaluated probabilistic models for base-pairing prediction incorporating adjacent residue SHAPE scores.

Main Results:

  • SHAPE signals strongly correlate with cis-Watson-Crick/Watson-Crick base-pairing.
  • SHAPE reactivity is largely independent of other structural features, except for stacking interactions.
  • Models considering adjacent residue SHAPE scores significantly improve base-pairing prediction accuracy compared to individual scores.

Conclusions:

  • RNA SHAPE reactivity is a robust indicator of Watson-Crick base-pairing.
  • Contextual information from neighboring residues enhances SHAPE-based structure prediction.
  • This study provides a framework for more accurate interpretation of SHAPE data in RNA structure analysis.