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Related Concept Videos

RNA Structure

RNA Structure

RNA Structure

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 Structure

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...

Nucleic Acid Structure

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...

Protein Folding

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 Folding

Protein Folding

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Related Experiment Video

Updated: Apr 4, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

SHAPE directed RNA folding.

Ronny Lorenz¹, Dominik Luntzer², Ivo L Hofacker¹

¹Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.

Bioinformatics (Oxford, England)

|September 11, 2015

Summary

This summary is machine-generated.

Chemical mapping experiments provide nucleotide-resolution RNA structure insights. Integrating probing data with RNA secondary structure prediction algorithms using soft constraints enhances accuracy, as demonstrated with SHAPE reactivities.

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Last Updated: Apr 4, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE

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Area of Science:

Biochemistry
Computational Biology
Molecular Biology

Background:

Chemical mapping experiments offer nucleotide-resolution assessment of RNA structure.
RNA secondary structure prediction is crucial for understanding RNA function.
Integrating experimental data with computational models improves prediction accuracy.

Purpose of the Study:

To demonstrate the implementation of soft constraints for integrating probing data with RNA secondary structure prediction algorithms.
To showcase the ViennaRNA Package's new feature for SHAPE-directed RNA folding.
To compare different strategies for utilizing SHAPE reactivities in structure prediction.

Main Methods:

Incorporation of pseudo-energies into the standard energy model for RNA secondary structures.
Utilizing Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reactivities.
Benchmarking the new tool on RNAs with known reference structures.

Main Results:

Different strategies for integrating probing data with thermodynamics-based prediction algorithms can be implemented using soft constraints.
The ViennaRNA Package now supports SHAPE-directed RNA folding.
Comparison of three distinct strategies for SHAPE reactivity utilization in structure prediction.

Conclusions:

Chemical mapping experiments combined with soft constraints provide accurate RNA structure assessment.
The ViennaRNA Package 2.2 offers a powerful new tool for RNA structure prediction.
This approach advances the field of RNA structure biology and computational prediction.