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Related Concept Videos

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...
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...
RNA Stability01:53

RNA Stability

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...
RNA Stability01:53

RNA Stability

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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Related Experiment Video

Updated: Jun 4, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

All-atom knowledge-based potential for RNA structure prediction and assessment.

Emidio Capriotti1, Tomas Norambuena, Marc A Marti-Renom

  • 1Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Principe Felipe, 46012 Valencia, Spain.

Bioinformatics (Oxford, England)
|February 26, 2011
PubMed
Summary
This summary is machine-generated.

A new computational tool, Ribonucleic Acids Statistical Potential (RASP), accurately assesses RNA 3D structures. RASP effectively ranks near-native models and distinguishes between destabilizing and compensatory mutations, aiding RNA structure prediction.

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Last Updated: Jun 4, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • The role of RNA has expanded beyond information transfer, highlighting the importance of understanding RNA sequence/structure/function relationships.
  • The increasing number of solved RNA structures and emerging prediction tools necessitates accurate methods for evaluating RNA structure models.

Purpose of the Study:

  • To introduce a novel all-atom knowledge-based potential for assessing the accuracy of three-dimensional (3D) RNA structures.
  • To provide a computational tool that aids in the evaluation and refinement of RNA structure predictions.

Main Methods:

  • Development of an all-atom knowledge-based potential named Ribonucleic Acids Statistical Potential (RASP).
  • Benchmarking RASP using decoy datasets of near-native RNA structures and a dataset of RNA motifs with non-canonical base pairs.
  • Evaluation of RASP's ability to discriminate between structure-destabilizing and compensatory mutations using specific RNA examples.

Main Results:

  • RASP successfully ranked the closest model to the X-ray structure as the best in ~93-95% of decoys across benchmark sets.
  • High correlation coefficients (0.85 and 0.89) were observed between RASP scores and established accuracy measures (RMSD, GDT-TS).
  • RASP outperformed the ROSETTA FARFAR force field in selecting accurate models on a diverse benchmark dataset and differentiated between mutation types.

Conclusions:

  • RASP is an effective tool for assessing RNA 3D structure accuracy.
  • The developed potential can be applied to both all-atom and coarse-grained RNA structures.
  • RASP is freely available and beneficial for both developers and users of RNA structure prediction methods.