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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...
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 18, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Predicting RNA structure by multiple template homology modeling.

Samuel C Flores1, Yaqi Wan, Rick Russell

  • 1Bioengineering Department, Stanford University, Clark Center S231, 318 Campus Drive, Stanford, California 94305-5444, USA.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|November 13, 2009
PubMed
Summary
This summary is machine-generated.

Predicting RNA 3D structure is crucial for understanding cellular functions. RNABuilder software models RNA structures using homology, accurately predicting the Azoarcus group I intron's topology and connections.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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10:34

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The ITS2 Database
16:17

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Published on: March 12, 2012

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Determining RNA 3D structure is vital for understanding cellular functions, but experimental methods like crystallography and NMR are often inaccessible.
  • RNA structure is modular, allowing local 3D structure prediction from existing solved structures of related or unrelated RNAs.

Purpose of the Study:

  • To predict the 3D structure of the Azoarcus group I intron using the RNABuilder software.
  • To evaluate the accuracy of RNABuilder's homology modeling approach for RNA structure prediction.

Main Methods:

  • Utilized RNABuilder software for RNA structure modeling.
  • Employed homology modeling against fragments of Twort and Tetrahymena group I introns.
  • Incorporated base pairing forces to refine the model.

Main Results:

  • The RNABuilder model accurately predicted the global topology, secondary, and tertiary connections of the Azoarcus group I intron.
  • Achieved an overall RMSD of 4.6 Å compared to the crystal structure, with higher accuracy in the intron core (3.5 Å).

Conclusions:

  • RNABuilder provides a reliable method for predicting RNA 3D structures, particularly for group I introns.
  • This approach is applicable to larger and more diverse RNA molecules and RNA-protein complexes.