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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-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
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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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Predicting and modeling RNA architecture.

Eric Westhof1, Benoît Masquida, Fabrice Jossinet

  • 1Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg, France. e.westhof@ibmc-cnrs.unistra.fr

Cold Spring Harbor Perspectives in Biology
|May 28, 2010
PubMed
Summary
This summary is machine-generated.

This study presents a new method for modeling large RNA structures by viewing them as assemblies of helical modules. This approach uses non-Watson-Crick base pairs and global constraints to accurately predict complex RNA architecture.

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biochemistry

Background:

  • RNA molecules fold into complex three-dimensional architectures essential for their function.
  • Predicting these structures from sequence remains a significant challenge due to extensive molecular neutrality.

Purpose of the Study:

  • To describe a general approach for modeling the architecture of large and structured RNA molecules.
  • To provide tools for sequence and structure analysis and interactive modeling of RNA.

Main Methods:

  • Modeling RNA architecture as the assembly of preformed double-stranded helices.
  • Utilizing Watson-Crick and non-Watson-Crick base pairs to define RNA modules.
  • Employing global constraints such as helix lengths and coaxiality for specificity.
  • Using the Assemble integrated suite of computer tools for analysis and modeling.

Main Results:

  • Demonstrated a method exploiting modularity and hierarchical folding for RNA architecture modeling.
  • Showcased the role of non-Watson-Crick pairs in guiding RNA formation.
  • Introduced metrics for assessing 3D model accuracy beyond RMSD.

Conclusions:

  • The described approach effectively models complex RNA architecture by integrating local and global structural features.
  • The Assemble tool facilitates accurate RNA modeling and analysis.
  • Non-Watson-Crick pairs play a crucial role in RNA structure specificity and model validation.