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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...
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...
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...

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Related Experiment Video

Updated: Jun 19, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology.

Michela Taufer1, Ming-Ying Leung, Thamar Solorio

  • 1Department of Computer and Information Sciences, University of Delaware, Newark, DE 19716, United States.

Parallel Computing
|November 4, 2009
PubMed
Summary

This study introduces RNAVLab, a virtual laboratory for predicting RNA secondary structures, including complex pseudoknots. RNAVLab enables efficient analysis of RNA structures and viral genome replication mechanisms.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Ribonucleic acid (RNA) secondary structures are crucial for biological processes like gene expression.
  • Predicting RNA secondary structures, especially with pseudoknots, is computationally challenging for long sequences.
  • Existing thermodynamic methods struggle with complex RNA motifs and long nucleotide sequences.

Purpose of the Study:

  • To present RNAVLab, a virtual laboratory designed for studying RNA secondary structures, including pseudoknots.
  • To demonstrate the versatility and functionality of RNAVLab through case studies.
  • To enable scientists to overcome computational limitations in RNA structure prediction.

Main Methods:

  • Development of RNAVLab, a virtual laboratory environment.
  • Utilizing grid technology for extensive sampling and rapid predictions.
  • Application of RNAVLab to analyze RNA secondary structures and viral genome replication.

Main Results:

  • RNAVLab successfully rebuilds longer RNA secondary structures from sampled nucleotide segments.
  • Grid technology facilitates feasible, extensive sampling and predictions in a short time.
  • RNAVLab aids in studying viral RNA genome replication mechanisms in Nodaviridae.

Conclusions:

  • RNAVLab provides a versatile platform for studying complex RNA secondary structures, including pseudoknots.
  • The virtual laboratory enhances the feasibility and efficiency of RNA structure prediction and analysis.
  • RNAVLab is a valuable tool for investigating RNA functions and viral mechanisms.