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Related Concept Videos

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 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...
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: May 12, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search.

Sebastian Will1,2, Michael F Siebauer3, Steffen Heyne2

  • 1Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16 -18, Leipzig D-04107, Germany.

Algorithms for Molecular Biology : AMB
|April 23, 2013
PubMed
Summary

This study explores using RNA secondary structure for homology searches, finding it feasible but limited by sequence information and structure prediction accuracy. Thermodynamic stability aids searches with minimal sequence data.

More Related Videos

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Related Experiment Videos

Last Updated: May 12, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Homology searches are crucial for genome annotation, especially for divergent homologs lacking sequence similarity.
  • Identifying novel RNA families (e.g., snoRNAs, microRNAs) is challenging due to sequence divergence.
  • Existing tools like Infernal combine sequence and structure, but sequence information often dominates.

Purpose of the Study:

  • To investigate if RNA secondary structure alone is sufficient for homology searches.
  • To determine the utility of thermodynamic propensity in detecting RNA structural homologs.
  • To assess the effectiveness of structure-based methods for discovering novel RNA members.

Main Methods:

  • Developed LocARNAscan, a tool for sequence-structure alignment using base pairing probability matrices.
  • Employed a semi-global scanning variant of LocARNA's algorithm for efficient searching.
  • Incorporated optional sequence information and pre-processed target sequences for local base pairing probabilities.

Main Results:

  • Purely structure-based homology search is demonstrated as feasible.
  • Thermodynamic stability is beneficial in homology searches with very limited sequence information.
  • Search sensitivity is constrained by the accuracy of predicted target RNA secondary structures.

Conclusions:

  • Structure-based homology search is viable but may not surpass sequence-heavy tools like Infernal in typical scenarios.
  • LocARNAscan's performance can be enhanced by high-throughput RNA secondary structure determination methods.
  • Accurate structure annotations from such methods are vital for transcriptome-wide applications.