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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 Structure01:23

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-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...
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: May 24, 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

Identifying complete RNA structural ensembles including pseudoknots.

Aditi Gupta1, Reazur Rahman, Kejie Li

  • 1Department of Biological Sciences; Purdue University; West Lafayette, IN, USA.

RNA Biology
|March 16, 2012
PubMed
Summary
This summary is machine-generated.

Predicting RNA structures, especially complex pseudoknots, is challenging. Suboptimal structure prediction offers a more comprehensive approach than minimum free energy methods for identifying RNA structural elements.

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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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Last Updated: May 24, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Published on: December 9, 2022

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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Accurate RNA structure prediction is crucial due to the direct link between RNA structure and function.
  • Pseudoknots are significant RNA structural motifs involved in various biological functions.
  • Existing pseudoknot prediction methods struggle with computational complexity and accuracy for longer RNA sequences.

Purpose of the Study:

  • To evaluate the performance of pseudoknot prediction methods on diverse, full-length RNA sequences.
  • To compare pseudoknot prediction methods against minimum free energy (MFE) and suboptimal secondary structure predictions.
  • To develop an improved strategy for identifying RNA structural elements within the suboptimal folding space.

Main Methods:

  • Surveyed pseudoknot prediction method performance on a dataset of full-length RNA sequences (RNase P RNA, Group I Intron, tmRNA, tRNA).
  • Compared pseudoknot prediction with MFE and suboptimal secondary structure prediction methods based on base-pair, stem, and pseudoknot accuracy.
  • Developed a heuristic strategy to identify a non-redundant set of stems from the suboptimal structure space by merging similar stems.

Main Results:

  • The ensemble of suboptimal structure predictions identified correct RNA structural elements often missed by MFE and specialized pseudoknot predictions.
  • The proposed strategy for identifying non-redundant stems in the suboptimal structure space outperformed specialized approaches.
  • Suboptimal folding space provides a more comprehensive representation of RNA structural diversity compared to optimal structure prediction alone.

Conclusions:

  • Suboptimal structure prediction is superior to MFE and specialized pseudoknot prediction for identifying diverse RNA structural elements.
  • A novel strategy leveraging suboptimal structures effectively identifies a comprehensive set of non-redundant stems.
  • The suboptimal folding space offers a robust framework for understanding the full structural diversity of RNA molecules.