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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-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...
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

Protein Folding

Overview

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Related Experiment Video

Updated: May 22, 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

Predicting folding pathways between RNA conformational structures guided by RNA stacks.

Yuan Li1, Shaojie Zhang

  • 1Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, FL 32816-2362, USA.

BMC Bioinformatics
|April 28, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces RNAEAPath, an algorithm that predicts RNA folding pathways by focusing on RNA stack formation and destruction. This method effectively identifies low energy barrier pathways, outperforming existing algorithms.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

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Last Updated: May 22, 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:

  • Computational Biology
  • Biophysics
  • Molecular Biology

Background:

  • Predicting RNA folding pathways is crucial for understanding RNA function.
  • Current methods often get trapped in local optima due to the complex RNA energy landscape.
  • Existing algorithms rely on free energy of intermediate structures, limiting their effectiveness.

Purpose of the Study:

  • To develop a novel algorithm for predicting low energy barrier folding pathways in RNA.
  • To overcome limitations of existing energy-guided heuristic algorithms.
  • To improve the accuracy and efficiency of RNA folding pathway prediction.

Main Methods:

  • Proposed an algorithm, RNAEAPath, that guides folding pathway construction.
  • Utilized the formation and destruction of RNA stacks as a coarse-grained movement strategy.
  • Reduced the search space by focusing on stack dynamics.

Main Results:

  • RNAEAPath successfully identifies lower energy barrier folding pathways.
  • The algorithm demonstrates improved performance over existing heuristic methods in test cases.
  • Coarse-grained movements of RNA stacks facilitate jumping out of local optima.

Conclusions:

  • RNAEAPath offers a new approach for predicting low-barrier RNA folding pathways.
  • The method provides valuable insights into RNA conformational changes.
  • Source code and data are available for reproducibility and further research.