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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 29, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Finding stable local optimal RNA secondary structures.

Yuan Li1, Shaojie Zhang

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

Bioinformatics (Oxford, England)
|September 10, 2011
PubMed
Summary
This summary is machine-generated.

Predicting RNA structures is challenging due to vast conformational spaces. This study introduces a novel method using local optimal stack configurations to efficiently identify stable RNA secondary structures, outperforming existing approaches in riboswitch prediction.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA molecules, like riboswitches, can adopt multiple stable conformations, enabling diverse biological functions.
  • Predicting these functional RNA secondary structures is complex due to the immense conformational space and the stability of native states.
  • RNA structure stability is largely determined by energetically favorable helical regions (stacks).

Purpose of the Study:

  • To develop an efficient algorithm for predicting functional RNA secondary structures.
  • To reduce the computational complexity of RNA structure prediction by focusing on a subset of configurations.
  • To identify stable RNA structures and estimate energy barriers between conformations.

Main Methods:

  • Representing RNA secondary structures using configurations of putative stacks.
  • Developing an algorithm to enumerate all possible local optimal stack configurations.
  • Implementing a heuristic algorithm to approximate energy barriers and identify stable structures.

Main Results:

  • The method successfully predicted native 'on' and 'off' secondary structures for RNA riboswitches.
  • Benchmark tests demonstrated superior performance in ranking alternate structures compared to state-of-the-art methods.
  • The approach effectively navigates the reduced conformational space of local optimal stack configurations.

Conclusions:

  • The proposed stack-based representation and algorithms offer an efficient and accurate approach to RNA secondary structure prediction.
  • This method aids in understanding the complex folding pathways and identifying biologically relevant RNA conformations.
  • The developed software is available for broader research applications.