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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...
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...
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jun 10, 2026

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

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

K-partite RNA secondary structures.

Minghui Jiang1, Pedro J Tejada, Ramoni O Lasisi

  • 1Department of Computer Science, Utah State University, Logan, Utah 84322-4205, USA. mjiang@cc.usu.edu

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|July 17, 2010
PubMed
Summary
This summary is machine-generated.

We introduce k-partite secondary structures, a classification for RNA with pseudoknots. Our methods efficiently predict these structures, outperforming existing tools in RNA secondary structure prediction.

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Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA
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Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA
08:17

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA

Published on: July 9, 2021

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • RNA structure analysis

Background:

  • RNA secondary structure prediction is crucial but complicated by pseudoknots.
  • Pseudoknots are formed by crossing base pairs, challenging standard prediction algorithms.
  • Existing methods struggle with the complexity introduced by pseudoknots in RNA.

Purpose of the Study:

  • To introduce and classify RNA secondary structures with pseudoknots using k-partite structures.
  • To analyze the computational complexity of recognizing k-partite RNA structures.
  • To develop and evaluate heuristics for predicting RNA secondary structures with pseudoknots.

Main Methods:

  • Defined k-partite secondary structures as unions of k pseudoknot-free substructures.
  • Characterized computational complexities by relating them to k-colorability on circle graphs.
  • Developed iterated peeling and first-fit packing heuristics for structure prediction.

Main Results:

  • Showed that any RNA secondary structure can be approximated by a k-partite structure with minimal free energy change.
  • Iterated peeling heuristic provides a constant approximation ratio for maximizing base pair stackings.
  • First-fit packing heuristic outperforms HotKnots in predicting pseudoknotted RNA secondary structures on PseudoBase data.

Conclusions:

  • K-partite structures offer a viable classification for understanding and predicting complex RNA secondary structures.
  • The developed heuristics provide efficient and effective methods for RNA secondary structure prediction, especially those with pseudoknots.
  • This work advances the field of structural bioinformatics by addressing the challenge of pseudoknots in RNA.