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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...
Nucleic Acids02:43

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Nucleic acids02:43

Nucleic acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...

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Related Experiment Video

Updated: Jun 13, 2026

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

Alignments of RNA structures.

Guillaume Blin1, Alain Denise, Serge Dulucq

  • 1Institut Gaspard Monge, UMR 8049 CNRS, Université Paris-Est, 5 Bd Descartes-Champs sur Marne, 77454 Marne La Vallée Cedex 2, France. gblin@univ-mlv.fr

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|May 1, 2010
PubMed
Summary
This summary is machine-generated.

We introduce alignment hierarchy, a new framework for comparing RNA structures using common supersequences. This approach unifies existing models and enables novel RNA structure analysis and comparison.

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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

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Last Updated: Jun 13, 2026

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
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Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Published on: February 27, 2026

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • RNA structure comparison is crucial for understanding RNA function.
  • Existing methods based on trees or arc-annotated sequences have limitations.
  • A unified framework is needed to encompass diverse comparison models.

Purpose of the Study:

  • To develop a theoretical unifying framework for RNA structure comparison.
  • To introduce the concept of alignment hierarchy based on common supersequences.
  • To explore novel edit operations and analyze their computational complexity.

Main Methods:

  • Defining a common supersequence framework for arc-annotated sequences.
  • Analyzing the computational complexity of RNA structure comparison within this hierarchy.
  • Developing a polynomial-time algorithm for RNA structure alignment.
  • Proving NP-completeness for certain variations of the problem.

Main Results:

  • The alignment hierarchy framework unifies existing RNA structure comparison models.
  • A new polynomial-time algorithm for RNA structure comparison was developed.
  • Biologically relevant edit operations like nucleotide pairing/unpairing are incorporated.
  • The framework gives rise to novel, unstudied edit models.

Conclusions:

  • The alignment hierarchy provides a comprehensive theoretical foundation for RNA structure comparison.
  • The developed algorithm and software (gardenia) offer efficient tools for RNA analysis.
  • This work advances the field of computational RNA biology by offering a unified perspective.