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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: Jul 4, 2026

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
09:04

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

Published on: September 21, 2017

Structural alignment of pseudoknotted RNA.

Buhm Han1, Banu Dost, Vineet Bafna

  • 1Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|June 14, 2008
PubMed
Summary
This summary is machine-generated.

This study introduces an efficient algorithm (PAL) to discover novel non-coding RNAs (ncRNAs) with complex pseudoknotted structures by analyzing sequence and structure conservation. PAL accurately predicts RNA secondary structures and identifies homologous ncRNAs across genomes.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Non-coding RNAs (ncRNAs) play crucial regulatory roles.
  • Identifying novel ncRNAs, especially those with complex pseudoknotted structures, remains challenging.
  • Conserved primary sequence and secondary structure are key indicators for ncRNA identification.

Purpose of the Study:

  • To develop an efficient algorithm for discovering novel pseudoknotted non-coding RNAs (ncRNAs).
  • To leverage both sequence and structural conservation for enhanced ncRNA detection.
  • To enable accurate inference of secondary structures for newly identified ncRNAs.

Main Methods:

  • Developed an efficient algorithm for optimal structural alignment of RNA sequences against genomic substrings.
  • Implemented the algorithm as a tool named PAL (Pseudoknotted RNA Alignment).
  • Tested PAL's performance on known pseudoknots and conducted genome-wide searches.

Main Results:

  • The PAL algorithm demonstrates near-perfect accuracy in predicting pseudoknot secondary structures.
  • PAL effectively detects homologous ncRNAs with high sensitivity and specificity.
  • Novel homologous pseudoknotted ncRNAs were identified in viral and mouse genomes.

Conclusions:

  • The developed algorithm provides an efficient and accurate method for discovering novel pseudoknotted ncRNAs.
  • PAL facilitates the identification of homologous ncRNAs and the inference of their secondary structures.
  • This approach significantly advances the field of ncRNA discovery in genomic data.