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Related Concept Videos

RNA Structure01:23

RNA Structure

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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
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RNA Structure01:19

RNA Structure

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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.
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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.
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RNA Stability01:53

RNA Stability

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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...
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DNA Topoisomerases

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Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
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Eukaryotic RNA Polymerases00:58

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures.

Takumi Otagaki1, Goro Terai1, Kiyoshi Asai1

  • 1Department of Computational Biology and Medical Sciences (CBMS), The University of Tokyo, Kashiwa, Chiba, Japan.

Plos Computational Biology
|November 20, 2025
PubMed
Summary
This summary is machine-generated.

PseudoknotVisualizer software identifies and colors RNA pseudoknots in 3D structures. This tool aids researchers in visualizing complex RNA architectures, improving structural analysis and molecular biology applications.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • RNA pseudoknots are crucial structural motifs impacting RNA function.
  • Visualizing pseudoknots in complex 3D RNA structures presents significant challenges.
  • Existing methods for pseudoknot identification and visualization are often limited.

Purpose of the Study:

  • To introduce PseudoknotVisualizer, a novel software for identifying and visualizing RNA pseudoknots.
  • To enable clear depiction of pseudoknot distribution within RNA tertiary structures.
  • To enhance RNA structural analysis and research productivity.

Main Methods:

  • Development of specialized software, PseudoknotVisualizer.
  • Decomposition of RNA secondary structures into pseudoknot-free layers.
  • Color-coding of base pairs within each pseudoknot layer for visualization.
  • Integration as a PyMOL extension and provision of a Command Line Interface (CLI).

Main Results:

  • Successful identification and visualization of pseudoknots in RNA 3D structures.
  • Facilitation of pseudoknot layer visualization through color-coding.
  • Generation of visualization commands for Chimera and PyMOL.

Conclusions:

  • PseudoknotVisualizer effectively addresses challenges in RNA pseudoknot visualization.
  • The tool enhances clarity in RNA structural analysis.
  • PseudoknotVisualizer has potential for broad applications in molecular biology research.