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Related Concept Videos

Nucleic Acid Structure01:25

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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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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.
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Updated: Oct 7, 2025

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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ONQUADRO: a database of experimentally determined quadruplex structures.

Tomasz Zok1, Natalia Kraszewska1, Joanna Miskiewicz1

  • 1Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland.

Nucleic Acids Research
|January 6, 2022
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Summary
This summary is machine-generated.

ONQUADRO is a comprehensive database for studying DNA quadruplex structures. It offers detailed information, analysis tools, and visualization for canonical and non-canonical quadruplexes, aiding structural biology research.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • Quadruplexes, including canonical and non-canonical forms, are crucial nucleic acid structures with significant biological roles.
  • Understanding the intricate 3D structures of quadruplexes is essential for deciphering their functions.

Purpose of the Study:

  • To introduce ONQUADRO, an advanced database system designed for the comprehensive study of quadruplex structures.
  • To provide researchers with a centralized, up-to-date resource for accessing and analyzing quadruplex data.

Main Methods:

  • Development of a relational database integrating information on tetrads, quadruplexes, and G4-helices.
  • Implementation of programs for structure parameter computation, data visualization, and statistical analysis.
  • Automated data retrieval from the Protein Data Bank, followed by processing, annotation, and completion.

Main Results:

  • As of August 2021, ONQUADRO contains data for 1,661 tetrads, 518 quadruplexes, and 30 G4-helices from 467 experimentally determined nucleic acid structures.
  • The database offers detailed descriptions including sequence, secondary and tertiary structure representations, planarity, twist, rise, chi angles, loop characteristics, and classification.
  • Includes metadata such as origin structure ID, experimental method, and molecule type.

Conclusions:

  • ONQUADRO serves as a valuable, self-updating resource for researchers studying quadruplex structures.
  • The database facilitates detailed analysis and visualization of quadruplexes, accessible via a user-friendly web interface on various devices.