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Related Concept Videos

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
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The DNA Helix01:16

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The DNA Helix01:07

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Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
The DNA Helix01:16

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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

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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.
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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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Updated: May 11, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Analyzing and building nucleic acid structures with 3DNA.

Andrew V Colasanti1, Xiang-Jun Lu, Wilma K Olson

  • 1Department of Chemistry & Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers - The State University of New Jersey. andrewco@rci.rutgers.edu

Journal of Visualized Experiments : Jove
|May 7, 2013
PubMed
Summary
This summary is machine-generated.

The 3DNA software package offers new features for analyzing and visualizing 3D nucleic acid structures and ensembles. This guide details installation and advanced protocols for bioinformatics research.

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Last Updated: May 11, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
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10:23

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Published on: May 8, 2015

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
11:25

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

Published on: January 25, 2020

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Chemistry

Background:

  • 3DNA is a widely used bioinformatics tool for analyzing, constructing, and visualizing 3D nucleic acid structures.
  • Recent advancements include features for handling ensembles of structures, crucial for NMR and molecular dynamics data.

Purpose of the Study:

  • To provide detailed protocols for new and popular features in the 3DNA software package, version 2.1.
  • To guide users through installation, structure analysis, model reconstruction, and ensemble manipulation.
  • To introduce the w3DNA web server and its capabilities, including building complex DNA-protein models.

Main Methods:

  • Detailed step-by-step protocols for software installation and usage.
  • Methods for analyzing nucleic acid structures, including base pairing and rigid-body parameter determination.
  • Protocols for reconstructing atomic models and manipulating structural ensembles.

Main Results:

  • Comprehensive protocols cover 3DNA installation, structure analysis, and model building.
  • New features for analyzing ensembles from NMR and MD simulations are presented.
  • The w3DNA web server offers user-friendly access to selected 3DNA functionalities.

Conclusions:

  • The 3DNA software package and w3DNA web server provide powerful tools for nucleic acid structure analysis and visualization.
  • Updated protocols facilitate the use of advanced features for individual structures and ensembles.
  • These resources support diverse bioinformatics and structural biology research applications.