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Nucleic Acid Structure

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.
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DNA...

Molecular Models

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Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Nucleic acids

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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.
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,...

Nucleic Acids and Nucleotides

Nucleic Acids and Nucleotides

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and have instructions for its functioning. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
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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.
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...

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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...

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Updated: Jun 24, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

FRET-guided modeling of nucleic acids.

Fabio D Steffen¹, Richard A Cunha¹, Roland K O Sigel¹

¹Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

Nucleic Acids Research

|June 13, 2024

Summary

This summary is machine-generated.

This study integrates single-molecule Förster resonance energy transfer (FRET) with computational modeling to map RNA structural dynamics. The approach refines RNA structure prediction by filtering models against experimental FRET data, enhancing mechanistic understanding.

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3D Printing of Biomolecular Models for Research and Pedagogy

3D Printing of Biomolecular Models for Research and Pedagogy

Published on: March 13, 2017

Area of Science:

Biophysics
Computational Biology
Structural Biology

Background:

RNA functional diversity arises from conformational heterogeneity.
Mapping structural transitions in nucleic acid ensembles is crucial for understanding function.
Single-molecule spectroscopy and computational modeling offer complementary approaches.

Purpose of the Study:

To develop a framework harmonizing single-molecule Förster resonance energy transfer (FRET) measurements with computational modeling.
To utilize FRET data for filtering de novo RNA structure prediction ensembles.
To improve the mechanistic understanding of nucleic acid structural dynamics and interactions.

Main Methods:

Integration of single-molecule FRET experiments with molecular dynamics simulations and de novo structure prediction (Rosetta).
In silico recreation of FRET experiments using all-atom or implicit fluorophore modeling.
Application of accessible-contact volumes as a post hoc scoring method for structure prediction.

Main Results:

Demonstrated FRET's utility in filtering RNA structure prediction ensembles by refuting incompatible models.
Successfully benchmarked the FRET-assisted modeling approach on DNA and validated it on a dynamic riboswitch.
Recapitulated the global fold of a riboswitch using a FRET coordinate for four-way junction assembly.

Conclusions:

Computational fluorescence spectroscopy enhances the interpretability of dynamic structural ensembles.
The developed pipeline improves mechanistic understanding of nucleic acid interactions.
This integrated approach provides a powerful tool for studying RNA structure and dynamics.