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Nucleic Acids

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,...

Nucleic acids

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,...

Nucleic Acids

Nucleic Acids

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.
DNA Structure
DNA...

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).
Deoxyribonucleic Acid (DNA)
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 the organelles such as chloroplasts and mitochondria....

Biosynthesis of Nucleic Acids

Biosynthesis of Nucleic Acids

Nucleic acid biosynthesis is a fundamental biochemical process that produces the purine and pyrimidine nucleotides essential for DNA and RNA synthesis. This pathway maintains a balanced nucleotide pool, preventing imbalances that could jeopardize genetic integrity and cellular function. Given the crucial role of nucleotides, their synthesis is tightly regulated to ensure proper cellular homeostasis.Purine BiosynthesisThe biosynthesis of purine nucleotides begins with ribose-5-phosphate, a...

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Related Experiment Video

Updated: Feb 14, 2026

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes

Kinetic Screening of Nuclease Activity using Nucleic Acid Probes

Published on: November 1, 2019

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.

Changsheng Zhang¹, Chao Lu², Zhifeng Jing¹

¹Department of Biomedical Engineering , University of Texas at Austin , Austin , Texas 78712 , United States.

Journal of Chemical Theory and Computation

|February 14, 2018

Summary

The AMOEBA force field accurately models nucleic acids using quantum mechanics and extensive simulations. It captures DNA and RNA structures, dynamics, and conformational changes, validating its use in molecular modeling.

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Last Updated: Feb 14, 2026

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Area of Science:

Computational Chemistry
Structural Biology
Biophysics

Background:

Accurate molecular modeling of nucleic acids is crucial for understanding biological processes.
Existing force fields often struggle to capture the complex behavior of DNA and RNA.

Purpose of the Study:

To present and validate the AMOEBA polarizable atomic multipole force field for nucleic acids.
To refine the force field using extensive molecular dynamics simulations.

Main Methods:

Determined valence and electrostatic parameters from high-level quantum mechanical calculations on nucleotide model compounds.
Incorporated previously derived parameters for phosphate groups and nucleobases.
Performed over 35 μs of condensed-phase molecular dynamics simulations of DNA and RNA in solution and crystal lattices.

Main Results:

Simulated structures of DNA and RNA duplexes and hairpins showed good agreement with NMR data (RMSD < 2.0 Å).
Key structural features like base pairing, sugar puckering, and backbone angles were accurately reproduced.
Observed DNA A-to-B form interconversion and accurately simulated crystal packing interactions.

Conclusions:

The AMOEBA force field provides a robust and accurate representation of nucleic acid structure and dynamics.
It is suitable for simulating various nucleic acid forms, conformational transitions, and interactions in condensed phases.
The validated force field advances the capabilities of molecular dynamics simulations in nucleic acid research.