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DNA as a Genetic Template

DNA as a Genetic Template

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...

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...

Noncovalent Attractions in Biomolecules

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Nucleosome Remodeling

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...

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,...

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Related Experiment Video

Updated: Mar 29, 2026

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Published on: October 25, 2017

Elastic Network Models of Nucleic Acids Flexibility.

Piotr Setny¹, Martin Zacharias²

¹Centre for New Technologies, University of Warsaw , 00-927 Warsaw, Poland.

Journal of Chemical Theory and Computation

|November 24, 2015

Summary

Elastic network models (ENMs) effectively capture RNA and DNA flexibility by optimizing coarse-grained parameters and introducing novel methods for force constant determination. This study validates ENMs for nucleic acid dynamics.

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Area of Science:

Biophysics
Computational Biology
Structural Biology

Background:

Elastic Network Models (ENMs) are widely used for protein dynamics.
Their application to nucleic acids (RNA and DNA) is less understood due to distinct structural properties.

Purpose of the Study:

To evaluate and optimize ENMs for capturing RNA and DNA flexibility.
To introduce novel ENM variants based on atomic-level distance distributions.
To determine optimal model parameters for accurate nucleic acid dynamics.

Main Methods:

Systematic evaluation of popular ENMs for RNA and DNA.
Development of coarse-grained models using atomic resolution distance distributions.
Optimization of spring connection lengths and force constant scaling.
Novel method for absolute force constant determination using Hessian matrix overlap.

Main Results:

Identified optimal ENM parameters for RNA and DNA flexibility.
Demonstrated improved agreement between ENM vibrational frequencies and atomic force field normal modes.
Validated novel ENM approaches for nucleic acid dynamics.

Conclusions:

ENMs can be effectively optimized to accurately model nucleic acid flexibility.
The introduced methods provide a robust framework for applying ENMs to RNA and DNA.
This work enhances the utility of ENMs in studying nucleic acid structural dynamics.