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Updated: Feb 4, 2026

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures

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Published on: January 19, 2019

Scalable Force Fields for Metal-Mediated DNA Nanostructures.

William Livernois¹, Olaiyan Alolaiyan^1,2, Arpan De¹

¹Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195, United States.

Journal of Chemical Theory and Computation

|February 2, 2026

Summary

This summary is machine-generated.

New computational force fields enhance the stability of metal-mediated DNA (mmDNA). These force fields accurately predict structural changes in mmDNA, aiding future research on DNA nanostructures.

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DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications

DNA Origami-Mediated Substrate Nanopatterning of Inorganic Structures for Sensing Applications

Published on: September 27, 2019

Area of Science:

Computational Chemistry
Biophysics
Molecular Modeling

Background:

Metal-mediated DNA (mmDNA) structures present unique challenges for computational modeling.
Accurate force fields are crucial for understanding the structural dynamics of mmDNA.

Purpose of the Study:

To develop and validate novel computational force fields for mmDNA structures.
To parametrize metal coordination using ab initio methods for cytosine/thymine mismatches with Ag and Hg.

Main Methods:

Ab initio calculations were used to parametrize metal coordination in mmDNA.
Developed force fields were validated through rigorous testing.
The computational framework was applied to model short mmDNA chains.

Main Results:

The developed force fields demonstrated enhanced structural stability in metalated base pairs.
Coordinated metals were observed to rotate into the major groove.
A higher propeller angle was found in metalated base pairs, consistent with experimental data.

Conclusions:

The new force fields provide a reliable tool for studying mmDNA.
These findings pave the way for investigating the structural dynamics of larger mmDNA systems, such as DNA nanowires.