Scalable Force Fields for Metal-Mediated DNA Nanostructures

18 March 2025, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Force fields were developed for metal-mediated DNA (mmDNA) structures, using ab-initio methods to parameterize metal coordination. Two mmDNA were considered, comprising of a cytosine/thymine mismatch with coordinated Ag/Hg metal atoms. These basepairs were parameterized with the proposed computational framework and subjected to multiple validation steps. The generated force fields result in enhanced structural stability, with metallated basepairs rotating into the major groove. Our findings show a higher propeller angle associated with metalated base pair, which agrees with previously reported experimental data. Molecular dynamics (MD) simulations showed that the metallated basepairs stabilized the DNA structure, with the mismatch bases locking together via metal coordination. We anticipate the developed force fields can help in unveiling the structural dynamics of long metallo-DNA nanowires.

Keywords

Density functional theory
Molecular Dynamics
Force Fields
DNA nanotechnology

Supplementary materials

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Description
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Suplementary Figures and Data
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Section I - Energy sampling data comparing parmBSC1 with the generated force field Section II - Force field parameters for the metallated cases Section III - Setup descriptions for the triple C-Ag2-T cases and corresponding orbital energy plots Section IV - Modifications applied to the MCPB.py software package to incorporate metals into DNA Section V - A descriptions of the metrics used for analysis of the MD trajectories Section VI - Addition RMSD data for the five cases
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Starting structures for the five seven basepair cases
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Coordinates are given in PDB format for the seven basepair cases: - Complementary case (Complementary.pdb) - Single CT mismatch case (SingleCT.pdb) - Single C-Ag2-T basepair case (SingleCAg2T.pdb) - Single C-Hg-T basepair case (SingleCHgT.pdb) - Triple C-Ag2-T basepair chain case (TripleCAg2T.pdb)
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Supplementary weblinks

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