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.
Supplementary materials
Title
Suplementary Figures and Data
Description
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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Title
Starting structures for the five seven basepair cases
Description
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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GitHub Repository
Description
This repository, forked from the original Python Metal Site Modeling Toolbox (pyMSMT), contains all of the updated files with the metal-modified DNA implementation as well as an installation guide for users.
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