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Abstract DNA double helices containing metal‐mediated DNA (mmDNA) base pairs are constructed from Ag+and Hg2+ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self‐assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X‐ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3‐dominant, centrosymmetric pairs and major groove binders driven by 5‐position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.
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This content will become publicly available on March 18, 2026
Scalable Force Fields for Metal-Mediated DNA Nanostructures
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.
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- Award ID(s):
- 2317843
- PAR ID:
- 10627383
- Publisher / Repository:
- chemrxiv
- Date Published:
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.more » « less
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