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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. 

Abstract An ion detection device that combines a DNA-origami nanopore and a field-effect transistor (FET) was designed and modeled to determine sensitivity of the nanodevice to the local cellular environment. Such devices could be integrated into a live cell, creating an abiotic-biotic interface integrated with semiconductor electronics. A continuum model is used to describe the behavior of ions in an electrolyte solution. The drift-diffusion equations are employed to model the ion distribution, taking into account the electric fields and concentration gradients. This was matched to the results from electric double layer theory to verify applicability of the model to a bio-sensing environment. The FET device combined with the nanopore is shown to have high sensitivity to ion concentration and nanopore geometry, with the electrical double layer behavior governing the device characteristics. A logarithmic relationship was found between ion concentration and a single FET current, generating up to 200 nA of current difference with a small applied bias. 

Abstract The rational design of molecular electronics remains a grand challenge of materials science. DNA nanotechnology has offered unmatched control over molecular geometry, but direct electronic functionalization is a challenge. Here a generalized method is presented for tuning the local band structure of DNA using transmetalation in metal‐mediated base pairs (mmDNA). A method is developed for time‐resolved X‐ray diffraction using self‐assembling DNA crystals to establish the exchange of Ag⁺ and Hg²⁺ in T:T base pairs driven by pH exchange. Transmetalation is tracked over six reaction phases as crystal pH is changed from pH 8.0 to 11.0, and vice versa. A detailed computational analysis of the electronic configuration and transmission in the ensuing crystal structures is then performed. This findings reveal a high conductance contrast in the lowest unoccupied molecular orbitals (LUMO) as a result of metalation. The ability to exchange single transition metal ions as a result of environmental stimuli heralds a means of modulating the conductance of DNA‐based molecular electronics. In this way, both theoretical and experimental basis are established by which mmDNA can be leveraged to build rewritable memory devices and nanoelectronics. 

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.