Exploring DNA-Carbon Nanotube Interfacial Interactions and Transport

In the rapidly changing world of combined scientific studies, two standout materials are drawing attention: DNA and carbon nanotubes (CNTs). DNA, known for its central role in carrying genetic information, is a wonder of nature's design. On the other hand, CNTs, recognized for their strength and electrical properties, represent the best of modern material advancements.<br/>Studying the interaction between DNA and carbon nanotubes (CNTs) presents a series of tangible challenges. One of the main obstacles is that the inherent differences in their chemical properties make direct interactions between them non-trivial. In addressing the challenges of understanding the intricate interactions between DNA and CNTs, our approach leverages the power of Molecular Dynamics (MD) simulations. MD simulations offer a dynamic and detailed perspective, allowing us to scrutinize the behavior of our DNA-CNT system. To initiate our study, we began by modeling the direct interaction between DNA and CNTs without forming any covalent bonds. This step was pivotal, setting the groundwork before introducing the linker and further constructing the comprehensive DNA-Linker-CNT system. The introduction of a linker in the system, studied under MD, can provide insights into creating stable bonds that bridge DNA and CNTs, ensuring their effective interaction without compromising their individual properties.<br/>In our comprehensive study on the DNA-Linker-CNT system, we utilize a systematic methodology to elucidate the behavior and stability of the structure complex. Each component of the system was carefully constructed: the DNA, in its B-form comprises a 12-basepair double-stranded sequence denoted as (3G3C3G3C). The linker, a 10-atom amino linker, served as the bridge in our system. The CNT has a chirality of (6,6) and is 10 primitive cells long. Crucially, to ensure accurate simulations, we employed specific force fields: the Amber force field bsc1 for DNA, and GAFF (General Amber Force Field) for the linker and CNT. By having the individual components, our next step was to bring them together into a cohesive environment. This involved forming bonds between the DNA, linker, and CNT, followed by the application of force fields – with specific force fields parameters calculated for the linker and CNT. To simulate a realistic biological environment, we introduced a water solvent using the TIP3P model, encapsulating our system in an octahedral geometry with a 15-angstrom buffer. Then we ionized the structure to ensure it was ready for the Molecular Dynamics (MD) simulations.<br/>The MD simulations were significant in revealing the dynamics of our system. Across multiple runs, a consistent observation was the pronounced attraction between the DNA and CNT, with the DNA segment nearing the CNT's surface, adopting a stable configuration involving the interaction between pi-orbitals on the DNA and CNT. This proximity between the pi-orbitals of the two subsystems, sustained over a significant portion of the simulation, is indicative of potential electron transport opportunities, a phenomenon further corroborated by RMSD analyses which underscored the stability of each component. Our observations so far paints a promising picture for the DNA-Linker-CNT system, hinting at potential channels for electron transport. Complementing our MD studies, we are performing transport calculations which will be presented to further enhance our understanding. These calculations shed light on the electron transfer between the DNA and nanotube subsystems under a variety of CNT-Linker-DNA-Linker-CNT configurations. Together, MD simulations and transport calculations provide a comprehensive and promising approach to unravel the complexities of the DNA-Linker-CNT interactions, paving the way for a deeper understanding of these systems. [We acknowledge NSF FMRG 2328217 and NSF SemiSynBio 2027165 grants.]