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Computational Studies of DNA Hybridization and Self-Assembly of DNA-Based Nanowires via Molecular Dynamics Simulations


DNA nanotechnology has been a rapidly growing field with many applications in drug delivery, energy, and molecular computing. First, a novel coarse-grained model of DNA is developed for elucidating the effects of sequence and environmental factors on DNA hybridization. This coarse-grained model has been integrated into our recently developed simulation package called BioModi (Biomolecular Multiscale Models at UC Irvine), enabling the study of the molecular interactions of large systems consisting of amino acids, nucleic acids, and polymers over long time scales. Second, for a design of organic nanowires, a DNA base surrogate, perylene-3,4,9,10-tetracarboxylic diimide, is parameterized and simulated via all-atom simulations to understand kinetic mechanisms of stacking and structural arrangement at equilibrium for optimized transfer of electrical charge.

DNA hybridization processes in a crowded environment are investigated using Biomodi. This model has been shown to capture the mechanical and thermal melting properties of DNA as compared to experimental data. Moreover, the effect of sequence, temperature and DNA concentration is elucidated in detail on the self-assembly process of DNA, giving insight to choosing the right environmental conditions for the formation of double helices. Furthermore, DNA hybridization processes demonstrate many kinetic pathways that are dependent on the sequence.

The overlapping π system of stacked natural DNA bases can mediate the transfer of electrical charge over long distances. To enhance such electron transport property, novel nanowires can be designed by replacing the sugar group and natural DNA bases with perylene-3,4,9,10-tetracarboxylic diimides. Therefore, it is necessary to understand the stacking kinetics of such perylenediimide DNA base surrogates and their equilibrium structures. Simulations demonstrate the different kinetic pathways for stacking depending on the length of the nanowire even when the base is PEGylated. Equilibrium structures obtained are shown to be similar to expected structures found in experiments.

Implementation of our newly developed coarse-grained models, BioModi, and insight gained from our simulations will provide key parameters and understanding to advance computer-aided design and development of innovative smart biomaterials. Moreover, our parameterization, simulation and analysis methods developed for DNA base surrogates will enable the creation and design of organic nanowires with enhanced electron transport properties.

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