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• W2800457054 abstract "Deoxyribonucleic acid (DNA) is arguably the most studied and most important biological molecule. Recently, it has also been established as a potential candidate for nanoconstruction. Self-assembly of DNA molecules has emerged as a simple yet elegant technique to organize matter with sub-nanometer precision. The unique base-pairing properties which helps DNA to carry genetic information, also makes it a suitable building block for creating stable and robust nanostructures. Recent decades have witnessed a major revolution in the synthesis of different topological structures made of DNA molecules at nanoscale like, two dimensional arrays, nanotubes, polyhedra, smiley faces, three dimensional crystals etc. Due to their easier design, high fidelity and automated chemistry, DNA nanostructures have proposed applications in diverse fields of bio-nanotechnology and synthetic biology. The field of structural DNA nanotechnology is just entering in adulthood and offer paramount challenge towards the journey of DNA-based nanostructures from the laboratory to their practical implementation in the real world. The aim of my dissertation is to develop a de novo computational framework to investigate the nanoscale structure and properties of DNA-based nanostructures. This will help to understand the molecular origin of interaction governing the structure and stability of DNA nanostructures. In this thesis, we have studied the in-solution behavior of self-assembled DNA nanostructures. The state of art all atom molecular dynamics (MD) simulation has been extensively implemented to understand the various thermodynamic properties of these self-assembled soft matter systems. We expect that the results presented here will lead to better design of self-assembled DNA nanostructures to address the real world challenges. In particular, we have developed algorithms to build very accurate atomistic models of various DNA nanostructures like crossover DNA molecules, DNA nanotubes (DNTs) and DNA icosahedron (IDNA). Further, we discuss a computational framework to understand the in situ structure and dynamics of these DNA nanostructures using state-of-art MD simulation. We carried out several hundred nanosecond long MD simulations on these systems which sometimes contains close to one million atoms. Following the trajectories of nanostructures in physiological conditions, we predicted numerous properties like equilibrium solution structure behavior and elastic properties which are difficult to measure in experiments. DNTs are self-assembled tubular templates where the circular double helical domains, kept at the vertices of a polygon, are connected at crossovers junctions. Ned Seeman and co-workers at New York University have synthesized different kind of DNTs using tile-based self-assembly of oligonucleotides. To investigate their microscopic structure, stability and mechanical properties, we have come up with 3d atomistic models of various DNTs which will facilitate further studies of these nanotubes towards their proposed nanotechnological and…" @default.
• W2800457054 created "2018-05-17" @default.
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• W2800457054 date "2017-01-01" @default.
• W2800457054 modified "2023-09-28" @default.
• W2800457054 title "Understanding DNA-Based Nanostructures using Molecular Simulation" @default.
• W2800457054 hasPublicationYear "2017" @default.
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