(706e) Sequence Effect on Self-Assembled DNA Nanostructures Via Molecular Dynamics Simulations

Authors: 
Markegard, C. B. - Presenter, University of California, Irvine
Nguyen, H. D., University of California, Irvine
Fu, I. W., University of California, Irvine

DNA nanotechnology is a rapidly growing field where a large variety of increasingly complex structures can be fabricated through self-assembly from single-strands of DNA. These structures have potential applications in nanoscience and nanotechnology to create analytical biosensors, to assemble biofuel cells and biomolecule-based devices, and to develop biocomputing systems for information processing. Currently, the thermodynamics and kinetics associated with DNA self-assembly are not fully understood. Through the use of a newly developed coarse-grained nucleic acid model, we aim to elucidate the fundamental principles that govern the self-assembly of DNA nanostructures. In particular, we examine the effect of sequence on the kinetic mechanisms of self-assembly of many single-stranded DNA into complex nanostructures. Our model has been shown to capture the persistence length of double-stranded and single stranded DNA in addition to thermal melting properties of double-stranded DNA as compared to experimental data.  Moreover, our results indicate that initial contacts between strands of DNA splits the kinetic pathways to either a zipping-like mechanism or a slithering-like mechanism. This kinetic partitioning, which is strongly dependent on the sequence, greatly affects the kinetic pathway and thus determines the yield of desired nanostructures. Finally, we have investigated structural stability of a 4x4 Holliday junction inspired structure using an all-atom model and assembly kinetics of forming lattice sheets using our coarse-grained model. The findings from our simulations will guide experimentalist in the mechanisms of DNA nanostructure formation and enable them to develop more novel biomaterials.