Engineering DNA-Based Self-Assembly Systems to Produce Nanostructures and Chemical Patterns
Embargo until
2019-05-01
Date
2017-01-03
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Publisher
Johns Hopkins University
Abstract
While commonly known as a material that stores biological information essential for life, few realize that deoxyribonucleic acid (DNA) is also a wonderful building (i.e., physical structures) and computing material. The field of DNA nanotechnology aims to use DNA primarily to build and control matter on the nanoscale. In 2006, a technique known as DNA origami was developed, which allows for the formation of about any shape on the nanoscale. Such DNA origami have been used in many applications: nanodevices, nanotubes, nanoreactors. However, the small surface area of the origami often limits its usefulness. One promising method for building large (micron-sized) DNA origami structures is to self-assemble multiple origami components into well-defined structures. To date, however, such structures suffer low yields, long reaction times and require experimental optimization with no guiding principles. One primary reason is that a governing theory and experimental measurements behind such a self-assembly process are lacking.
In this work, we develop coarse-grained computational simulations to describe and understand the self-assembly of finite-sized, multicomponent complexes (e.g., nine different DNA-origami components that form a square grid complex). To help inform the model, we experimentally investigate how various interface architectures between two self-assembling DNA origami components affect the reaction kinetics and thermodynamics. We further develop the accuracy of our simulations by incorporating these measurements and other thermodynamic measurements from our group and implement a computational algorithm that optimizes the interaction strengths between self-assembling components for reaction efficiency (i.e., speed and yield of the complex). With these experimentally-informed simulations, we suggest design improvements and provide yield predictions to an experimentally demonstrated tetrameric complex.
Finally, with the overarching idea of using DNA-based components to self-assemble to produce ordered structures and patterns, we build a reaction-diffusion system whose reactions are programmed using DNA strand displacement and diffusion which occurs in a hydrogel, wherein patterns develop, and liquid reservoirs, which are used to supply the high energy components. With this reaction-diffusion system we create stable (i.e., unchanging in space and time) one and two-dimensional patterns of DNA molecules with millimeter-scale features.
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Keywords
Self-Assembly, Chemical Patterns, Reaction-Diffusion, DNA Nanotechnology,