Strategies of Programmed Self-assembly of Complex DNA Nanostructures

Abstract

DNA with its special base pairing capability has been proved to be one of the best material for programmed self-assembly into various customized nanostructures. Since the concept been established, a great variety of DNA nanostructures with well-defined shape and size has been fabricated with different approaches. Motif-based DNA self-assembly is one of the classic strategy for fabricating DNA nanostructures. However, previous study of DNA motifs focused heavily on utilizing the intrinsic symmetry to simplify the system and build highly ordered structures. So in my research, I explored what can be done with asymmetric DNA motif design and pushed the limit of the method in complexity.

In this thesis, we designed 3 types of asymmetrical 3-arm DNA motifs. Based on 4 rules we established for DNA motif design and assemble condition, we analyzed the possible assemble pathway for each of the motifs and proposed potential assemble conditions for the complex structures we were interested in. By screening from these potential conditions, we managed to build a new 2D array and 3 new complex polyhedron cages which verified our rules for DNA motif design. These new structures showed much higher complexity than any other structures built with DNA motif-based assembly. And the rules we established are expected to guild the future design of DNA nanostructures.

DNA can be easily conjugated to other nanomaterial via chemical modification thus it’s also a great tool to programmable assemble various other material. Gold nanoparticle is one of the popular material that has been studied a lot and compatible with DNA coating. In this thesis, we explored the assembly of gold nanoparticle via specific DNA binding. A linear gold nanoparticle chain was fabricated via very long single strand DNA interaction. Also an alternating pattern was built with 2 different sized gold nanoparticle with complementary DNA linkers. Additionally, we attempted to align gold nanoparticles on a 2-unit double crossover DNA 2D array, in order to establish parallel gold nanowires with nanometer scale resolution. This study has provided some new strategy and important new data in the DNA based gold nanoparticle assembly research.