Programmed DNA 3D self-assembly

Xiang Li, Purdue University

Abstract

The field of DNA nanotechnology, which utilizes synthetic DNA strands as build-blocks for nanostructure construction, has developed rapidly in the past decades and has drawn great interest from many other areas. It provides people with unparalleled ability to assemble nano-scale structures with high programmability and precise control. Such versatile and well-defined DNA nanostructures are widely applied in nanofabrication, nano-device, molecular computation and diagnosis. My major researches focus on developing methods for assembly of 3D DNA nanostructures, including individual 3D nano-particles and 3D DNA lattices. I further explored the application of assembled structures to serve as scaffolds for guest molecule organization and structural characterization. In this thesis, we firstly developed a strategy for DNA self-assembly with T-linkage to replace commonly used sticky-end cohesion. To demonstrate the strategy, a range of DNA polyhedra with T-linkage were assembled and characterized. In addition, the above DNA polyhedra have potential for introducing well-structured guest molecules. We tested the idea by successful preparation of DNA polyhedra with thrombin aptamer and proved the thrombin binding activity. Besides 3D DNA nano-particles, we designed a DNA triangle motif associated with T-linkage based on previous work of tensegrity triangle crystal. By incorporating T-junction structure into the crystal, we can apply the DNA crystal as a scaffold to characterize unknown T-junction structure with X-ray diffraction. The result showed the detailed structure of T-junction. The proposed method can be applied as a general method for structural study of unknown biomarcomolecules. To demonstrate the programmability and application of rational designed DNA 3D crystals, we further modified the design and prepared various versions of triangle crystals. The length and orientation of out-pointing DNA hairpin spikes can be finely tuned by adjusting DNA length and position. Moreover, tails have been introduced to the triangle crystal design, which can further be modified with functional group to arrange guest molecules. Finally, we reported an assembly method, Vernier assembly, for the preparation of repetitive DNA duplexes with defined lengths. Two DNA strands with integer number copies of complimentary repeating unit will assemble into a controlled length duplex, which is the lowest common multiple length of two component strands. We proved the strategy by preparation of a 12-unit DNA strand from 3-unit and 4-unit component strands. Furthermore, a range of Vernier combinations were carried out to study the assembly efficiency.

Degree

Ph.D.

Advisors

Mao, Purdue University.

Subject Area

Chemistry

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