Rationally Designed DNA Crystals and the Applications

Jiemin Zhao, Purdue University

Abstract

The ability to self-assemble into pre-programmed architectures has made DNA become a useful molecule to build 2D and 3D nanostructures. In the last decade, the development of several types of 3D DNA crystals extends the applications, including as scaffolds for small-molecule structure determination, as filter unit, and as controllable device system. My major researches focus on self-assembled 3D DNA crystals. I developed methods to improve properties of rationally designed DNA crystals and explored the applications of these crystals. I also built a 3D DNA crystal involving with the melamine-mediated T-T base pair and solved its structures. In this thesis, I developed approaches to improve properties of existing rationally designed DNA crystals. My work was mainly based on triangle crystal. The building motif of the crystal is a triangular shaped rigid DNA structure. The crystal extends in 3D space by interaction between sticky ends. One of the projects was increasing the stability of crystal through post-assembly approach. Triplex was formed in the link places between triangle motifs to stable the crystals after assembly. Stabilized crystals can survive in solution with low ionic strength. I also developed a general strategy for morphology control and resolution improvement of rationally designed DNA crystal. Improving quality and diffraction resolution of DNA crystals is crucial for their applications. In the strategy, the presence of hairpin shaped “blocking strands” that block building motifs helps to get less and larger crystals. The key of this success is the unstable Watson-Crick pairing between building motifs and blocking strands. It contributes to reach the thermodynamic equilibrium, the less-defective crystals. When applied to particular sticky ends of asymmetric triangular motif, blocking strands slow down the growth of corresponding facets that leads to modified crystal morphology. Finally, I explored applications of DNA crystals in macro-biomolecule structure determination. X-ray diffraction is a good way to solve the structure of macro-biomolecules. I grew a 3D DNA crystal involving with the melamine-mediated T-T base pair. I solved the structure of the melamine-mediated T-T base pair by solving structure of the crystal, by X-ray diffraction and molecular replacement method. Six hydrogen bonds are observed in each melamine-mediated base pair. The near-atomic details of the poly-T-melamine structure are basis of designing DNA nanostructures involved with melamine-mediated T-T base pair.

Degree

Ph.D.

Advisors

Mao, Purdue University.

Subject Area

Chemistry

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