DNA Self-Assembly Driven by Base Stacking

Longfei Liu, Purdue University

Abstract

DNA nanotechnology has provided programming construction of various nanostructures at nanometer-level precision over the last three decades. DNA self-assembly is usually implemented by annealing process in bulk solution. In recent several years, a new method thrives by fabricating two-dimensional (2D) nanostructures on solid surfaces. My researches mainly focus on this field, surface-assisted DNA assembly driven by base stacking. I have developed methods to fabricate DNA 2D networks via isothermal assembly on mica surfaces. I have further explored the applications to realize quasicrystal fabrication and nanoparticles (NPs) patterning.In this dissertation, I have developed a strategy to assemble DNA structures with 1 or 2 pair(s) of blunt ends. Such weak interactions cannot hold DNA motifs together in solution. However, with DNA-surface attractions, DNA motifs can assemble into large nanostructures on solid surface. Further studies reveal that the DNA-surface attractions can be controlled by the variety and concentration of cation in the bulk solution. Moreover, DNA nanostructures can be fabricated at very low motif concentrations, at which traditional solution assembly cannot render large nanostructures. Finally, assembly time course is also studied to reveal a superfast process for surface-assisted method compared with solution assembly.Based on this approach, I have extended my research scope from 1D to 2D structures assembled from various DNA motifs. In my studies, I have successfully realized conformational change regulated by DNA-surface interaction and steric effect. By introduction of DNA duplex “bridges” and unpaired nucleotide (nt) spacers, we can control the flexibility/rigidity of DNA nanomotifs, which helps to fabricate more delicate dodecagonal quasicrystals. The key point is to design the length of spacers. For 6-point-star motif, a rigid structure is required so that only 1-nt spacers are added. On the other hand, 3-nt spacers are incorporated to enable an inter-branch angle change from 60°to 90°for a more flexible 5-point-star motif. By tuning the ratio of 5 and 6 -pointstar motifs in solution, we can obtain 2D networks from snub square tiling, dodecagonal tiling, a mixture of dodecagonal tiling and triangular tiling, and triangular tiling.Finally, I have explored the applications of my assembly method for patterning NPs. Tetragonal and hexagonal DNA 2D networks have been fabricated on mica surfaces and served as templates. Then modify the surfaces with positively-charged “glues”, e.g. poly-L-lysine (PLL) or Ni2+. After that, various NPs have been patterned into designated lattices, including individual DNA nanomotifs, gold NPs (AuNPs), proteins, and silica complexes. Observed NP lattices and fast Fourier Transform (FFT) patterns have demonstrated the DNA networks’ patterning effect on NPs.

Degree

Ph.D.

Advisors

Mao, Purdue University.

Subject Area

Design|Nanotechnology|Genetics

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