DNA Self-Assembly on Surface

DNA nanotechnology has rendered programmable, bottom-up self-assembly of nanostructures in various morphology, versatile functionalization, and atomic level precision over the last forty years. DNA nanostructures are usually assembled in solution by the thermodynamic process in a specific solution. In recent years, DNA two-dimensional (2D) structures on the surface have been widely applied in semiconductors, electronic devices, and biomedical studies. My research mainly focused on novel DNA nanostructures assembly on the surface and their applications. I have developed an equilibrium-enabled flexibly curved DNA homopolymer. I have further developed a novel method to determine the interhelical angle of DNA secondary structure by DNA 2D-array.

In this thesis, I have envisioned a strategy to prepare DNA linear polymers with flexible curvature and further assembled them into spiral or concentric rings on the surface. In DNA double crossover-like (DXL) homopolymers, an aromatic chemical group was introduced to the 3'-end in each strand. The planar group could stack into the DNA homopolymer, which increases the length on one side of the DXL polymer and further bend the structure by uneven-length stress. Moreover, the stacking in is under the equilibrium with flipping out, endowing the dynamic change and flexibility to the curvature of the DNA homopolymer, which could be a benefit in the surface-assisted construction of spirals or concentric rings.

With the appropriate design, DNA could be self-assembled on the surface into 2D crystals in a certain periodicity. Such a structure could be applied in nucleic acid secondary structure determination as a crystallography-like method. In this work, I have successfully incorporated the 10-23 DNAzyme, a common-used RNA-cleavage DNA sequence into DNA 2D arrays. In the brick-wall-like DNA 2D arrays, the repeating distance determined the interhelical angle of the 10-23 DNAzyme flanks. By 2D fast Fourier transform (FFT), this repeating distance could be measured and calibrated, following the deduction of the target angle. This approach had been validated with well-known DNA secondary structures.