Date of Graduation


Document Type


Degree Name

Master of Science in Cell & Molecular Biology (MS)

Degree Level



Biological Sciences


Jin-Woo Kim

Committee Member

Jingyi Chen

Second Committee Member

Matthew Patitz

Third Committee Member

Joshua Sakon


DNA-Linked Nanoparticle Building Blocks, nBLOCKs, Structural DNA Nanotechnology


Controlling the shapes and sizes of nanomaterials often enables controlling their properties for certain applications. The most promising methods for controlling the shapes and sizes of nanostructures use base-pairing between complementary DNA strands to self-assemble nanostructures from DNA and nanoparticles. DNA Brick-based self-assembly is a particularly useful method for creating DNA nanostructures. It offers a large amount of control over the final shapes and sizes because it uses building blocks that are anisotropic and have predictable geometry. However, this control has not been extended to the self-assembly of nanostructures from nanoparticles. Applying DNA Brick based self-assembly to the self-assembly of nanostructures from nanoparticles would require DNA-linked nanoparticles that are anisotropic and have predictable geometry.

To this end, Solidworks models were used to study the interactions between DNA Bricks so that detailed information could be gained about their mode of self-assembly. This information was used to generate Solidworks models of DNA-linked nanoparticle building blocks (nBLOCKs) that can be used for DNA Brick-based self-assembly. These nBLOCKs could be created by attaching a single 43 base pair (bp) long DNA strand to gold nanoparticles using the anisotropic monofunctionalization technique. However, accomplishing this feat would require improving the efficiency of the anisotropic monofunctionalization method first.

Attempts to improve all three steps of the anisotropic monofunctionalization technique yielded mixed results. The efficiency of the first step, binding DNA to a solid support, was improved by implementing the photocleavable (PC) biotin – streptavidin interaction. UV-Vis absorbance spectroscopy revealed that the PC biotinylated DNA strands became bound to streptavidin-coated magnetic beads with nearly 100% efficiency. However, the second and third steps, binding gold nanoparticles (AuNPs) to DNA and cleaving DNA-linked AuNPs from the beads, still suffer from low yields. The efficiency of the second step was incrementally improved from 3% to 25% by tuning the reaction conditions. The third step was carried out at a maximum of 10% efficiency. The method was successfully used to generate nBLOCKs but the overall yield was less than 5%. Explanations of and possible solutions to the low-yield are suggested for future experiments.