The Efficiency of Pooled vs. Unpooled Staple Strands for Folding DNA Nanostructures
Dr. Eric Hayden
Due to its non-volatile nature, high information density, durability, and energy efficiency, DNA is a promising material to address the growing demands for data storage. Recently the Nucleic Acid Memory Institute developed an innovative DNA data storage system: digital Nucleic Acid Memory (dNAM). dNAM uses DNA origami breadboards that encode data by using a ssDNA scaffold, staple strands, and different patterns of protruding strands. These patterns are then revealed by fluorescence signals using DNA-PAINT super-resolution microscopy. A 7.2 kilobase (kb) M13 ssDNA scaffold and a plate of individual staple strands are currently used to produce dNAM. Recently, dNAM expanded their effort to encode more data by creating a larger p11 kb scaffold that will allow for 60% more possible data points and more customization. A larger scaffold, however, also requires more staples which demands a significant amount of time and money to assemble. In order to make origami assembly more efficient, we decided to use pooled staple strands to test their folding capability and quality. We successfully determined, from preliminary data, that using pooled and unpooled staple strands result in the formation of DNA origami. Further experiments are needed to compare their possible defects and ability to encode data. Utilizing pooled staple strands should streamline the production of dNAM to even further extend its practicality and adaptability.
Wolf, Amanda; Hayden, Eric; Kobernat, Sarah; Piantanida, Luca; and Balzer, Ben, "The Efficiency of Pooled vs. Unpooled Staple Strands for Folding DNA Nanostructures" (2022). 2022 Undergraduate Research Showcase. 101.