Faculty Mentor Information
Dr. Eric Hayden (Mentor), Boise State University; and Dr. Maryna Lazouskaya (Mentor), Boise State University
Additional Funding Sources
This work has been supported by the National Science Foundation (Awards #1807809 and #2227626), by the Higher Education Council (HERC-2016) and by the Idaho Global Entrepreneurial Mission (IGEM-2016).
Abstract
The limitations of conventional memory materials, both in physical and economic aspects, necessitate the development of novel memory materials and methods. Digital Nucleic Acid Memory (dNAM) is one such memory method, which leverages DNA’s high information density, stability, and energy efficiency for non-volatile long-term memory applications, such as archival storage. dNAM uses DNA origami to form an information matrix where fluorescent DNA strands can bind to represent Binary 1’s and 0’s. This process is dependent on the size of the DNA Origami, therefore being dependent on the size of the ssDNA scaffold. The custom novel ssDNA scaffold P11453.1 is synthesized at BSU through a Biological Bacteria/Bacteriophage system in E. coli, producing small quantities of the desired scaffold at a time. Future dNAM requirements demand larger amounts of concentrated scaffold. Upscaling ssDNA scaffold synthesis, if possible, would provide high-yield samples and save time-per-preparation of the same amount of ssDNA. This work shows two different methods for upscaling ssDNA scaffold production. By utilizing pre-growth techniques and a refined Phenol-Chloroform extraction, along with the utilization of a commercial kit for the isolation of ssDNA, both methods were performed in replicates. The quality and quantity of P11453.1 scaffold was evaluated by spectrophotometry, densitometry, and gel electrophoresis. DNA Origami folded using ssDNA scaffold produced by these methods act as a final verification of our methods.
Digital Nucleic Acid Memory: Up-Scaling ssDNA Synthesis of Novel P11453.1 Scaffold for DNA Origami
The limitations of conventional memory materials, both in physical and economic aspects, necessitate the development of novel memory materials and methods. Digital Nucleic Acid Memory (dNAM) is one such memory method, which leverages DNA’s high information density, stability, and energy efficiency for non-volatile long-term memory applications, such as archival storage. dNAM uses DNA origami to form an information matrix where fluorescent DNA strands can bind to represent Binary 1’s and 0’s. This process is dependent on the size of the DNA Origami, therefore being dependent on the size of the ssDNA scaffold. The custom novel ssDNA scaffold P11453.1 is synthesized at BSU through a Biological Bacteria/Bacteriophage system in E. coli, producing small quantities of the desired scaffold at a time. Future dNAM requirements demand larger amounts of concentrated scaffold. Upscaling ssDNA scaffold synthesis, if possible, would provide high-yield samples and save time-per-preparation of the same amount of ssDNA. This work shows two different methods for upscaling ssDNA scaffold production. By utilizing pre-growth techniques and a refined Phenol-Chloroform extraction, along with the utilization of a commercial kit for the isolation of ssDNA, both methods were performed in replicates. The quality and quantity of P11453.1 scaffold was evaluated by spectrophotometry, densitometry, and gel electrophoresis. DNA Origami folded using ssDNA scaffold produced by these methods act as a final verification of our methods.