Increased DNA Origami Data Storage for Nucleic Acid Memory
Additional Funding Sources
This research was funded in part by the National Science Foundation (ECCS 1807809), the Semiconductor Research Corporation, and the State of Idaho through the Idaho Global Entrepreneurial Mission and Higher Education Research Council.
Presentation Date
7-2022
Abstract
The fabrication of new data is greatly increasing and yet the available capacity of current data storage methods fails to meet the high demand. Due to its non-volatile nature, high information density, and durability, DNA is a promising material to address our worldwide data storage deficit. To confront this issue, the Nucleic Acid Memory Institute at Boise State University developed a novel DNA data storage system: digital Nucleic Acid Memory (dNAM). dNAM encodes data using DNA origami breadboards, designed with a 7.2 kilobase (kb) M13 scaffold, many shorter staple strands, and varying patterns of protruding strands. While this method of data storage has proven effective, there are some limitations. dNAM currently uses a commercial M13 scaffold, which limits size and customizability. For the prototypical message “Data is in our DNA!\n” it requires 15 distinctive origamis with unique groups of staple strands. Additionally, creating the 15 unique groups of staple strands demands a significant amount of time and liquid handling. Recently, we addressed these inefficiencies by creating a larger custom 11 kb scaffold that will allow for 60% more possible data sites, while decreasing the number of origamis needed from 15 to 6 for the prototypical message. To reduce the number of liquid handling steps, we also shifted to using staple strands synthesized in pools (IDT) instead of individually adding each staple. The utilization of these two advancements in origami production should streamline the assemblage of dNAM to significantly extend its data storage capacity and practicality. In the future, the combination of these advances and using multiple orthogonal 11 kb scaffolds will allow us to encode data in a one-pot synthesis moving the dNAM system even closer to practical applications.
Increased DNA Origami Data Storage for Nucleic Acid Memory
The fabrication of new data is greatly increasing and yet the available capacity of current data storage methods fails to meet the high demand. Due to its non-volatile nature, high information density, and durability, DNA is a promising material to address our worldwide data storage deficit. To confront this issue, the Nucleic Acid Memory Institute at Boise State University developed a novel DNA data storage system: digital Nucleic Acid Memory (dNAM). dNAM encodes data using DNA origami breadboards, designed with a 7.2 kilobase (kb) M13 scaffold, many shorter staple strands, and varying patterns of protruding strands. While this method of data storage has proven effective, there are some limitations. dNAM currently uses a commercial M13 scaffold, which limits size and customizability. For the prototypical message “Data is in our DNA!\n” it requires 15 distinctive origamis with unique groups of staple strands. Additionally, creating the 15 unique groups of staple strands demands a significant amount of time and liquid handling. Recently, we addressed these inefficiencies by creating a larger custom 11 kb scaffold that will allow for 60% more possible data sites, while decreasing the number of origamis needed from 15 to 6 for the prototypical message. To reduce the number of liquid handling steps, we also shifted to using staple strands synthesized in pools (IDT) instead of individually adding each staple. The utilization of these two advancements in origami production should streamline the assemblage of dNAM to significantly extend its data storage capacity and practicality. In the future, the combination of these advances and using multiple orthogonal 11 kb scaffolds will allow us to encode data in a one-pot synthesis moving the dNAM system even closer to practical applications.