Abstract Title

Enhancement of Digital Nucleic Acid Memory by Customizing DNA Origami Scaffolds

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.

Abstract

DNA origami is a promising novel biotechnology because DNA is a small, stable, and dense biomaterial. DNA origami is made from a scaffold, a piece of single stranded DNA (ssDNA), and staple strands, short oligonucleotides, that together fold into a predefined shape. Our lab developed digital Nucleic Acid Memory (dNAM), which uses DNA origami as a breadboard for data storage by creating a matrix of locations that fluoresce. Some DNA staples that are used to fold the scaffold have a protruding segment, allowing for oligonucleotide strands with fluorophores attached to them, called imager strands, to anneal to the protruding segment. The DNA origami is read with DNA-PAINT super resolution microscopy; if a fluorophore is present at a protruding strand a 1 is recorded, and if not a zero is recorded for that data point on the breadboard. The dNAM project currently relies on the M13 scaffold which has a fixed length of 7.2 kilo bases (kb), limiting size and customization of the DNA origami. Creating larger scaffolds will expand the storage capacity and versatility of the dNAM project. In order to create larger scaffolds we used a phagemid/helper phage system to produce ssDNA in bacteria and then export it from the cell. Using this system, we produced ssDNA between 3 kb and 10 kb in length. In the future, the goal is to clone different phagemids to create larger, custom scaffolds to expand the data storage capacity of dNAM.

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Enhancement of Digital Nucleic Acid Memory by Customizing DNA Origami Scaffolds

DNA origami is a promising novel biotechnology because DNA is a small, stable, and dense biomaterial. DNA origami is made from a scaffold, a piece of single stranded DNA (ssDNA), and staple strands, short oligonucleotides, that together fold into a predefined shape. Our lab developed digital Nucleic Acid Memory (dNAM), which uses DNA origami as a breadboard for data storage by creating a matrix of locations that fluoresce. Some DNA staples that are used to fold the scaffold have a protruding segment, allowing for oligonucleotide strands with fluorophores attached to them, called imager strands, to anneal to the protruding segment. The DNA origami is read with DNA-PAINT super resolution microscopy; if a fluorophore is present at a protruding strand a 1 is recorded, and if not a zero is recorded for that data point on the breadboard. The dNAM project currently relies on the M13 scaffold which has a fixed length of 7.2 kilo bases (kb), limiting size and customization of the DNA origami. Creating larger scaffolds will expand the storage capacity and versatility of the dNAM project. In order to create larger scaffolds we used a phagemid/helper phage system to produce ssDNA in bacteria and then export it from the cell. Using this system, we produced ssDNA between 3 kb and 10 kb in length. In the future, the goal is to clone different phagemids to create larger, custom scaffolds to expand the data storage capacity of dNAM.