Synthesis of Custom Single Stranded DNA for Nucleic Acid Memory
Additional Funding Sources
This project is supported by a 2018-2019 STEM Undergraduate Research Grant from the Higher Education Research Council, the National Science Foundation (NSF), Semiconductor Research Corporation (SRC), and the State of Idaho through Idaho Global Entrepreneurial Mission and Higher Education Research Council (IGEM-HERC).
Abstract
The demand for memory storage will soon outrun the supply of naturally occurring silicon on Earth (Zhirnov et al. 2016). It is now apparent that a more dense and less power-consuming memory storage technology will be necessary. DNA is an incredible natural memory storage material with the ability to encode all the information needed for every function of all organisms on our planet. Information can even be recovered from ancient fossils demonstrating the durability of DNA. The research presented here is a part of a larger Nucleic Acid Memory (NAM) project, which aims to use small structures built out of DNA (origami) as a memory storage technology. The goal of our research is the production of long single-stranded DNA of arbitrary sequences. Analogous to an electronic breadboard, these long DNA molecules act as a "scaffold" upon which our origami structures are built. Multiple long scaffolds are needed for more dense and reliable information storage. Here we show the production, purification, and characterization of custom DNA scaffolds of variable lengths. These scaffolds are expressed from phage derived plasmids in E. coli. We optimized a protocol based on several that were previously reported in the literature. We found that DNA size did not limit the yield or quality of our purified scaffolds indicating the feasibility of further increases in size. Next, the scaffolds will be combined with small synthetic DNA oligonucleotide "staples" to build origami structures, and visualize them by Atomic Force Microscopy and Super Resolution Fluorescence Microscopy. Based on the outcome of this microscopy, we will use computer aided design and synthetic biology to build novel scaffold sequences with improved properties. To continue this research cycle into the future, we plan to pass on our knowledge to future research students and help develop a sustainable, transdisciplinary Vertically Integrated Project (VIP) program at Boise State University.
Synthesis of Custom Single Stranded DNA for Nucleic Acid Memory
The demand for memory storage will soon outrun the supply of naturally occurring silicon on Earth (Zhirnov et al. 2016). It is now apparent that a more dense and less power-consuming memory storage technology will be necessary. DNA is an incredible natural memory storage material with the ability to encode all the information needed for every function of all organisms on our planet. Information can even be recovered from ancient fossils demonstrating the durability of DNA. The research presented here is a part of a larger Nucleic Acid Memory (NAM) project, which aims to use small structures built out of DNA (origami) as a memory storage technology. The goal of our research is the production of long single-stranded DNA of arbitrary sequences. Analogous to an electronic breadboard, these long DNA molecules act as a "scaffold" upon which our origami structures are built. Multiple long scaffolds are needed for more dense and reliable information storage. Here we show the production, purification, and characterization of custom DNA scaffolds of variable lengths. These scaffolds are expressed from phage derived plasmids in E. coli. We optimized a protocol based on several that were previously reported in the literature. We found that DNA size did not limit the yield or quality of our purified scaffolds indicating the feasibility of further increases in size. Next, the scaffolds will be combined with small synthetic DNA oligonucleotide "staples" to build origami structures, and visualize them by Atomic Force Microscopy and Super Resolution Fluorescence Microscopy. Based on the outcome of this microscopy, we will use computer aided design and synthetic biology to build novel scaffold sequences with improved properties. To continue this research cycle into the future, we plan to pass on our knowledge to future research students and help develop a sustainable, transdisciplinary Vertically Integrated Project (VIP) program at Boise State University.
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