Dynamic and scalable DNA-based information storage

Abstract

The physical architectures of information storage systems often dictate how information is encoded, databases are organized, and files are accessed. Here we show that a simple architecture comprised of a T7 promoter and a single-stranded overhang domain (ss-dsDNA), can unlock dynamic DNA-based information storage with powerful capabilities and advantages. The overhang provides a physical address for accessing specific DNA strands as well as implementing a range of in-storage file operations. It increases theoretical storage densities and capacities by expanding the encodable sequence space and simplifies the computational burden in designing sets of orthogonal file addresses. Meanwhile, the T7 promoter enables repeatable information access by transcribing information from DNA without destroying it. Furthermore, saturation mutagenesis around the T7 promoter and systematic analyses of environmental conditions reveal design criteria that can be used to optimize information access. This simple but powerful ss-dsDNA architecture lays the foundation for information storage with versatile capabilities.

DNA stability: a central design consideration for DNA data storage systems

“…The active development of DNA-based computation preceded the development of DNA storage systems by over a decade 5,6,43,44 . The idea of now merging these two fields to perform in-storage computation has intriguing implications including potentially providing the ability to directly search 45 and edit 46 DNA databases. In addition to computation, there is also the hope that DNA storage systems may be capable of dramatically lower latencies of operation than the current multi-hour to multi-day process of reading and writing information.…”

“…To function at reasonable temperature ranges (<100°C) the addresses are generally limited to <25 nt as longer sequences would require higher temperatures to 'melt' during PCR cycling. However, addresses cannot be much shorter without sacrificing diversity in addresses 46 . The addresses take up space on each strand and do not encode data (e.g., overhead).…”

Decoding DNA data storage for investment

“…The technology is based on an elegant design of DNA blocks with recognition sequences that can be altered via PCR ( Yazdi et al, 2015 ). More recent advances include a dynamic storage system based on a T7 promoter sequence with a single-stranded overhang, unlocking versatile editing and rewriting capabilities ( Lin et al, 2020 ).…”

Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage

“…DNA is a naturally selected molecule for storing our gene information, which serves as the blueprint to construct and maintain the most intricate biological system. DNA-related biotechnologies such as synthesis ( 5 , 6 ), polymerase chain reaction (PCR) ( 7 , 8 ), and sequencing ( 9 , 10 ) can facilitate efficient writing, reading, editing, and random access of data encoded in DNA sequences ( 11 , 12 ). The theoretical data density in DNA is as high as ~455 EB (exabyte) g −1 ( 13 – 15 ), and DNA is also very stable when preserved under proper conditions, so the information encoded in it can be still readable after a long time (e.g., over 2 million years in Global Seed Vault) ( 16 , 17 ).…”