An alternative approach to nucleic acid memory

George D Dickinson,Luca Piantanida,William Clay,Reza Zadegan,Golam Md Mortuza,Eric J Hayden,William L Hughes,Tim Andersen,Wan Kuang,Elton Graugnard,Christopher M Green,Chad Watson

doi:10.1038/s41467-021-22277-y

Abstract

DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency. Previous studies have used artificially synthesized DNA to store data and automated next-generation sequencing to read it back. Here, we report digital Nucleic Acid Memory (dNAM) for applications that require a limited amount of data to have high information density, redundancy, and copy number. In dNAM, data is encoded by selecting combinations of single-stranded DNA with (1) or without (0) docking-site domains. When self-assembled with scaffold DNA, staple strands form DNA origami breadboards. Information encoded into the breadboards is read by monitoring the binding of fluorescent imager probes using DNA-PAINT super-resolution microscopy. To enhance data retention, a multi-layer error correction scheme that combines fountain and bi-level parity codes is used. As a prototype, fifteen origami encoded with ‘Data is in our DNA!\\n’ are analyzed. Each origami encodes unique data-droplet, index, orientation, and error-correction information. The error-correction algorithms fully recover the message when individual docking sites, or entire origami, are missing. Unlike other approaches to DNA-based data storage, reading dNAM does not require sequencing. As such, it offers an additional path to explore the advantages and disadvantages of DNA as an emerging memory material.

Highlights

DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency
By combining the spatial control of DNA nanotechnology with our error-correction algorithms, we demonstrate digital Nucleic Acid Memory (dNAM) as an alternative approach to prototyping DNA-based storage for applications that require a limited amount of data to have high information density, redundancy, and copy number
High-resolution atomic force microscopy (AFM) was used in tapping mode to confirm the structural integrity of the origami and the presence of the data domains (Fig. 1d). 40,000 frames from a single field of view were recorded using DNA-PAINT (~4500 origami identified in 2982 μm2)

Summary

Introduction

DNA is a compelling alternative to non-volatile information storage technologies due to its information density, stability, and energy efficiency. In dNAM, data is encoded by selecting combinations of single-stranded DNA with (1) or without (0) docking-site domains. In dNAM, non-volatile information is digitally encoded into specific combinations of single-stranded. When formed into origami, the staple strands are arranged at addressable locations (Fig. 1) that define an indexed matrix of digital information. Extended staple strands have two domains: the first domain forms a sequence-specific double helix with the scaffold and determines the address of the data within the origami; the second domain extends above the origami and, if present, provides a docking site for fluorescently labeled single-stranded DNA imager strands. As an integrated memory platform, data is entered into dNAM when the staple strands encoding 1 or 0 are selected for each addressable site. The origami is optically imaged below the diffraction limit of light using DNA-PAINT (Fig. S1)

Methods

Results

Conclusion