Integrated Microfluidic DNA Storage Platform with Automated Sample Handling and Physical Data Partitioning

Abstract

Biopolymers are considered a promising alternative for information storage, and the most successful implementation has been using chemically synthesized DNA to represent binary data, which has achieved tremendous progress at multiple fronts bridging biotechnology with digital information. Currently, a majority of these systems are lacking the system integration and process automation expected by users of digital data and overly use tubes/vials for DNA storage. Herein, we present a microfluidic platform for automated storage and retrieval of data-encoding oligonucleotide samples enabled by a microvalve network architecture. Our platform, equipped with individually addressable compartments, offers an orthogonal strategy of data partitioning and file indexing with respect to the molecular-based random access implementation, with each partition amounting to an equivalence of 9.5 TB data within a 4 × 2 mm2 area. We examined the functionality of the presented platform and its compatibility with the DNA storage workflow coupled with nanopore sequencing to fully recover the stored files, demonstrating a significantly enhanced degree of function integration and process automation compared to that of the existing microfluidic approach.

Metal–Organic Frameworks in Microfluidics Enable Fast Encapsulation/Extraction of DNA for Automated and Integrated Data Storage

“…To automate and integrate the DNA storage process, we devised an integrated microfluidics-based DNA storage system, enabling fast encapsulation within 10 min for enhanced DNA stability to do away with specialized equipment and fast DNA extraction within 5 min. Previous studies focused either on automation of the DNA storage channel , or on improving DNA stability, but have not placed great emphasis on automation or integration of the complex manual operations required for DNA preservation and data access. The detailed procedure can be found in Supplementary Note 2.…”

“…However, several technical limitations also exist for the DNA microlibrary@MOFs: (1) the coding capacity of 3D barcodes is limited by available fluorescence; (2) retrieval of a target file depends on a large-scale commercial and expensive flow cytometer. Alternatively, microfluidic chip-based sorting with the integrated and miniaturized feature may be explored in the future. − We’ve made some progress on sample handling and physical data partitioning recently . We expect that microfluidic technologies will allow for DNA-based storage to be miniaturized, automated, and integrated in practical applications.…”

“…63−65 We've made some progress on sample handling and physical data partitioning recently. 19 We expect that microfluidic technologies will allow for DNA-based storage to be miniaturized, automated, and integrated in practical applications. We believe the DNA microlibrary@MOFs is a promising platform for DNA-based data storage with lower energy consumption and cost.…”

“…A DNA storage system demands a high degree of automation and integration, miniaturization, and robust and economical storage. Recent studies on automation or integration of synthesis, sample handling, and sequencing have been reported. − Here we focus on DNA stability and develop a robust preservation and data access method for economical and practical DNA storage.…”

A nanoparticle-coated microfluidic chip for automated, non-destructive extraction of encapsulated DNA in data storage

“…This device demonstrates that 1 TB of data could be stored and retrieved 8 . Another microfluidic platform composed of two-layer PDMS has been developed for automated storage and retrieval of data encoding DNA based on the combinatorial valve network 9 . Compared to other platforms, compact disk (CD)-microfluidics stands out by the degree of maturity in which unit operations such as fluidic displacement, mixing, separation, and metering can be implemented, scaled, and standardized 10,11 .…”