DNA storage in thermoresponsive microcapsules for repeated random multiplexed data access

Abstract

DNA has emerged as an attractive medium for archival data storage due to its durability and high information density. Scalable parallel random access to information is a desirable property of any storage system. For DNA-based storage systems, however, this still needs to be robustly established. Here we report on a thermoconfined polymerase chain reaction, which enables multiplexed, repeated random access to compartmentalized DNA files. The strategy is based on localizing biotin-functionalized oligonucleotides inside thermoresponsive, semipermeable microcapsules. At low temperatures, microcapsules are permeable to enzymes, primers and amplified products, whereas at high temperatures, membrane collapse prevents molecular crosstalk during amplification. Our data show that the platform outperforms non-compartmentalized DNA storage compared with repeated random access and reduces amplification bias tenfold during multiplex polymerase chain reaction. Using fluorescent sorting, we also demonstrate sample pooling and data retrieval by microcapsule barcoding. Therefore, the thermoresponsive microcapsule technology offers a scalable, sequence-agnostic approach for repeated random access to archival DNA files.

Timed Pulses in DNA Strand Displacement Reactions

“…Due to the fact that nucleic acid SDRs are the key processes of dynamic DNA nanotechnology, − the possibility to achieve temporally programmed pulse outputs could find different applications. For example, being able to intermittently activate DNA-based signaling with specific temporal features could be used to improve multiplexing in DNA-based imaging systems (such as DNA paint) or to temporally control inputs/outputs in DNA-encoded systems with possible applications in DNA computing and drug-delivery. − Finally, inspired by the temporal program of gene expression, our strategy can be used to control over time the pulse activation of synthetic genes for different synthetic biology applications, including diagnostic, therapeutic, and biofuel production. , …”

Data Storage Using DNA

“…Adapted with permission. [ 45 ] Copyright 2023, Springer Nature. D) Content‐addressable DNA data storage system.…”

“…For example, Bögels et al. recently demonstrated that storing DNA data in thermoresponsive microcapsules enables multiplexed and repeated random data access [ 45 ] (Figure 5C). They achieved this by enhancing the fidelity of PCR amplification through constraining the reaction into microreactors.…”

“…[ 18,35b ] The presence of PCR bias also presents challenges for multiplexed data retrieval. [ 115 ] While strategies like emulsion PCR [ 35b,36 ] and the use of specific microcapsules [ 45 ] can help mitigate these issues, their implementation may pose obstacles, and they cannot resolve all the challenges associated with PCR‐based random access. As alternative random access methods, various physical isolation strategies have been developed.…”

“…Furthermore, their platform is compatible with fluorescent barcoding and sorting, further enhancing the capability of random data retrieval. [ 45 ] Banal et al. achieved random access by barcoding silica‐encapsulated DNA data with three 25‐nucleotide single‐stranded DNA (ssDNA) sequences [ 46 ] (Figure 5D).…”