Publications
Nano SelectNov 2021 DOI:
10.1002/nano.202100275

Current and emerging opportunities in biological medium‐based computing and digital data storage

Bennet, Devasier; Vo‐Dinh, Tuan; Zenhausern, Frederic
Product Used
NGS
Abstract
Exciting data storage applications can be seen in the increasing interest in DNA computation, barcoding, and the advent of “DNA of Everyday Things” (Figure 3). The emerging technology that combines nanomaterials and DNA labeling uses silica to encapsulate and protect DNA molecules that contain information for item authenticity and verification.[6, 46] The DNA component encapsulated in these silica-based "synthetic fossils" can withstand high temperatures and aggressive radical oxygen species (ROS) and resist a wide range of otherwise dangerous chemical conditions. Also, it is quickly released without harm by using fluoride-containing buffered oxide etch solutions.[103] Puddu et al.[94] have demonstrated the potential of such nanoparticles for barcoding valuable and dangerous goods (e.g., Barcoding of fuel (gasoline), cosmetic oil (bergamot oil), and food-grade oil (extra virgin olive oil) to protect against fakes. Mikutis et al.[96] developed silica-encapsulated DNA for use in environmental tracing for underground water contamination (Figure 8A-i). Multiple groups have reported several approaches of implementing DNA-based authentication, with tags being used in barcoding directly (e.g., naked DNA tracers) or with protective materials (e.g., PLA or silica-encapsulated DNA tracers).[96, 104] This concept was extended with developing the DNA-of-things storage architecture to create materials with embedded information.[47] This novel storage architecture was achieved by encapsulating DNA using silica beads and mixed with the material used to print the target 3D Stanford Bunny and spectacle lenses, which can substantially enhance DNA stability. Thus, existing methods for encoding digital information in materials, including silica-encapsulated DNA,[94, 96] DNA embedded in 3D printed material (Figure 8A-ii),[47] allow storing data as DNA in any physical object essentially and potentially opening up new areas for DNA storage, molecular identification. Potentially it could be applied to store electronic health records in implants. However, in any application using encapsulated DNA, DNA molecules should be released from the protective materials before qPCR measurements. Also, existing digital encoding information methods require access to specialized labs and equipment to decode. In most molecular tagging cases, the protocol prevents real-time use; for example, it requires a PCR-based or SHERLOCK-based detection system.[105] An ideal molecular tagging system should be inexpensive and reliable, with fast readout and user-controlled encoding and decoding from end-to-end with minimal reliance on lab equipment. To address this, Doroschak et al.[106] developed a Porcupine's encoding scheme, an end-to-end encoding and decoding system featuring DNA-based tags (Figure 8A-iii) readable within 10-15 seconds using a portable nanopore device. The Porcupine digital bits tagging scheme relies on the presence or absence of short distinct DNA strands (40 nt) called molecular bits (molbits), which can rapidly be read by nanopore. They reported this molecular tagging method is inexpensive, fast, and reliable to decode and requires minimal resources to create or read tags. However, this portable nanopore device is limited by its ability to deliver very high-molecular-weight DNA to the pore, and its accuracy has not yet been extensively tested. [image] [/cms/asset/dbfe9736-5d4a-43ef-a47e-0f55dda92fe2/nano202100275-fig-0008-m.jpg]
Product Used
NGS

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