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Advancing synthesis-free and enzyme-free rewritable DNA memory through frameshift encoding and nanopore duplex

Kai Tian1,2,3, Sicheng Zhang4, Sally Chen1,2

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This study introduces a novel DNA memory system using frameshift encoding for rapid, cost-effective data writing on universal DNA templates. This DNA hard drive technology enables efficient rewriting and has potential in computing and encryption.

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Area of Science:

  • Biomolecular Engineering
  • Data Storage Technologies
  • Molecular Computing

Background:

  • DNA data storage offers high density and durability but faces limitations in cost and rewrite capability for non-archival applications.
  • Existing DNA hard drive strategies often involve complex methods, low data density, and expensive instrumentation.
  • There is a need for cost-effective, rapid, and rewritable DNA data storage solutions.

Purpose of the Study:

  • To develop a DNA memory system enabling rapid, cost-effective, and parallel data writing on a universal DNA template without de novo synthesis.
  • To demonstrate efficient data rewriting capabilities using a novel frameshift encoding strategy.
  • To explore the potential of this DNA hard drive technology in applications beyond archival storage.

Main Methods:

  • Utilized frameshift encoding, inspired by viral ribosomal frameshifting, to encode information as checkpoint frameshifts on a DNA template.
  • Employed microstaples of varying lengths annealed at specific sites on a long template strand for data encoding.
  • Developed data decoding using MspA nanopore duplex interruption sequencing with a novel unzipping marker and frameshift-induced current signatures.

Main Results:

  • Successfully demonstrated a DNA memory system based on frameshift encoding for data writing without synthesis or enzymatic processing.
  • Achieved efficient, bit-specific rewriting through toehold-mediated strand displacement enabled by the duplex structure.
  • Validated data decoding using nanopore sequencing, resolving individual bits via frameshift signatures.

Conclusions:

  • The frameshift encoding DNA memory system provides a scalable and versatile framework for DNA-based hard drives.
  • This technology overcomes limitations of previous DNA storage methods, offering cost-effectiveness and rewrite capability.
  • Potential applications include in-memory computing, encryption, and dynamic biomolecular sensing.