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Selective Capture of 5-hydroxymethylcytosine from Genomic DNA
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A practical DNA data storage using an expanded alphabet introducing 5-methylcytosine.

Deruilin Liu1,2, Demin Xu2,3, Liuxin Shi2

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This study introduces R+, a DNA data storage method using modified bases like 5-methylcytosine (5mC) to boost information density. Experimental results show high data recovery rates, proving 5mC

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Area of Science:

  • Biotechnology
  • Data Storage
  • Molecular Engineering

Background:

  • DNA is a promising medium for next-generation data storage.
  • Expanding the DNA alphabet with modified bases can increase information density.
  • Synthesizing non-natural DNA sequences presents significant challenges.

Purpose of the Study:

  • To describe and validate a practical DNA data storage transcoding scheme named R+.
  • To demonstrate the use of 5-methylcytosine (5mC) as an expanded molecular letter.
  • To assess the feasibility of using modified bases for high-density DNA data storage.

Main Methods:

  • Developed the R+ transcoding scheme based on an expanded molecular alphabet including 5mC.
  • Encoded a representative file into 1.3–1.6 kbps in vitro DNA fragments.
  • Utilized nanopore sequencing for DNA data retrieval.
  • Implemented R+ in Python with code available under MIT license.

Main Results:

  • Achieved an average data recovery rate of 98.97% with reference.
  • Achieved an average data recovery rate of 86.91% without reference.
  • Validated the experimental practicability of 5mC in DNA data storage systems.

Conclusions:

  • The R+ scheme effectively utilizes 5mC for practical DNA data storage.
  • The use of modified bases like 5mC is feasible and enhances storage capacity.
  • This approach has potential for wide-ranging applications in data archiving.