DNA diamond formulates a decomposable composite letter constellation model for DNA data storage.

Area of Science:

• Biotechnology
• Data Storage
• Molecular Engineering

Background:

• Oligonucleotide multiplicity is inherent in DNA synthesis, offering potential for data storage.
• Current composite letter DNA storage faces challenges in letter indistinguishability and molecular diversity, hindering reliable data recovery.

Purpose of the Study:

• To develop a novel composite letter DNA storage model for improved data density and recovery reliability.
• To address limitations of existing DNA data storage systems through a new constellation model and detection framework.

Main Methods:

• Formulated a 15-point composite letter constellation model named DNA diamond.
• Proposed a two-stage letter detection framework using set partitioning based on discrete entropy.
• Incorporated encoded double-end indices and length filtering to mitigate crosstalk and error propagation.

Main Results:

• Validated eight-letter and 15-letter composite letter DNA storage systems.
• The eight-letter system achieved 2.5 bits per letter payload density with error-free recovery at 14× coverage.
• The 15-letter system achieved 3.125 bits per letter payload density, with 2.23 bits per letter (payload plus indices) at 33× coverage.

Conclusions:

• The DNA diamond model offers a practical and scalable framework for high-density composite DNA data storage.
• The proposed methods significantly improve storage density and data recovery accuracy compared to prior systems.
• This advancement paves the way for more efficient and reliable DNA-based data archiving solutions.