Oligo Design with Single Primer Binding Site for High Capacity DNA-Based Data Storage

Area of Science:

• Biotechnology
• Data Storage
• Molecular Engineering

Background:

• DNA offers high density and longevity for long-term data archiving.
• Current DNA data storage methods use two primer binding sites (PBSs), reducing data density.
• Existing methods limit homopolymer runs to three nucleotides, further impacting storage efficiency.

Purpose of the Study:

• To enhance data density in DNA-based storage systems.
• To develop and validate a novel oligonucleotide design with a single PBS.
• To increase the maximum allowable homopolymer run length.

Main Methods:

• Devised and tested an oligonucleotide design appending a single PBS to the data block.
• Increased the maximum homopolymer run length to four nucleotides.
• Developed an oligo assembly algorithm for error-prone sequencing data.
• Conducted wet lab experiments with 398KB of data stored in 10,750 oligos.

Main Results:

• Experimental validation confirmed the feasibility of the single PBS design.
• Achieved over 99% accurate recovery of oligo sequences.
• Demonstrated that a single PBS is sufficient for DNA data storage.
• Showcased a data density gain of 14.3% to 140.2% compared to existing schemes.

Conclusions:

• A single PBS is sufficient for effective DNA data storage.
• Relaxing the homopolymer run constraint to four nucleotides is viable.
• The proposed method significantly improves data density in DNA storage systems.