Massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS)

Area of Science:

• Biotechnology
• Information Storage
• Genomics

Background:

• Chip-scale DNA synthesis is a promising high-throughput, cost-effective method for large-scale DNA data storage.
• Unbiased retrieval of low-copy-number DNA sequences is a major challenge, primarily due to DNA amplification limitations.

Purpose of the Study:

• To develop a novel amplification strategy for unbiased, high-throughput retrieval of DNA data from low-copy sequences.
• To enable efficient and accurate storage and retrieval of multimedia data using DNA.

Main Methods:

• Devised a simulation-guided quantitative primer-template hybridization strategy for massively parallel homogeneous amplification of chip-scale DNA (MPHAC-DIS).
• Utilized a fixed-energy primer design to demonstrate unbiased amplification of 100,000-plex sequences.
• Employed machine learning in conjunction with low sequencing depths for data decoding.

Main Results:

• MPHAC achieved a fold-80 value of 1.0, significantly outperforming conventional primers (3.2).
• Demonstrated cost reduction by up to four orders of magnitude through reduced over-sequencing.
• Achieved high decoding accuracy for multimedia files (text, images, videos) even at a sequencing depth of ~1×, reaching ~80% with machine learning.

Conclusions:

• The MPHAC-DIS method provides a programmable and predictable solution for unbiased DNA amplification in DNA data storage.
• This approach significantly enhances the cost-effectiveness and accessibility of large-scale DNA-based information storage.
• The technology shows potential for industrial applications in DNA data storage.