DNA punch cards for storing data on native DNA sequences via enzymatic nicking

Area of Science:

• Biotechnology
• Molecular Biology
• Data Storage

Background:

• Synthetic DNA data storage offers high density but faces challenges with cost and speed.
• Native DNA presents an alternative for data storage by modifying its structure rather than sequence.

Purpose of the Study:

• To develop a cost-effective and efficient data storage system using native DNA.
• To explore DNA topology modification for information encoding.

Main Methods:

• Introduction of DNA punch cards: a system encoding data via nicks on native double-stranded DNA.
• Utilizing Pyrococcus furiosus Argonaute for DNA nicking and enzymatic toehold creation.
• Employing high-throughput sequencing and read alignment for data reconstruction.

Main Results:

• Successful encoding and accurate retrieval of data using the DNA punch card system.
• Demonstration of parallel nicking and single-bit random access capabilities.
• Validation of the method on PCR products of Escherichia coli genomic DNA.

Conclusions:

• DNA punch cards offer a viable, low-cost approach to native DNA data storage.
• The platform enables efficient data writing and reading, overcoming limitations of synthetic DNA systems.
• This technology holds potential for future data archival and in-memory computing applications.