DNA Backbone Editing for Data Storage Throughput
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Solution Overview
Problem
Current DNA data storage methods are inefficient, requiring an 8 to 9 order of magnitude improvement to match the speed of magnetic disk drives and tapes, as a single DNA base pair can store only 2 bits, necessitating the storage of 4000 Giga-base pairs in an hour to compete with existing storage technologies.
Innovation Solution
The method involves cleaving a DNA backbone into segments and inserting data-encoding oligos with terminal ends that join homologous terminal ends, allowing for the synthesis of a DNA strand encoding data in a massively parallel manner using techniques like CRISPR/Cas9 and homology-directed repair, enabling faster data storage by positioning data-encoding symbols between segments.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Speed
If current DNA synthesis methods are used to write data to DNA strands, then data can be stored in DNA molecules, but the writing speed is extremely slow (15 base pairs per hour) compared to magnetic storage technologies
Solution Approach 1:
The patent divides the DNA backbone into multiple segments and processes them in parallel. By cleaving the backbone into numerous smaller segments simultaneously and performing independent synthesis operations on each segment, the system achieves massive parallelization of the data writing process, increasing overall throughput from 15 base pairs per hour to potentially millions of base pairs per hour across parallel reactions
Solution Approach 2:
The patent performs preliminary preparation of DNA segments and data-encoding oligos before the actual assembly process. Backbone segments are pre-cleaved and prepared with terminal ends, and data-encoding oligos are pre-synthesized with complementary terminal ends, enabling rapid assembly without time-consuming preparation during the writing process
2Productivity
If 4000 Giga-base pairs need to be stored in an hour to match disk drive capabilities, then DNA data storage can compete with magnetic technologies, but current methods cannot achieve this throughput
Solution Approach 1:
The patent combines multiple operations into a single integrated process. The cleavage of backbone, preparation of segments, synthesis of data-encoding oligos, and assembly operations are merged into a coordinated workflow that can be executed in parallel across thousands of reactions simultaneously, achieving the necessary throughput to write 4000 Giga-base pairs in an hour
Solution Approach 2:
The patent transitions from sequential single-strand processing to massively parallel multi-strand processing. By organizing the synthesis across multiple dimensions (multiple backbones, multiple segments per backbone, multiple oligos per segment), the system achieves exponential increases in throughput capability
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach significantly enhances the data storage rate by allowing for the parallel synthesis of DNA strands, potentially making DNA data storage more viable by increasing the speed at which data can be written to DNA strands.
Implementation Method 1
cleaving a DNA backbone into multiple segments... using techniques like CRISPR/Cas9
Implementation Method 2
pasting a plurality of data-encoding symbols having terminal ends between the multiple segments, with the terminal ends of the segments joining homologous terminal ends of the symbols
Implementation Method 3
moving, via voltage, at least one of the DNA backbone and a Cas9 across a hydrophobic fluidic platform
Data Source
AI summary
Methods of writing data to a DNA strand by inserting data-encoding oligos or symbols into a DNA backbone. One particular method of synthesizing a DNA strand encoding data includes cleaving a DNA backbone into multiple segments, and pasting a plurality of data-encoding oligo symbols between the multiple segments, with the terminal ends of the segments joining homologous terminal ends of the symbols, resulting in the DNA strand encoding data comprising alternating segments and symbols.