Flow Cell Selective Nucleotide Deposition for DNA Data Storage
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Solution Overview
Problem
Current data storage methods, such as magnetic, optical, and solid-state storage, face limitations in read-write speed, data retention, power usage, and data density, while existing DNA reading techniques are inefficient for machine-written DNA.
Innovation Solution
A flow cell system with selectively activatable or depositable nucleotides, utilizing electrodes, light sources, and pH control to write and read machine-written DNA, enabling precise deposition and activation of nucleotides for enhanced data storage capabilities.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If traditional magnetic, optical, or solid-state storage is used, then data storage is achievable, but read-write speed, data retention, power usage, and data density are limited
Solution Approach 1:
The patent replaces mechanical data storage systems (magnetic, optical, solid-state) with a biochemical system using DNA synthesis and sequencing. The flow cell enables direct writing of DNA sequences representing data, eliminating mechanical read/write heads and moving parts, thereby achieving faster access speeds and eliminating mechanical wear limitations
Solution Approach 2:
The patent changes the fundamental parameter of data storage from physical states (magnetic fields, optical reflections, electrical charges) to chemical sequences (DNA nucleotide sequences). This parameter change enables vastly superior data density since DNA can store information at the molecular level, and improves data retention through the natural stability of DNA molecules
2Productivity
If DNA sequencing is performed using traditional array-based cyclic methods, then DNA can be read, but the process is inefficient for machine-written DNA
Solution Approach 1:
The patent applies preliminary action by performing flow-cell-based enrichment and preparation of machine-written DNA sequences before sequencing. The system pre-processes the DNA in the flow cell to concentrate and organize the machine-written sequences, making them readily available for rapid sequencing without requiring time-consuming traditional library preparation steps
Solution Approach 2:
The patent introduces an intermediary flow cell system that acts as a bridge between DNA synthesis and sequencing. The flow cell contains controlled environments with specific enzymes, buffers, and conditions that facilitate the transition from machine-written DNA to sequencer-ready samples, enabling faster and more efficient processing than direct array-based methods
3Quantity of substance
If selective deposition of nucleotides is implemented, then data density increases, but device complexity increases
Solution Approach 1:
The patent applies segmentation by dividing the flow cell into multiple discrete wells, each capable of independent nucleotide deposition. This segmentation allows parallel processing of multiple data sequences simultaneously, increasing overall data density while managing complexity through modular well structures that can be independently controlled and monitored
Solution Approach 2:
The patent implements universality by designing the flow cell to perform multiple functions: it serves as both the synthesis chamber for selective nucleotide deposition and the preparation chamber for subsequent sequencing. The same flow cell structure accommodates different nucleotide types, enzymes, and buffer conditions, reducing the need for separate specialized components and thereby managing overall device complexity
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 provides faster read-write speeds, longer data retention, reduced power usage, and higher data density by leveraging the flow cell system's ability to selectively deposit and activate nucleotides, overcoming limitations in existing data storage technologies.
Implementation Method 1
each electrode of the plurality of electrodes may be positioned in a corresponding well of the plurality of wells, the plurality of electrodes to effect writing of polynucleotides in the corresponding wells of the plurality of wells
Implementation Method 2
the integrated circuit may drive the selective deposition or activation of selected nucleotides by activating the at least one light source
Implementation Method 3
the integrated circuit to drive the selective deposition or activation of selected nucleotides by applying a change in pH within the corresponding well of the plurality of wells
Data Source
AI summary
An apparatus includes a flow cell body, a plurality of electrodes, an integrated circuit, and an imaging assembly. The flow cell body defines one or more flow channels and a plurality of wells. Each flow channel is configured to receive a flow of fluid. Each well is fluidically coupled with the corresponding flow channel. Each well is configured to contain at least one polynucleotide. Each electrode is positioned in a corresponding well of the plurality of wells. The electrodes are operable to effect writing of polynucleotides in the corresponding wells. The integrated circuit is operable to drive selective deposition or activation of selected nucleotides to attach to polynucleotides in the wells to thereby generate polynucleotides representing machine-written data in the wells. The imaging assembly is operable to capture images indicative of one or more nucleotides in a polynucleotide.