DNA Data Storage Electrode Array for Scalable Polynucleotide Synthesis
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Solution Overview
Problem
Existing biomolecule-based information storage systems lack scalability, automation, and efficiency for generating biomolecules, necessitating a need for larger capacity and more stable storage solutions.
Innovation Solution
The development of devices and methods utilizing a solid support with addressable loci and electrodes for polynucleotide synthesis, enabling high-density polynucleotide storage and synthesis through localized electrochemical control and digital fluidics, reducing cycle times and reagent usage.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If traditional biomolecule-based information storage systems are used, then storage capacity is limited, but increasing storage capacity requires more complex and less scalable systems
Solution Approach 1:
The system divides the storage surface into discrete addressable loci (e.g., 100 x 100 micrometer squares) that can be independently addressed and controlled. Each locus can hold polynucleotides, and the grid structure enables scalable expansion without increasing overall system complexity. This segmentation allows the system to achieve high storage capacity while maintaining manageable complexity through modular addressing.
Solution Approach 2:
The patent transitions from linear or simple 2D storage arrangements to a structured 2D grid system with precise addressing capabilities. By organizing loci in a dimensional grid (e.g., 1000 x 1000 addressable locations), the system exponentially increases storage capacity while maintaining systematic control. This dimensional organization enables scalable expansion by simply adding more grid positions rather than complicating the control architecture.
2Productivity
If manual or less automated methods are used for polynucleotide synthesis, then system simplicity is maintained, but productivity and synthesis efficiency are low
Solution Approach 1:
The system employs electrochemical generation of reagents directly at the addressable loci, where electrical potentials applied to electrodes locally generate cleavage and deprotection reagents on-demand. This eliminates the need for complex automated reagent delivery systems while maintaining high productivity. The synthesis process serves itself by using electricity (a simple utility) to generate the necessary chemical reagents at the point of use, dramatically simplifying automation requirements.
Solution Approach 2:
The patent replaces mechanical reagent delivery systems (pumps, valves, fluid handling) with electrochemical generation at the locus level. Instead of mechanically transporting reagents to each location, the system uses electrical potentials to generate reagents in-situ through electrochemical reactions. This substitution dramatically reduces the complexity of automated fluid handling while maintaining high synthesis productivity and precision.
3Loss of substance
If conventional synthesis methods are used, then reagent usage is high, but reducing reagent usage requires more precise localized control
Solution Approach 1:
The system applies electrical potentials to specific electrodes corresponding to individual addressable loci, generating reagents only where needed. Each locus receives reagents locally through electrochemical generation at its specific position, rather than flooding the entire surface. This localized reagent generation dramatically reduces overall reagent consumption while requiring precise control of electrical potentials at each electrode location, which is achieved through the addressable electrode array.
Solution Approach 2:
The electrodes serve as intermediaries between the electrical control system and the chemical synthesis process. Electrical potentials applied to electrodes generate reagents in-situ at each addressable locus through electrochemical reactions. This intermediary mechanism enables precise localized reagent generation without requiring complex fluid delivery systems, reducing reagent waste while maintaining the precision needed for selective polynucleotide synthesis at specific loci.
4Productivity
If longer synthesis cycles are used, then manufacturing precision can be maintained, but productivity and throughput decrease
Solution Approach 1:
The system enables continuous synthesis operations by rapidly cycling through the steps of nucleoside coupling, cleavage, and deprotection at each addressable locus. Electrical potentials are applied in rapid succession to generate reagents and drive reactions without long idle periods. The electrochemical generation of reagents on-demand eliminates waiting times for reagent delivery and preparation, maintaining continuous productive action while ensuring each synthesis step completes with sufficient precision through controlled potential application.
Solution Approach 2:
The synthesis process uses periodic application of electrical potentials to drive sequential reactions at each locus. Electrical pulses are applied in a repeating cycle: coupling potential, cleavage potential, deprotection potential, then repeat for the next nucleoside. This periodic electrochemical driving enables rapid cycling through synthesis steps, increasing throughput while maintaining precision through controlled pulse timing and potential magnitudes that ensure complete reaction at each stage.
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 enhances storage capacity and efficiency by allowing for higher polynucleotide densities and reduced synthesis times, providing a stable and scalable solution for biomolecule-based information storage.
Implementation Method 1
The bottom electrode is in addressable communication with the synthesis surface
Implementation Method 2
the at least one sidewall electrode is 50 nm to 200 nm from the bottom region
Data Source
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AI summary
Provided herein are compositions, devices, systems and methods for generation and use of biomolecule-based information for storage. Further provided are devices comprising addressable electrodes controlling polynucleotide synthesis (deprotection, extension, or cleavage, etc.) The compositions, devices, systems and methods described herein provide improved storage, density, and retrieval of biomolecule-based information.