Nanopore DNA Encoding via Voltage-Controlled Ion Migration
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Solution Overview
Problem
There is a need for efficient and accurate nanopore-based information encoding and storage methods, as existing technologies face challenges in archiving, maintenance, and retrieval of complex digital media, with nucleic acids like DNA offering high-density encoding capabilities but requiring improved encoding and storage solutions.
Innovation Solution
A scalable nanopore-based information encoding method using an enzymatic approach, involving an encoding unit with an enzyme, single-stranded DNA, and a nanopore within a lipid bilayer, where a voltage is applied to facilitate the migration of activating ions and catalyze nucleotide addition, enabling DNA synthesis and information encoding.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If DNA is used for information storage, then high-density encoding capability is achieved, but challenges in archiving, maintenance, and retrieval remain
Solution Approach 1:
The patent segments the encoding process into distinct functional modules: a nanopore for ion flux control, an enzyme (DNA polymerase) for catalysis, and a template strand for information encoding. This segmentation allows each component to be optimized independently while working together to achieve reliable high-density storage
Solution Approach 2:
The patent introduces activating ions (such as Mg2+ or Mn2+) as intermediaries that migrate through the nanopore to activate the enzyme. These ions serve as a controllable mediator between the applied voltage and the DNA synthesis reaction, enabling precise control over the encoding process while maintaining system reliability
2Productivity
If nanopore-based encoding is implemented, then scalable information storage is achieved, but efficiency and accuracy of encoding need improvement
Solution Approach 1:
The patent utilizes parameter changes in the form of applied voltage to control ion flux through the nanopore. By modulating the voltage, the system can control the concentration and flux of activating ions, thereby regulating enzyme activity and nucleotide incorporation rate. This enables dynamic adjustment of encoding speed and accuracy to optimize both throughput and precision
Solution Approach 2:
The patent implements continuous DNA synthesis by maintaining a steady flux of activating ions through the nanopore. The enzyme remains continuously active as long as ions are supplied, allowing uninterrupted nucleotide addition to the template strand. This continuous action increases encoding throughput while maintaining accuracy through consistent reaction conditions
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 method enables efficient and accurate DNA synthesis and information encoding, allowing for high-throughput nanopore measurement and storage of data in a scalable and reliable manner, addressing the challenges of complex digital media management.
Implementation Method 1
applying a voltage across the lipid bilayer via an electrode wherein the electrode can modulate the voltage across the lipid bilayer to cause migration of or influx of activating ions from the second reservoir through the nanopore and through the lipid membrane and into the first reservoir
Implementation Method 2
the enzyme is activated in the presence of the activating ions and catalyzes addition of one or more nucleotides present in the first reservoir to the single-stranded DNA
Data Source
AI summary
This invention provides methods and systems of DNA synthesis including providing an encoding unit comprising an enzyme, a single-stranded DNA (ssDNA) and a nanopore, providing a lipid bilayer having on opposite sides a cis and a trans reservoir each having a different buffer composition, wherein the nanopore is within the lipid bilayer and the enzyme and the ssDNA are in the cis reservoir, providing an electrode over the lipid bilayer wherein the electrode can modulate voltage across the lipid bilayer, wherein the enzyme catalyzes DNA synthesis in response to the voltage.