Nanopore DNA Data Reading with Controlled Polymer Translocation
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Solution Overview
Problem
Current DNA data storage methods using nanopore devices face challenges in achieving high-quality, reliable, and scalable DNA data reading due to difficulties in detecting small changes in current or capacitance, and the speed at which DNA moves through nanopores, leading to inaccuracies and errors in reading long DNA sequences.
Innovation Solution
A nanofluidic system with nanopore readers that synthesizes and reads long DNA strands by using a nanochip with separate reaction compartments and nanopores, allowing for controlled movement of DNA molecules and enzymes, and employing capacitive variance measurement for rapid and accurate sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If nanopore devices are used to read DNA data, then data storage density is improved, but measurement precision deteriorates due to difficulty in detecting small changes in current or capacitance
Solution Approach 1:
The patent introduces an intermediary mechanism by using nanopore devices that convert DNA sequence information into measurable electrical signals (current or capacitance changes). The nanopore acts as a mediator between the DNA molecule and the detection system, enabling indirect measurement of DNA sequences through electrical property changes as DNA passes through the nanopore.
Solution Approach 2:
The patent employs parameter changes by measuring variations in electrical properties (current or capacitance) that occur when DNA sequences pass through the nanopore. Different DNA sequences cause different parameter changes in the electrical signal, allowing discrimination and identification of the stored data through these parameter variations.
2Productivity
If DNA moves through nanopores at high speed, then productivity is improved, but measurement precision deteriorates due to inability to accurately read long DNA sequences
Solution Approach 1:
The patent implements feedback mechanisms by continuously monitoring the electrical signals (current or capacitance) as DNA passes through the nanopore and using this information to track and analyze the DNA sequence in real-time. The system provides feedback on the position and identity of nucleotides as they translocate through the nanopore, enabling accurate reading despite high-speed movement.
3Ease of manufacture
If conventional DNA storage methods are used, then ease of manufacture is improved, but reliability deteriorates due to data corruption after prolonged storage
Solution Approach 1:
The patent replaces conventional mechanical/digital storage systems with a biochemical storage system using DNA molecules. Instead of storing data on physical media like hard drives or tapes, the invention encodes data directly into the molecular structure of DNA sequences, which are then stored in a biological medium, fundamentally substituting the storage mechanism to achieve long-term stability.
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 enables high-density data storage with improved accuracy and speed, allowing for the reliable reading of long DNA sequences and the storage of data in a binary code format, overcoming previous limitations of existing methods.
Implementation Method 1
Measurements based on changes in capacitance have been proposed but are not commercial; the changes are in the range of pico/fempto/atto-farads.
Implementation Method 2
typically a nanopore is used in a fluid-filled cell to read the DNA data by measuring a change in current as the DNA passes through the nanopore, which are typically in the range of nano-amps
Implementation Method 3
one or more electrodes to draw the electrically charged polymer into the chamber
Implementation Method 4
A nanofluidic system with nanopore readers that synthesizes and reads long DNA strands by using a nanochip with separate reaction compartments and nanopores, allowing for controlled movement of DNA molecules and enzymes
Data Source
AI summary
The disclosure provides novel DNA sequences, synthesized in the 3′ to 5′ direction using topoisomerase, comprising a sequence of oligomeric cassettes, wherein each oligomeric cassette comprises a topoisomerase recognition sequence and an informational sequence, and methods for making and using the same.