Multi-Nanopore Sequencing for DNA Data Storage
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Solution Overview
Problem
Nanopore sequencing for DNA data storage faces challenges such as high costs, slow read and write times, and sensitivity to errors, primarily due to the complexity of current base-calling algorithms and the need for numerous neural networks in commercial devices, which makes it impractical for large-scale implementation.
Innovation Solution
A nucleic acid digital data storage system utilizing a multi-nanopore arrangement with stacked nanopores of varying sizes and translocation speeds, combined with post-processing systems, joint symbol detection, and Error Correction Coding, to improve data retrieval efficiency and reduce error rates.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If nanopore sequencing is used for DNA data storage, then cost-effectiveness and storage density are improved, but error sensitivity and translocation speed control become problematic
Solution Approach 1:
The patent divides the single nanopore sequencing task into multiple parallel nanopores, each handling a portion of the DNA strand. This segmentation allows simultaneous sequencing of multiple DNA segments, improving throughput while distributing the computational burden across multiple simpler detection channels rather than one complex base-calling system
Solution Approach 2:
The patent transitions from two-dimensional (single nanopore, sequential reading) to three-dimensional sequencing architecture by stacking nanopores vertically. This spatial arrangement enables parallel processing of multiple DNA strands through different pore layers, effectively adding a spatial dimension to the sequencing process that improves throughput without proportionally increasing algorithmic complexity
2Productivity
If commercial nanopore sequencing devices are implemented, then data retrieval capability is achieved, but device complexity and computational requirements become impractical
Solution Approach 1:
The patent merges multiple nanopore detection signals into a unified sequencing output by coordinating the readings from stacked nanopores. This consolidation allows the system to process multiple DNA strands simultaneously through a single integrated analysis pipeline, improving data read rate without requiring proportionally more neural networks
Solution Approach 2:
The stacked nanopore configuration creates a multi-functional system where each nanopore layer can process different DNA strands or different regions of the same strand. This universal architecture allows a single device to perform multiple sequencing operations in parallel, achieving high productivity with a standardized, scalable design rather than requiring specialized neural networks for each function
3Measurement precision
If DNA strands are threaded through nanopores, then sequencing capability is enabled, but translocation speed variability causes errors
Solution Approach 1:
The patent implements error correction codes and redundancy mechanisms before the sequencing process to cushion against translocation speed variability. By encoding the DNA data with redundant information in advance, the system can tolerate variations in translocation speed and still accurately reconstruct the original sequence, preventing speed-related errors rather than attempting to eliminate them
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
The system enhances data retrieval speed and accuracy by decoupling detection stages, reducing complexity, and introducing spatial and temporal redundancies, thereby achieving lower error rates and making nanopore sequencing more viable for practical use.
Implementation Method 1
a voltage is applied across the pore which ends up creating an electrical field across pore ends
Implementation Method 2
This voltage (the field itself) creates an ionic current to pass through the pore (movement of charges due to the field)
Implementation Method 3
a strand of DNA molecules passes through a specially designed pore
Implementation Method 4
different current blockade levels and translocation speeds can be measured
Data Source
AI summary
A nucleic acid storage system (100) that uses nanopore sequencing to read data values chemically embedded in oligonucleotides includes a membrane (102), a voltage source (108), and a nucleic acid strand (110). The membrane (102) has a plurality of nanopores (104) that are stacked upon one another in a multi-nanopore arrangement. The voltage source (108) is configured to direct voltage across the plurality of nanopores (104). The nucleic acid strand (110) including the oligonucleotides is threaded through each of the plurality of nanopores (104) within the membrane (102). A separate base signal (118) is generated from the nucleic acid strand (110) being threaded through each of the plurality of nanopores (104), and Recursive Neural Networks can be used to estimate a signal shape for each oligonucleotide. Recurrent Convolutional Neural Networks and noise predictive data detection algorithms can be used based on the estimated signal shapes to sequence the oligonucleotides.