Double-Nanopore DNA Threading for Repeat-Read Sequencing Fidelity
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Solution Overview
Problem
Conventional nanopore sequencing technologies face limitations in accuracy of raw reads and detection of nucleotide modifications, with existing systems often providing a single pass of the molecule through a nanopore, which limits fidelity.
Innovation Solution
A double-nanopore apparatus is employed, where a molecule is pulled back and forth between two nanopores, allowing multiple reads of the same DNA fragment, facilitated by independent control of voltage and pressure differentials across channels, enabling high-fidelity capture and threading.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional single-nanopore sequencing is used, then the device complexity is low, but the measurement precision and reliability are insufficient due to single-pass sequencing
Solution Approach 1:
The system divides the sequencing function into two independent nanopores (first nanopore and second nanopore), each capable of independently capturing and sequencing the same DNA molecule. This segmentation enables multiple independent reads of the same molecule, improving measurement precision through consensus sequencing while distributing the complexity across modular components
Solution Approach 2:
The patent implements a nested structure where two nanopores are integrated within a single membrane substrate, sharing common fluidic channels and control systems. The first and second nanopores are embedded in the same membrane, with shared inlet/outlet channels, creating a compact nested architecture that improves precision without proportionally increasing overall device complexity
2Reliability
If conventional single-nanopore sequencing is used, then the device structure is simple, but the reliability of nucleotide identification is insufficient
Solution Approach 1:
The sequencing function is segmented into two independent nanopore measurement systems that can independently capture and sequence the same DNA molecule. Each nanopore provides an independent measurement, and the combination of multiple independent measurements improves reliability through statistical consensus, reducing errors from single-pass sequencing
Solution Approach 2:
The system employs feedback mechanisms where voltage differentials are dynamically adjusted based on capture events detected by each nanopore. When a DNA molecule is captured by the first nanopore, the system can adjust voltages to facilitate subsequent capture by the second nanopore, creating a coordinated feedback loop that enhances reliability of nucleotide identification
3Measurement precision
If multiple reads of the same DNA fragment are enabled, then the accuracy of nucleotide identification improves, but the device complexity increases due to independent voltage and pressure control
Solution Approach 1:
The system employs universal control mechanisms where a single controller manages both voltage sources and pressure differentials for both nanopores. The same control architecture and software algorithms are used to coordinate both nanopores, enabling multi-functionality that achieves high measurement precision without proportionally increasing control system complexity
Solution Approach 2:
The patent merges the control systems for both nanopores into a unified architecture, where voltage sources and pressure control are coordinated through a single control unit. This consolidation allows the system to manage multiple reads and independent nanopore operations while avoiding the complexity of completely separate control systems, achieving precision through integrated rather than distributed control
4Manufacturing precision
If a double-nanopore apparatus is used for high-fidelity capture, then the threading precision improves to nearly 100%, but the device complexity increases
Solution Approach 1:
Two nanopores are nested within a single membrane substrate with shared fluidic infrastructure. The first and second nanopores are embedded in the same membrane, sharing common inlet and outlet channels, which achieves high threading precision through coordinated dual-nanopore capture while containing device complexity within a compact nested architecture rather than requiring fully independent systems
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 achieves nearly 100% fidelity in threading and sequencing, improving the accuracy of nucleotide identification and detection of modifications by enabling repeat exposure of DNA fragments to the nanopore sensing volume.
Implementation Method 1
a first voltage source configured to apply a first voltage differential in a first vicinity of the first pore between the first channel and the third channel; a second voltage source configured to apply a second voltage differential in a second vicinity of the second pore between the second channel and the third channel
Implementation Method 2
a first pressure differential between a first end of the first channel and a second end of the first channel; and a second pressure differential between a first end of the second channel and a second end of the second channel
Data Source
AI summary
Aspects of the subject disclosure may include, for example, an apparatus comprising: a membrane, wherein the membrane has a first side and a second side, wherein the membrane has a first pore disposed therein, wherein the first pore extends through the membrane from the first side of the membrane to the second side of the membrane, wherein the membrane has a second pore disposed therein, and wherein the second pore extends through the membrane from the first side of the membrane to the second side of the membrane; a first channel disposed on the first side of the membrane, wherein the first channel is along a first longitudinal axis; a second channel disposed on the first side of the membrane, wherein the second channel is along a second longitudinal axis, and wherein the first channel and the second channel are disposed side by side adjacent to each other; a third channel disposed on the second side of the membrane, wherein the third channel is along a third longitudinal axis, wherein the third channel is in first fluid communication with the first channel via the first pore, and wherein the third channel is in second fluid communication with the second channel via the second pore; and one or more sensors disposed at one or more locations to facilitate sequencing of a molecule that extends from the first channel, through the first pore across at least a portion of the third channel, and through the second pore into the second channel. Additional embodiments are disclosed.