Nanopore Polynucleotide Scanning With Voltage-Pulse Recapture Control
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Solution Overview
Problem
Existing methods for precise mapping of molecular motifs along long, individual dsDNA strands in heterogeneous samples face challenges such as inconsistent linearization, molecular fluctuations leading to random errors, and the need for accurate genomic distance calibration in nanopore-based sequencing.
Innovation Solution
An automated method for mapping and sequencing polynucleotides using a nanopore device with multiple pores and controlled voltage adjustments to recapture and linearize polynucleotides, allowing for precise feature detection and genomic distance calibration through controlled translocation and recapture.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Speed
If voltage is applied to translocate polynucleotide through nanopore, then translocation speed increases, but mapping precision deteriorates due to molecular fluctuations
Solution Approach 1:
The system applies periodic voltage pulses to translocate the polynucleotide through the nanopore in discrete steps rather than continuous flow. This allows the molecule to pause at regular intervals, enabling multiple measurements at each position and reducing the impact of molecular fluctuations on mapping precision.
Solution Approach 2:
The system uses real-time current measurements from the nanopore to provide feedback on polynucleotide position and orientation. This feedback is used to dynamically adjust voltage application and trigger recapture events when positioning accuracy thresholds are met, ensuring high mapping precision while maintaining efficient translocation.
2Productivity
If polynucleotide translocation is performed in heterogeneous samples, then throughput increases, but mapping consistency deteriorates due to inconsistent linearization
Solution Approach 1:
The system performs preliminary actions including applying voltages to capture and linearize polynucleotides before they enter the nanopore, and pre-positioning them in optimal orientations. This ensures that even in heterogeneous samples, all molecules are properly prepared for consistent mapping, maintaining linearization consistency across diverse sample types.
Solution Approach 2:
The system dynamically changes voltage parameters (magnitude, polarity, duration) based on detected polynucleotide states and sample characteristics. This allows optimization of linearization and translocation conditions for different molecule types and sizes, ensuring consistent mapping performance across heterogeneous samples while maintaining high throughput.
3Measurement precision
If recapture and retranslocation is performed to improve mapping accuracy, then measurement precision increases, but processing time increases
Solution Approach 1:
The system uses the nanopore current measurements themselves to trigger recapture decisions, making the system self-regulating. When measurement precision thresholds are met, the system automatically proceeds without unnecessary recaptures. When thresholds are not met, recapture is automatically triggered, eliminating the need for external intervention and optimizing the balance between accuracy and time.
Solution Approach 2:
The system replaces mechanical manipulation with electrical field control for recapture and repositioning. By using voltage pulses to electrically guide and recapture polynucleotides, the system achieves faster and more precise control compared to mechanical methods, reducing processing time while maintaining or improving mapping accuracy.
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
Enhances the accuracy and efficiency of polynucleotide mapping and sequencing by reducing random errors and enabling precise genomic distance calibration, facilitating the detection of molecular features with improved consistency.
Implementation Method 1
a sensor configured to provide: a voltage between the electrode within the first fluidic volume and the electrode within the chamber, and a current measurement that detects capture and translocation of the polynucleotide into and through the first pore
Implementation Method 2
applying a first voltage to capture and translocate the polynucleotide from the chamber in a first direction through the first pore and into the first fluidic volume
Data Source
AI summary
The present disclosure provides an automated method of mapping one or more features of a target polynucleotide. Also provided in the present disclosure are automated methods for sequencing a polynucleotide sequence. Also provided in the present disclosure are methods of extended recapture of a polynucleotide in a nanopore device. Also provided in the present disclosure are devices and systems for carrying out the methods of the present disclosure.