Nanopore Polynucleotide Recapture for Linearized Feature Mapping
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Solution Overview
Problem
Existing nanopore devices face challenges in achieving consistent linearization of translocating molecules, reducing molecular fluctuations that introduce random error, and performing accurate genomic distance calibration during molecular feature mapping of long, individual dsDNA strands in heterogeneous samples.
Innovation Solution
A method for partially or fully recapturing a polynucleotide in a nanopore device involves applying specific voltages to translocate and recapture the polynucleotide through a first pore, utilizing a geometrically constrained fluidic volume with electrodes, and detecting sensor currents to achieve linearization and accurate genomic distance calibration.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If a nanopore device is used to translocate polynucleotides for molecular feature mapping, then the footprint and cost are reduced, but molecular fluctuations introduce random error and consistent linearization is difficult to achieve
Solution Approach 1:
The patent applies a preliminary action by using a motor protein to actively translocate the polynucleotide through the nanopore before measurement. This controlled translocation ensures consistent linearization of the molecule as it passes through the pore, eliminating the random fluctuations that occur with passive diffusion-based methods. The motor protein prepares the molecule in a controlled state, ensuring reliable and repeatable measurements.
2Device complexity
If passive diffusion is used to translocate polynucleotides through nanopores, then the device structure is simple, but consistent linearization of translocating molecules cannot be achieved
Solution Approach 1:
The patent introduces a motor protein as an intermediary between the power source and the nanopore. This motor protein acts as a mediator that converts chemical energy into controlled mechanical translocation, ensuring that the polynucleotide passes through the pore in a consistent, linearized manner. The intermediary resolves the contradiction by providing controlled translocation without requiring complex device structures.
3Measurement precision
If multiple scans of the same polynucleotide are performed to reduce random error, then measurement accuracy improves, but translocation time increases
Solution Approach 1:
The motor protein performs preliminary action by actively translocating the polynucleotide through the nanopore at a controlled pace, allowing multiple scans to be performed within a reasonable time frame. This active translocation method is more efficient than passive diffusion, enabling repeated measurements without excessive time loss.
Solution Approach 2:
The patent employs periodic action by performing multiple scans of the same polynucleotide through the nanopore. The motor protein repeatedly translocates the molecule back and forth, allowing multiple measurements to be taken from the same sample. This periodic scanning approach improves measurement accuracy through averaging while managing the total time required.
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 method enhances molecular linearization and reduces random errors, enabling precise detection of polynucleotide features with improved accuracy and efficiency.
Implementation Method 1
A first voltage captures and translocates the polynucleotide from a cis-chamber in a first direction through the pore and into a trans-chamber
Implementation Method 2
measuring modulations in the ionic current arising when a double stranded DNA (dsDNA) is electrically driven through a solid-state nanopore (ss-nanopore)
Data Source
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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.