Nanopore Mass Spectrometry Sequencing Single Molecules
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Solution Overview
Problem
Conventional DNA sequencing methods require multiple copies of the target sequence and are limited by the rate of chemical reactions and the cost of reagents, making them inefficient for high-speed and low-cost sequencing.
Innovation Solution
A method involving passing a polymer through a non-naturally occurring pore with a diameter of less than 1 micrometer, where the polymer is cleaved using a laser or electric field, and the fragments are analyzed using mass spectrometry to determine the sequence.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If conventional DNA sequencing methods are used, then sequencing can be performed with existing technology, but multiple copies of the target sequence are required and the process is limited by chemical reaction rates and reagent costs
Solution Approach 1:
The patent replaces conventional chemical sequencing methods with a physical approach using mass spectrometry. A single polymer molecule is passed through a nanopore and sequentially cleaved by controlled fragmentation, with each fragment detected by mass spectrometry to determine its identity. This physical measurement approach eliminates the need for multiple copies and chemical amplification reactions.
Solution Approach 2:
The patent changes the detection parameter from optical/chemical signals requiring multiple copies to mass-to-charge ratio measurements that can identify single molecules. By using mass spectrometry to measure the precise mass of sequentially released fragments, the system can determine the polymer sequence from a single molecule, fundamentally changing how sequencing information is extracted.
2Productivity
If conventional sequencing methods are used, then chemical reactions can be performed, but the cost of reagents and labor is high
Solution Approach 1:
The patent replaces costly chemical reagents and multiple reaction steps with a physical nanopore-based system. The nanopore provides a confined space where a single polymer molecule can be sequentially fragmented and detected, eliminating the need for expensive enzymes, dNTPs, and other chemical reagents required by conventional sequencing methods.
Solution Approach 2:
The nanopore system inherently provides the sequencing function through physical principles rather than requiring external chemical assistance. The confined pore structure naturally guides the polymer through sequential fragmentation, and the mass spectrometer automatically detects each fragment's mass, reducing the need for external reagents and manual intervention.
3Quantity of substance
If single-molecule analysis is performed, then multiple copies are not needed, but the detection of single ions requires highly sensitive mass spectrometry
Solution Approach 1:
The patent uses a nanopore with dimensions specifically optimized for single-molecule analysis. The pore's confined space creates a localized environment where a single polymer molecule can be held and sequentially fragmented, concentrating the signal from individual fragments. This local confinement enhances the detectability of single ions by the mass spectrometer.
Solution Approach 2:
The nanopore acts as an intermediary structure that facilitates single-molecule analysis. It provides a confined environment that enhances the signal from single ions by preventing diffusion and concentrating fragments in a small detection volume, thereby improving the sensitivity required for detecting single molecules without requiring multiple copies.
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 fast and cost-effective sequencing of polymers like DNA by efficiently cleaving and analyzing single molecules, improving sequencing speed and reducing the need for multiple copies and costly reagents.
Implementation Method 1
cleaving the polymer in sequence to produce one or more fragments, wherein the polymer is cleaved using a laser or an electric field
Implementation Method 2
cleaving the polymer in sequence to produce one or more fragments, wherein the polymer is cleaved using a laser or an electric field
Implementation Method 3
a fragment is ionized to form a single ion
Implementation Method 4
obtaining a mass spectrograph based on the signal, indicative of the single ion
Implementation Method 5
an electric field or a pressure difference urges the polymer through the pore
Implementation Method 6
an electric field or a pressure difference urges the polymer through the pore
Data Source
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AI summary
The present invention generally relates to mass spectrometry and related techniques, and in some cases, to determining single species using mass spectrometry. In certain instances, polymers such as DNA or RNA can also be sequenced. Certain embodiments of the invention relate to passing a polymer, such as DNA, RNA, a protein, a polypeptide, a polysaccharide, etc., through a pore and cleaving the polymer in sequence. For instance, the polymer may be cleaved using a laser or an electric field. In some embodiments, a property of at least one subunit of a polymer is determined using mass spectrometry. In some embodiments, a single ion (which may be a subunit of a polymer, or an ion based on another species) can be isolated in a mass spectrometer and a signal generated from the single ion.