Membrane-Coupled Analyte Detection for Higher Nanopore Capture
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Solution Overview
Problem
Existing nucleic acid sequencing technologies are slow and expensive due to reliance on amplification techniques and require high quantities of fluorescent chemicals, and nanopore detection is limited by the concentration of analytes, especially in samples like cancer cell DNA, leading to inefficient sequencing.
Innovation Solution
Coupling the analyte to a membrane where the detector is present, allowing for increased interaction frequency and concentration of analytes, thereby enhancing nanopore sequencing efficiency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If nanopore detection is used for DNA sequencing, then direct electrical detection is achieved, but the capture frequency is limited by low analyte concentration
Solution Approach 1:
The invention transitions from three-dimensional bulk solution detection to two-dimensional surface-confined detection by immobilizing DNA analytes on a surface. This dimensional reduction increases the effective concentration and residence time of analytes near the nanopore, thereby enhancing capture frequency and sequencing throughput without requiring higher bulk concentrations.
Solution Approach 2:
The DNA analytes are pre-immobilized on the surface before the sequencing process begins. This preliminary action ensures that analytes are already positioned in close proximity to the nanopore when the measurement starts, eliminating the need for continuous diffusion from bulk solution and maximizing capture frequency from the outset.
2Measurement precision
If amplification techniques are used to increase analyte quantity, then detection sensitivity improves, but sequencing speed decreases and cost increases
Solution Approach 1:
Instead of using biological amplification techniques that replicate DNA sequences, the invention creates multiple copies of the detection interface by implementing an array of nanopores in the membrane. Each nanopore can independently detect and sequence DNA molecules, providing parallel detection capability that maintains sensitivity while dramatically increasing throughput and speed.
Solution Approach 2:
The detection system is divided into multiple independent nanopore units arranged in an array. Each nanopore operates as an independent detection channel, allowing simultaneous sequencing of multiple DNA molecules. This segmentation enables parallel processing that increases overall productivity without compromising the detection sensitivity of individual pores.
3Illumination intensity
If high quantities of fluorescent chemicals are used for signal detection, then signal strength increases, but cost and complexity increase
Solution Approach 1:
The invention replaces the optical/chemical detection system (fluorescent chemicals and illumination) with an electrical detection system based on ionic current measurements through the nanopore. This substitution eliminates the need for fluorescent chemicals and complex optical instrumentation, reducing both cost and device complexity while maintaining detection capability through direct electrical signal measurement.
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 method significantly reduces the required amount of analyte by several orders of magnitude, increasing capture frequency by ~4 orders of magnitude and improving sequencing duty cycle, making it suitable for ultra-sensitive detection and diagnostic applications.
Implementation Method 1
When a potential is applied across a nanopore, there is a drop in the current flow when an analyte, such as a nucleotide, resides transiently in the barrel for a certain period of time. Nanopore detection of the analyte gives a current blockade of known signature and duration.
Implementation Method 2
Capture of a 92-nucleotide synthetic piece of single strand DNA (ssDNA) by a protein nanopore (hemolysin) was determined to be at a frequency of 3.0±0.2 s−1 uM−1
Data Source
AI summary
The invention relates to a new method of determining the presence, absence or characteristics of an analyte. The analyte is coupled to a membrane. The invention also relates to nucleic acid sequencing.