Nanopore Sequencing With Feedback-Controlled Polymer Translocation
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Solution Overview
Problem
Existing nanopore sequencing methods struggle with controlling the rate of polynucleotide analysis, leading to variable translocation rates and challenges in resolving nucleotide composition and spatial relationships within polynucleotides.
Innovation Solution
The use of thin film devices with cis and trans chambers separated by a thin film containing pores or channels, along with controlled electric fields, allows for precise regulation of polymer passage and enzyme binding, enabling controlled translocation rates and sequencing of polynucleotides.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If nanopore sequencing is used to rapidly determine polynucleotide sequence, then productivity is improved, but measurement precision deteriorates due to variable translocation rates
Solution Approach 1:
The patent introduces a motor protein as an intermediary between the polynucleotide and the nanopore. The motor protein binds to the polynucleotide and controls its translocation through the nanopore at a regulated rate, allowing rapid sequencing while maintaining measurement precision through controlled movement
Solution Approach 2:
The patent employs feedback control mechanisms where the translocation rate is monitored and adjusted in real-time. The system detects the position and movement of the polynucleotide through the nanopore and regulates the motor protein activity to maintain optimal translocation speed for accurate nucleotide identification
2Productivity
If high translocation rates are used for rapid sequencing, then productivity is improved, but measurement precision deteriorates due to inability to resolve spatial relationships
Solution Approach 1:
The patent implements dynamic control of the translocation process by using motor proteins that can adjust their movement speed and direction. This allows the system to slow down at critical measurement points to resolve spatial relationships while maintaining overall high productivity through efficient transit between measurement points
3Productivity
If multiple molecules are analyzed simultaneously, then productivity is improved, but measurement precision deteriorates due to lack of single-molecule control
Solution Approach 1:
The patent divides the analysis into independent single-molecule events by using the nanopore to sequentially process individual polynucleotide molecules. Each molecule is captured, analyzed, and released in discrete steps, allowing high throughput through repeated cycles while maintaining the measurement precision of single-molecule analysis
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 precise control over the analysis rate of polymers, enhancing the resolution of nucleotide sequencing and spatial relationships, facilitating accurate determination of polynucleotide sequences.
Implementation Method 1
the polynucleotide partially blocked the nanopore aperture, resulting in a transient decrease of ionic current
Implementation Method 2
by using an electric field to force single stranded RNA and DNA molecules through a 1.5 nanometer diameter nanopore aperture
Data Source
AI summary
Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.