Edge Sequencing with Immobilized Translocator
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Solution Overview
Problem
Current nucleic acid sequencing techniques require significant rebuilding of sequences from small reads or repeated runs to achieve single base pair resolution, which is inefficient and not highly accurate.
Innovation Solution
A system and method for nucleic acid sequencing that includes an oxidizing electrode, a reducing electrode, and a dielectric member with a translocating protein attached to its surface, allowing for the controlled translocation of polynucleotide strands with redox labels through a sensing zone where rapid electron transfer occurs, enabling single base pair resolution sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional sequencing techniques are used, then sequencing can be performed, but single base pair resolution cannot be achieved without significant rebuilding of sequences from small reads or repeated runs
Solution Approach 1:
The polynucleotide strand is pre-modified with redox labels on the nucleoside bases before translocation. This preliminary labeling enables direct detection of single base pairs during translocation, eliminating the need for subsequent sequence rebuilding or repeated runs, thus achieving both high resolution and efficiency
Solution Approach 2:
A translocating protein serves as an intermediary that binds to the redox-labeled polynucleotide strand and controls its movement through the sensing zone. The protein mediates between the electrode system and the polynucleotide, enabling controlled translocation at speeds optimized for detection, thereby achieving single base pair resolution without sacrificing sequencing throughput
2Productivity
If the translocation speed is increased to improve productivity, then sequencing efficiency improves, but single base pair resolution is lost
Solution Approach 1:
The translocation speed is optimized by adjusting the electric field parameters (voltage, current) applied across the sensing zone. By controlling the electric field strength and distribution, the system achieves an optimal translocation velocity that maintains single base pair resolution while enabling continuous sequencing at high productivity
Solution Approach 2:
The translocating protein acts as a mediator that regulates the interaction between the polynucleotide strand and the electric field. The protein controls the translocation velocity by binding to the redox-labeled nucleotides and moving them through the sensing zone at a speed that allows detection, thus decoupling translocation speed from detection precision
3Speed
If the distance between electrodes is reduced to at most 10 nm for rapid electron transfer, then electron transfer speed improves, but device fabrication complexity increases
Solution Approach 1:
The patent employs a disposable sensor cartridge containing the pre-fabricated electrode assembly with the precisely controlled 10 nm gap. This disposable approach eliminates the need for complex, reusable fabrication equipment and allows for mass production of standardized sensors with precise electrode spacing, reducing overall device complexity while maintaining rapid electron transfer speeds
Solution Approach 2:
A dielectric member is introduced as an intermediary between the two electrodes to precisely control and maintain the 10 nm separation distance. The dielectric provides mechanical support and electrical insulation, enabling accurate electrode spacing without requiring complex alignment mechanisms, thus simplifying device fabrication while ensuring rapid electron transfer
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 allows for long read sequencing with single base pair resolution, providing a controlled localization and translocation rate, thereby enhancing sequencing fidelity and efficiency.
Implementation Method 1
electron transfer from the reducing electrode, to redox label, and to oxidizing electrode
Implementation Method 2
rapid electron transfer (i.e., nearly simultaneously) from the reducing electrode to redox label to the oxidizing electrode
Implementation Method 3
a dielectric member positioned between the oxidizing electrode and reducing electrode. Characteristically, the dielectric member separates the reducing electrode from the oxidizing electrode by a first distance of at most 10 nm
Data Source
AI summary
The present disclosure relates to systems, devices, and methods for nucleic acid sequencing including polynucleotide strands having a nucleotide(s) modified with a redox label(s) attached thereto or capable of receiving the modified nucleotide(s) with a redox label(s) attached thereto. The systems, devices, and methods include a dielectric member with an attached translocating protein positioned between oxidizing and reducing electrodes. The oxidizing and reducing electrodes generate an electrical field extending to a reaction area where the translocation of the polynucleotide strand through the protein occurs such the modified nucleotide(s) with redox label(s) attached thereto are identified by changes in current flow in the oxidizing and reducing electrodes, wherein the changes identify electron transfer from the reducing electrode, to redox label, and to oxidizing electrode when the modified nucleotide with a redox label covalently bonded to the nucleoside base of the modified nucleotide of the polynucleotide strand is at the reaction area.