Modified Nanopore Sensing for Heteropolymeric DNA Sequencing

Solution Overview

Problem

Current DNA sequencing technologies are slow and expensive due to reliance on amplification techniques and high quantities of specialist chemicals, while stochastic sensing has the potential to provide rapid and cost-effective sequencing but lacks methods for sequencing heteropolymeric nucleic acid sequences.

Innovation Solution

A method involving a transmembrane pore with modified sites capable of discriminating between different nucleotides, allowing for the sequencing of heteropolymeric nucleic acid sequences by passing the target sequence through the pore and measuring current fluctuations during nucleotide interactions.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Quantity of substance

If amplification techniques are used for DNA sequencing, then the quantity of nucleic acid signal is increased, but the sequencing speed decreases and cost increases

Engineering Contradiction:

Improvequantity of nucleic acid signalVSAvoidsequencing speed

Core Design Contradiction:

Quantity of substanceVSProductivity

Solution Approach 1:

The invention extracts and detects individual nucleotides directly from the heteropolymeric sequence without performing amplification. By using a nanopore to translocate single-stranded nucleic acid and detect nucleotides one at a time through current blockage patterns, the method eliminates the amplification step entirely, thereby maintaining signal quantity sufficient for detection while dramatically improving sequencing speed and reducing reagent consumption.

Inventive Principle:

Principle #2Taking out (Extraction)

2Quantity of substance

If amplification techniques are used for DNA sequencing, then the quantity of nucleic acid signal is increased, but the cost increases due to specialist chemicals

Engineering Contradiction:

Improvequantity of nucleic acid signalVSAvoidsequencing cost

Core Design Contradiction:

Quantity of substanceVSEase of manufacture

Solution Approach 1:

The invention extracts and detects individual nucleotides directly from the heteropolymeric sequence without performing amplification. By using a nanopore to translocate single-stranded nucleic acid and detect nucleotides one at a time through current blockage patterns, the method eliminates the amplification step entirely, thereby maintaining signal quantity sufficient for detection while dramatically improving sequencing speed and reducing reagent consumption.

Inventive Principle:

Principle #2Taking out (Extraction)

3Quantity of substance

If a pore is used for stochastic sensing of nucleic acids, then the quantity of reagents required is reduced, but the ability to sequence heteropolymeric sequences is lost

Engineering Contradiction:

Improvequantity of reagentsVSAvoidnucleotide discrimination ability

Core Design Contradiction:

Quantity of substanceVSMeasurement precision

Solution Approach 1:

The invention applies local quality by engineering specific recognition sites within the nanopore structure that can distinguish between different nucleotide bases (A, T, G, C). The pore contains multiple binding sites with specific chemical properties (charged residues, hydrophobic regions) that create distinctive current blockage patterns for each nucleotide type, enabling precise discrimination of heteropolymeric sequences while maintaining low reagent consumption through stochastic sensing.

Inventive Principle:

Principle #3Local quality

4Device complexity

If a single pore is used for stochastic sensing, then the device complexity is reduced, but the nucleotide recognition precision is insufficient

Engineering Contradiction:

Improvepore system complexityVSAvoidnucleotide discrimination accuracy

Core Design Contradiction:

Device complexityVSMeasurement precision

Solution Approach 1:

The invention applies local quality by engineering specific recognition sites within the nanopore structure that can distinguish between different nucleotide bases (A, T, G, C). The pore contains multiple binding sites with specific chemical properties (charged residues, hydrophobic regions) that create distinctive current blockage patterns for each nucleotide type, enabling precise discrimination of heteropolymeric sequences while maintaining low reagent consumption through stochastic sensing.

Inventive Principle:

Principle #3Local quality

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 enables efficient sequencing of heteropolymeric nucleic acid sequences by accurately determining the sequence through stochastic sensing, improving nucleotide recognition and reducing the need for large volumes of reagents.

Implementation Method 1

measuring voltage-driven ionic transport through the pore in the presence of analyte molecules

Methodology Applied

Scientific EffectIonic transport: Conduction (electrical)

Implementation Method 2

The frequency of occurrence of fluctuations in the current reveals the concentration of an analyte that binds within the pore. The identity of an analyte is revealed through its distinctive current signature, notably the duration and extent of current block

Methodology Applied

Scientific EffectCurrent block: Electrical Resistance

Data Source

PatentUS20250215490A1Method for sequencing a heteropolymeric target nucleic acid sequence

Publication Date: 2025.07.03 OXFORD UNIVERSITY INNOVATION LTD

AI summary

The invention relates to a method for sequencing a heteropolymeric target nucleic acid sequence that involves stochastic sensing. The invention also relates to a method for improving a pore for sequencing a target nucleic acid sequence by modifying one or more sites in the pore.