Single-Chain Msp Nanopores for Rapid DNA Sequencing

Solution Overview

Problem

Existing DNA sequencing technologies require substantial amounts of DNA and several lengthy steps to construct just several tens of bases out of the full sequence, which is expensive and time-consuming, especially for sequencing mammalian genomes.

Innovation Solution

A nucleic acid encoding a single-chain Mycobacterium smegmatis porin (Msp) is developed, comprising different Msp monomer sequences linked by an amino acid linker, which can be expressed in a mutant bacterial strain and used to sequence DNA through a nanopore system.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Productivity

If traditional DNA sequencing technologies are used, then sequencing can be performed, but the process requires substantial amounts of DNA and several lengthy steps making it time-consuming and expensive

Engineering Contradiction:

Improvesequencing speedVSAvoidtime required for sequencing

Core Design Contradiction:

ProductivityVSLoss of time

Solution Approach 1:

The patent employs Msp porins, which are protein structures forming nanopores with specific geometries (vestibule and constriction zone), to enable direct translocation of DNA molecules through the pore under an electric field, eliminating the need for traditional multi-step sequencing preparation and assembly processes

Inventive Principle:

Principle #31Porous materials

Solution Approach 2:

The patent extracts and utilizes only the essential pore-forming functionality of the Msp porin protein, creating a simplified system where DNA translocation occurs directly through the nanopore without requiring complex enzymatic reactions, fragment assembly, or substantial DNA amplification steps

Inventive Principle:

Principle #2Taking out (Extraction)

2Productivity

If traditional DNA sequencing technologies are used, then sequencing can be performed, but it requires substantial amounts of DNA and multiple lengthy steps

Engineering Contradiction:

Improvesequencing efficiencyVSAvoidnumber of sequencing steps

Core Design Contradiction:

ProductivityVSDevice complexity

Solution Approach 1:

The patent extracts and utilizes only the essential pore-forming functionality of the Msp porin protein, creating a simplified system where DNA translocation occurs directly through the nanopore without requiring complex enzymatic reactions, fragment assembly, or substantial DNA amplification steps

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent employs Msp porins, which are protein structures forming nanopores with specific geometries (vestibule and constriction zone), to enable direct translocation of DNA molecules through the pore under an electric field, eliminating the need for traditional multi-step sequencing preparation and assembly processes

Inventive Principle:

Principle #31Porous materials

3Productivity

If traditional DNA sequencing technologies are used, then sequencing can be performed, but it is expensive especially for mammalian genomes

Engineering Contradiction:

Improvesequencing throughputVSAvoidDNA amount required

Core Design Contradiction:

ProductivityVSQuantity of substance

Solution Approach 1:

The patent modifies parameters of the porin structure (amino acid composition, vestibule size, constriction zone dimensions) to optimize DNA translocation efficiency and conductance, enabling effective sequencing with smaller DNA amounts and shorter translocation times

Inventive Principle:

Principle #35Parameter changes

Solution Approach 2:

The patent employs Msp porins, which are protein structures forming nanopores with specific geometries (vestibule and constriction zone), to enable direct translocation of DNA molecules through the pore under an electric field, eliminating the need for traditional multi-step sequencing preparation and assembly processes

Inventive Principle:

Principle #31Porous materials

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 system enables efficient and cost-effective sequencing of DNA by translocating nucleic acids through a nanopore tunnel, allowing for rapid and accurate determination of nucleotide sequences.

Implementation Method 1

applying an electric field to a Mycobacterium smegmatis porin (Msp) porin having a vestibule and a constriction zone that define a tunnel

Methodology Applied

Scientific EffectElectric field: Electric Field

Implementation Method 2

wherein the Msp porin is positioned between a first conductive liquid medium and a second conductive liquid medium

Methodology Applied

Scientific EffectElectrical conduction: Conduction (electrical)

Data Source

PatentEP3686602B1Msp nanopores

Publication Date: 2026.05.20 THE UAB RESEARCH FOUNDATION INC

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Figure 3(a)~3(b)

AI summary

Provided herein are Mycobacterium smegmatis porin nanopores, systems that comprise these nanopores, and methods of using and making these nanopores. Such nanopores may be wild-type MspA porins, mutant MspA porins, wild-type MspA paralog porins, wild-type MspA homolog porins, mutant MspA paralog porins, mutant MspA homolog porins, or single-chain Msp porins. Also provided are bacterial strains capable of inducible Msp porin expression.