Magnetic Bead Substrate Enrichment via Interference Probe

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Solution Overview

Problem

Current methods for isolating and analyzing small concentrations of compounds, such as DNA, RNA, and proteins, face challenges in efficiently enriching substrates bound to analytes, particularly in separating amplified substrates from unamplified ones to enhance detection sensitivity and sequencing accuracy.

Innovation Solution

The method involves emulsion amplification of substrates with target polynucleotides, followed by the application of an interference probe in a breaking solution to separate amplified substrates from unamplified ones, utilizing surfactants and magnetic separation techniques to enrich the amplified substrates for loading onto biosensors.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Quantity of substance

If emulsion amplification is performed to enrich substrates bound to target polynucleotides, then the concentration of amplified substrates increases, but unamplified substrates without target sequences remain mixed in the dispersion making separation difficult

Engineering Contradiction:

Improveconcentration of amplified substratesVSAvoidpurity of substrate enrichment

Core Design Contradiction:

Quantity of substanceVSReliability

Solution Approach 1:

A magnetic separation bead is introduced as an intermediary component that specifically binds to amplified substrates containing target polynucleotides. This magnetic bead acts as a mediator between the amplified substrates and the magnetic field, enabling selective separation of enriched substrates from unamplified ones in the dispersion without compromising the concentration achieved through emulsion amplification

Inventive Principle:

Principle #24Intermediary (Mediator)

2Measurement precision

If separation techniques are applied to isolate amplified substrates from unamplified ones, then detection sensitivity improves, but the complexity of the isolation process increases

Engineering Contradiction:

Improvedetection sensitivityVSAvoidcomplexity of isolation process

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The isolation process replaces complex mechanical separation methods with a magnetic field-based system. Magnetic separation beads coupled with target polynucleotides allow amplified substrates to be separated from unamplified ones through simple magnetic field application, significantly reducing procedural complexity while maintaining high detection sensitivity through effective enrichment

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

3Measurement precision

If substrates are bound to compounds for analysis, then trace amounts of chemical agents can be detected, but the time required for binding and isolation increases

Engineering Contradiction:

Improvedetection of trace amountsVSAvoidtime for binding and isolation

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The method performs preliminary emulsion amplification of target polynucleotides bound to substrates before the actual detection step. By pre-enriching the target sequences through amplification within the emulsion, the system reduces the time required for subsequent binding and isolation steps, as the target compounds are already concentrated and ready for rapid magnetic separation and analysis

Inventive Principle:

Principle #10Preliminary action

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 significantly enriches amplified substrates, improving the sensitivity of detection and sequencing by isolating and loading enriched substrates onto biosensors, thereby enhancing the analysis of target polynucleotides.

Implementation Method 1

amplified substrates are conjugated with copies of a target sequence through emulsion amplification

Methodology Applied

Scientific EffectEmulsion amplification: Emulsion

Implementation Method 2

interference probes that limit binding of unbound template polynucleotides to unamplified substrates

Methodology Applied

Scientific EffectHybridization: Absorption (physical)

Implementation Method 3

The amplified substrates are separated from the unamplified substrates, thus enriching the amplified substrates

Methodology Applied

Scientific EffectMagnetic separation: Magnetism

Data Source

PatentUS10184146B2Systems and methods for substrate enrichment

Publication Date: 2019.01.22 LIFE TECHNOLOGIES CORP

AI summary

A method of separating bead substrates includes applying an emulsion to an emulsion-breaking solution. A dispersed phase of the emulsion includes an unbound polynucleotide, a first set of bead substrates and a second set of bead substrates. The unbound polynucleotide includes a segment complementary to a coupling oligonucleotide. The first set of bead substrates includes the coupling oligonucleotide extended to include a segment complementary to a portion of the unbound polynucleotide. The second set of bead substrates includes the coupling oligonucleotide. The emulsion-breaking solution includes an interference probe having a sequence similar to the coupling oligonucleotide or complementary to the coupling oligonucleotide. The method further includes binding beads of the first set of bead substrates to separation substrates and separating unbound beads of the second set of bead substrates from the beads of the first set of bead substrates bound to the separation substrates.