In Situ Biomolecule Proximity Detection Using Rolling Circle Amplification

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Solution Overview

Problem

Current technologies lack the ability to provide reliable specificity, high throughput, and high sensitivity for studying cellular biomolecular interaction networks, particularly in clinical settings, which hampers the discovery of biomarkers for disease diagnostics and treatment response prediction.

Innovation Solution

A method involving the use of extended oligonucleotides conjugated to biomolecules within cells or tissues, utilizing rolling circle amplification to create localized DNA-nanoballs for enhanced detection of biomolecules, enabling the study of protein interactions beyond traditional limits.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If traditional detection methods are used, then the detection process is simple, but the sensitivity and specificity are insufficient

Engineering Contradiction:

Improvedetection sensitivityVSAvoiddetection method complexity

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent introduces circular polynucleotide intermediaries that mediate between target biomolecules and detection systems. These circular polynucleotides serve as amplifiable intermediaries that convert single biomolecule binding events into multiple detectable signals through rolling circle amplification, thereby enhancing sensitivity without requiring direct detection of the target molecule itself

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The patent employs rolling circle amplification to generate multiple copies of circular polynucleotide signals from single binding events. This copying mechanism amplifies the detection signal by producing numerous identical copies of the circular polynucleotide, each containing detection sequences, thereby significantly increasing detection sensitivity and signal-to-noise ratio

Inventive Principle:

Principle #26Copying

2Productivity

If traditional detection methods are used, then the method is easy to operate, but the throughput is limited

Engineering Contradiction:

Improvedetection throughputVSAvoiddetection system complexity

Core Design Contradiction:

ProductivityVSDevice complexity

Solution Approach 1:

The patent performs preliminary conjugation of oligonucleotides to biomolecules before the actual detection process. This pre-preparation step allows the detection system to be ready for high-throughput operation, as the conjugated biomolecules can be immediately used in detection assays without requiring time-consuming preparation during the measurement phase

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent changes the physical state and concentration parameters of detection signals through rolling circle amplification. By converting single binding events into high concentrations of amplified circular polynucleotide copies, the system achieves high throughput detection with improved signal strength, allowing parallel processing of multiple samples

Inventive Principle:

Principle #35Parameter changes

3Length of moving object

If traditional detection methods are used, then the detection range is limited, but the method is straightforward

Engineering Contradiction:

Improvedetection distanceVSAvoiddetection accuracy

Core Design Contradiction:

Length of moving objectVSMeasurement precision

Solution Approach 1:

The patent extends detection from direct spatial proximity to a new dimension of detection through rolling circle amplification. Instead of relying solely on physical distance, the system uses the amplification of circular polynucleotide signals to detect biomolecules at extended distances (beyond 40 nm), adding a signal amplification dimension that decouples detection range from direct spatial proximity

Inventive Principle:

Principle #17Another dimension (Dimensionality change)

4Reliability

If specificity is improved through conventional methods, then false positives are reduced, but the detection sensitivity decreases

Engineering Contradiction:

Improvedetection specificityVSAvoiddetection sensitivity

Core Design Contradiction:

ReliabilityVSMeasurement precision

Solution Approach 1:

The patent segments the detection system into distinct functional modules: specific binding of oligonucleotides to target biomolecules, formation of circular polynucleotide intermediaries, and rolling circle amplification. This segmentation allows each module to optimize for its specific function - binding specificity in the first module and signal amplification in the second - thereby achieving both high specificity and high sensitivity simultaneously

Inventive Principle:

Principle #1Segmentation

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

Enables the detection of biomolecules with improved specificity and sensitivity, allowing for the study of protein interactions at distances greater than 40 nm, facilitating the identification of new biomarkers for disease diagnostics and treatment response prediction.

Implementation Method 1

hybridizing a first sequence of a first probe oligonucleotide to the first oligonucleotide and hybridizing a second sequence of the first probe oligonucleotide to a second oligonucleotide

Methodology Applied

Scientific EffectDNA hybridization:

Implementation Method 2

amplifying the second circular polynucleotide to form an extension product

Methodology Applied

Scientific EffectRolling circle amplification:

Implementation Method 3

hybridizing a first sequence of a first probe oligonucleotide to the first oligonucleotide and hybridizing a second sequence of the first probe oligonucleotide to a second oligonucleotide, wherein the second oligonucleotide is attached to a second biomolecule

Methodology Applied

Scientific EffectNucleic acid hybridization: