Capture and Assist Probe Hybridization for Intact Oligonucleotide Detection

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Solution Overview

Problem

Conventional methods for detecting oligonucleotides struggle to distinguish between intact and metabolized forms, leading to inaccurate measurements and high cross-reactivity with metabolites, especially when drug concentrations are low, necessitating a more sensitive and specific detection method.

Innovation Solution

A hybridization method using a capture probe and an assist probe with specific positional relationships, where the capture probe has a short nucleotide length, allowing differentiation between intact oligonucleotides and metabolites by hybridizing at the site of nucleotide deficiency.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If conventional measurement systems are used, then measurement can be performed, but intact oligonucleotide and metabolite cannot be distinguished leading to inaccurate measurements

Engineering Contradiction:

Improvedetection accuracyVSAvoidspecificity

Core Design Contradiction:

Measurement precisionVSReliability

Solution Approach 1:

The detection system is segmented into two distinct probes: a capture probe that binds to the intact oligonucleotide and an assist probe that binds to the metabolite. This segmentation allows separate detection and quantification of intact form versus metabolite, resolving the inability to distinguish between them using conventional single-probe systems.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The capture probe acts as an intermediary that specifically captures intact oligonucleotides, while the assist probe serves as another intermediary that binds to metabolites. These intermediary probes enable indirect detection and differentiation of the two forms through their specific binding preferences, achieving both measurement precision and reliability.

Inventive Principle:

Principle #24Intermediary (Mediator)

2Measurement precision

If high sensitivity detection is required for low drug concentrations, then detection limit is improved, but cross-reactivity with metabolites increases

Engineering Contradiction:

Improvedetection sensitivityVSAvoidcross-reactivity

Core Design Contradiction:

Measurement precisionVSObject-affected harmful factors

Solution Approach 1:

Each probe is designed with local quality - the capture probe has high affinity for intact oligonucleotide sequences while the assist probe has high affinity for metabolite sequences. This localized specificity at the molecular binding level allows high sensitivity detection of target molecules without cross-reactivity interference, as each probe operates in its optimized binding niche.

Inventive Principle:

Principle #3Local quality

3Reliability

If enzymatic treatments are used to distinguish intact and metabolized forms, then specificity is improved, but measurement complexity increases

Engineering Contradiction:

ImprovespecificityVSAvoidmeasurement complexity

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The invention replaces the mechanical/enzymatic treatment system with a molecular recognition system. Instead of using enzymes to physically or chemically modify molecules for differentiation, the system uses the natural molecular recognition properties of nucleic acid probes to specifically bind and differentiate intact oligonucleotides from metabolites through sequence-specific hybridization.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

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 achieves high sensitivity and specificity in detecting oligonucleotides with minimal cross-reactivity, enabling accurate measurement of intact forms without enzymatic treatments, suitable for low drug concentrations.

Implementation Method 1

A method for detecting or quantifying a target oligonucleotide in a sample using a capture probe and an assist probe in combination by the principle of hybridization

Methodology Applied

Scientific EffectHybridization:

Data Source

PatentUS20250230490A1Method for detecting oligonucleotide using probes

Publication Date: 2025.07.17 SEKISUI MEDICAL CO LTD

AI summary

A method for measuring an oligonucleotide which is simpler and more sensitive and has excellent specificity and quantitative capability compared to the conventional measurement method is provided. Moreover, a method for measuring an oligonucleotide having excellent specificity which can distinguish the intact target oligonucleotide (unchanged form) and a metabolite thereof and detect the unchanged form only is provided. In a hybridization method using a capture probe and an assist probe, by using a capture probe having a short nucleotide length in a certain range and the assist probe and causing hybridization under a specific positional relationship between the nucleotide-lacking-site in a metabolite of a nucleic acid drug and the capture probe, it becomes possible not only to detect the target oligonucleotide in a sample but also to distinguish from a metabolite of the nucleic acid drug.