RNA Blocking Molecules for Precise In Situ Small RNA Detection

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Solution Overview

Problem

Existing in situ hybridization (ISH) techniques face challenges in accurately detecting small RNA molecules like miRNA, siRNA, and piRNA due to high off-target binding of probes, leading to inaccurate diagnostic and therapeutic information.

Innovation Solution

The use of RNA blocking molecules with non-probe-targeting and probe-targeting regions that are complementary to non-target and target RNA molecules, respectively, to reduce off-target binding and enhance the detection of target RNA molecules.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If standard ISH probes are used to detect small RNA molecules, then detection coverage is achieved, but off-target binding increases leading to reduced measurement precision

Engineering Contradiction:

Improvedetection accuracyVSAvoidoff-target binding

Core Design Contradiction:

Measurement precisionVSObject-generated harmful factors

Solution Approach 1:

The patent introduces blocking molecules as intermediary substances that bind to non-target RNA sequences, preventing standard ISH probes from binding to off-target sites. The blocking molecule contains a blocking sequence complementary to non-target RNA and a spacer sequence, creating a physical barrier that eliminates harmful off-target binding while preserving on-target detection accuracy

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The blocking molecules are applied before the detection probes to pre-block off-target binding sites. By performing the blocking action in advance, the system prevents harmful off-target interactions from occurring, allowing the subsequent probe to bind only to the intended target sequence with high precision

Inventive Principle:

Principle #9Preliminary anti-action

2Measurement precision

If probe length is increased to improve target binding, then on-target detection sensitivity improves, but off-target binding also increases

Engineering Contradiction:

Improvedetection sensitivityVSAvoidnon-specific binding

Core Design Contradiction:

Measurement precisionVSObject-generated harmful factors

Solution Approach 1:

The detection system is segmented into distinct functional components: a blocking molecule with blocking sequence and spacer, and a detection probe with probe sequence. This segmentation allows the probe to be optimized for sensitivity (longer length) while the blocking molecule separately handles specificity by blocking off-target sites, resolving the contradiction between sensitivity and non-specific binding

Inventive Principle:

Principle #1Segmentation

3Measurement precision

If probe concentration is increased to enhance signal strength, then detection sensitivity improves, but non-specific binding increases reducing measurement precision

Engineering Contradiction:

Improvesignal efficiencyVSAvoidnon-specific probe binding

Core Design Contradiction:

Measurement precisionVSObject-generated harmful factors

Solution Approach 1:

The blocking molecule acts as an intermediary that selectively binds to non-target RNA sequences, creating a protective barrier that allows higher probe concentrations to be used without increasing non-specific binding. The blocking molecule absorbs the harmful effect, enabling the probe to work at optimal concentrations for maximum signal efficiency and measurement precision

Inventive Principle:

Principle #24Intermediary (Mediator)

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

Enhances the signal efficiency and accuracy of ISH by reducing non-specific probe binding, thereby improving the detection of target RNA molecules such as mRNA, miRNA, sncRNA, piRNA, and siRNA.

Implementation Method 1

the non-probe-targeting region of the RNA blocking domain is complementary to a non-probe-targeting region of a target RNA molecule

Methodology Applied

Scientific EffectComplementary base pairing:

Implementation Method 2

the probe-targeting region of the RNA blocking domain is complementary to a portion of a probe-targeting region of a target RNA molecule

Methodology Applied

Scientific EffectComplementary base pairing:

Data Source

PatentUS20260078430A1Methods for detecting target nucleic acids using RNA blocking molecules

Publication Date: 2026.03.19 ADVANCED CELL DIAGNOSTICS INC

AI summary

Embodiments of the present disclosure include compositions and methods for performing in situ hybridization reactions. In particular, the present disclosure provides RNA blocking molecules that enhance detection of a target RNA molecule (e.g., an mRNA molecule, a microRNA (miRNA) molecule, a small non-coding RNA (sncRNA) molecule, a PIWI-interacting RNA (piRNA) molecule, a small interfering RNA (siRNA) molecule, and/or an anti-sense oligo (ASO) molecule) by reducing binding of a target probe to a non-target RNA molecule in a sample.