Blocked Nucleic Acid Cascade Assay for Rapid Target Detection

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Solution Overview

Problem

Existing nucleic acid detection methods rely on target nucleic acid amplification for sensitivity, which increases detection time and can lead to artifacts or inaccurate results, necessitating improved technologies for rapid and accurate pathogen detection.

Innovation Solution

A cascade assay using two ribonucleoprotein complexes and blocked nucleic acid molecules that allow target nucleic acid detection at attamolar limits without amplification, utilizing cis- and trans-cleavage activities to detect DNA, RNA, and cDNA within 10 minutes.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If nucleic acid amplification is used to enhance detection sensitivity, then detection sensitivity is improved, but detection time increases and artifacts may occur

Engineering Contradiction:
Improvedetection sensitivityVSAvoiddetection time
Core Design Contradiction:
Measurement precisionVSLoss of time

Solution Approach 1:

The patent extracts and eliminates the amplification step from the detection process. By using a cascade assay with two ribonucleoprotein complexes and blocked nucleic acid molecules, the system achieves detection sensitivity without requiring target nucleic acid amplification, thus reducing detection time and avoiding artifacts caused by amplification.

Inventive Principle:
Principle #2Taking out (Extraction)

Solution Approach 2:

The patent introduces blocked nucleic acid molecules as intermediaries that mediate the detection process. These blocked molecules are cleaved by the first ribonucleoprotein complex when bound to the target, releasing unblocked molecules that activate the second complex, enabling signal amplification without target nucleic acid amplification.

Inventive Principle:
Principle #24Intermediary (Mediator)

2Measurement precision

If nucleic acid amplification is used to enhance detection sensitivity, then detection sensitivity is improved, but artifacts and inaccurate results may occur

Engineering Contradiction:
Improvedetection sensitivityVSAvoidaccuracy of results
Core Design Contradiction:
Measurement precisionVSReliability

Solution Approach 1:

The patent removes the amplification step that causes artifacts. By using a direct detection cascade assay with blocked nucleic acid molecules, the system achieves high sensitivity without the artifacts and inaccuracies introduced by conventional nucleic acid amplification methods.

Inventive Principle:
Principle #2Taking out (Extraction)

Solution Approach 2:

The patent converts the blocking function of blocked nucleic acid molecules from a hindrance into a beneficial mechanism. The blocked molecules are designed to be cleaved only when the target nucleic acid is present, transforming the blocking state into a controlled signal activation mechanism that improves detection accuracy.

Inventive Principle:
Principle #22Blessing in disguise (Convert harm into benefit)

3Productivity

If conventional detection methods are used, then assay simplicity is maintained, but detection speed is slow

Engineering Contradiction:
Improvedetection speedVSAvoidassay complexity
Core Design Contradiction:
ProductivityVSDevice complexity

Solution Approach 1:

The patent segments the detection process into two distinct ribonucleoprotein complexes with specialized functions. The first complex handles target binding and initial cleavage, while the second complex provides signal amplification, enabling rapid detection through functional segmentation rather than simple sequential steps.

Inventive Principle:
Principle #1Segmentation

Solution Approach 2:

The patent employs preliminary action by pre-assembling the two ribonucleoprotein complexes and blocked nucleic acid molecules before target introduction. This pre-preparation allows the cascade reaction to proceed rapidly once the target is added, achieving fast detection without requiring complex real-time assembly steps.

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

The assay provides rapid and accurate detection of target nucleic acids without amplification, avoiding primer-dimerization and maintaining assay components' modularity across different targets, enabling timely diagnosis and treatment of diseases.

Implementation Method 1

the first nucleic acid-guided nuclease exhibits both cis-cleavage activity and trans-cleavage activity

Methodology Applied
Scientific EffectCis-cleavage activity:

Implementation Method 2

the first nucleic acid-guided nuclease exhibits both cis-cleavage activity and trans-cleavage activity

Methodology Applied
Scientific EffectTrans-cleavage activity:

Implementation Method 3

the second nucleic acid-guided nuclease exhibits both cis-cleavage activity and trans-cleavage activity

Methodology Applied
Scientific EffectCis-cleavage activity:

Implementation Method 4

the second nucleic acid-guided nuclease exhibits both cis-cleavage activity and trans-cleavage activity

Methodology Applied
Scientific EffectTrans-cleavage activity:

Data Source

PatentUS12410464B2Detection assays
Publication Date: 2025.09.09 VEDABIO INC
  • US12410464B2 patent drawing
  • US12410464B2 patent drawing
  • US12410464B2 patent drawing

AI summary

Presented is a nucleic acid-guided nuclease cascade assay that can detect one or more target nucleic acids of interest of interest without the need for amplifying the target nucleic acids of interest. The nucleic acid-guided nuclease cascade assays utilize signal amplification mechanisms comprising various components including nucleic acid-guided nucleases and guide RNAs (gRNAs) forming ribonucleoprotein complexes, blocked primer molecules, template molecules, polymerases and reporter moieties.