DNA Loop Transducer for Enzyme Activity Detection

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Solution Overview

Problem

Current enzyme detection systems are limited in their ability to efficiently detect enzyme activity, particularly in vivo, and lack sophistication for broad biomedical applications, with a need for new techniques that can provide optical or electrical outputs with improved performance and cost-effectiveness.

Innovation Solution

A DNA-based enzyme detection method that converts enzyme activity into a DNA signal, utilizing a loop transducer composed of DNA with stiffening and hybridizing domains, allowing for amplification and processing, and capable of detecting endonucleases and proteases with high specificity and sensitivity.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Adaptability or versatility

If conventional enzyme detection systems are used, then detection can be performed, but the systems lack sophistication for in vivo applications and broad biomedical uses

Engineering Contradiction:

Improveapplicability to in vivo and broad biomedical applicationsVSAvoiddetection performance and low false positives

Core Design Contradiction:

Adaptability or versatilityVSReliability

Solution Approach 1:

The patent introduces a DNA loop transducer as an intermediary component that converts enzyme activity into a detectable DNA signal. The loop transducer contains a recognition domain that specifically binds to the target enzyme, and upon binding, undergoes a conformational change that produces a measurable signal. This intermediary mechanism enables sophisticated in vivo detection while maintaining high reliability through specific enzyme-DNA interactions.

Inventive Principle:

Principle #24Intermediary (Mediator)

2Measurement precision

If existing optical and electrical enzyme detection methods are used, then enzyme activity can be detected, but new approaches are needed to improve performance and cost-effectiveness

Engineering Contradiction:

Improveenzyme activity detection precisionVSAvoidcost-effectiveness

Core Design Contradiction:

Measurement precisionVSEase of manufacture

Solution Approach 1:

The patent changes the detection parameter from conventional optical or electrical signals to DNA-based signals. The loop transducer produces a DNA signal upon enzyme binding, which can then be amplified using established DNA amplification techniques. This parameter change enables both high measurement precision through DNA's inherent specificity and cost-effectiveness by leveraging existing, well-established DNA amplification methods.

Inventive Principle:

Principle #35Parameter changes

3Productivity

If conventional detection systems are used, then detection is possible, but they lack the capability for signal amplification and logical processing

Engineering Contradiction:

Improvesignal amplification capabilityVSAvoiddetection system sophistication

Core Design Contradiction:

ProductivityVSDevice complexity

Solution Approach 1:

The patent segments the detection system into distinct functional modules: the loop transducer for enzyme recognition, the DNA signal generation component, and the amplification/processing component. This segmentation allows the system to achieve high productivity through DNA amplification while managing complexity by separating the recognition function from the amplification function, enabling modular design and implementation.

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

The method provides robust, scalable, and cost-effective enzyme detection with low false positives and negatives, enabling in vivo applications and broad applicability to various enzymes, and allows for logical processing and amplification of signals.

Implementation Method 1

A DNA-based enzyme detection method that converts enzyme activity into a DNA signal, utilizing a loop transducer composed of DNA with stiffening and hybridizing domains

Methodology Applied

Scientific EffectDNA hybridization:

Implementation Method 2

allowing for amplification and processing, and capable of detecting endonucleases and proteases with high specificity and sensitivity

Methodology Applied

Scientific EffectStrand displacement:

Data Source

PatentUS11255786B2Detection of enzyme activity with DNA loops

Publication Date: 2022.02.22 THE GOVERNMENT OF THE UNITED STATES OF AMERICA AS REPRESENTED BY THE SECRETARY DEPARTMENT OF HEALTH & HUMAN SERVICES

AI summary

The stiffness and topology of ultra-small circular DNAs and DNA/peptide hybrids are exploited to create a transducer of enzyme activity with low error rates. The modularity and flexibility of the concept are illustrated by demonstrating various transducers that respond to either specific restriction endonucleases or to specific proteases. In all cases the output is a DNA oligo signal that, as we show, can readily be converted directly to an optical readout, or can serve as input for further processing, for example, using DNA logic or amplification. By exploiting the DNA hairpin (or stem-loop) structure and the phenomenon of strand displacement, an enzyme signal is converted into a DNA signal, in the manner of a transducer. This is valuable because a DNA signal can be readily amplified, combined, and processed as information.