3D DNA Nanostructures for Multiplex mRNA Detection
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Solution Overview
Problem
Current gene expression profiling (GEP) methods face challenges in achieving precise, sensitive, and efficient detection of mRNA molecules, including false positive and false negative counting events, with limitations in scalability, speed, and cost-effectiveness.
Innovation Solution
The use of 3D DNA nanostructures with inwardly disposed fluorescence dye molecules, specifically bound to target structures, allows for precise quantification by distinguishing fluorescence signals, reducing false positives and enhancing sensitivity through the strategic arrangement of dye molecules to prevent interaction and quenching.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If multiple DNA nanostructures are used for multiplex detection, then the number of detectable targets increases, but false positive and false negative counting events increase
Solution Approach 1:
The patent applies local quality by creating distinct spatial zones within the DNA nanostructure - the core region contains densely packed fluorescent dyes that serve as a reference signal, while the periphery contains adapter binding sites for target molecules. This spatial differentiation allows the system to simultaneously perform multiplex detection while maintaining reliability through internal reference comparison that corrects for counting errors.
Solution Approach 2:
The patent implements feedback through the reference signal mechanism. The fluorescent dyes embedded in the DNA nanostructure core provide a continuous reference signal that feeds back into the detection algorithm, allowing real-time correction of false positives and false negatives. This internal feedback loop ensures reliable quantification even when multiple different targets are detected simultaneously.
2Measurement precision
If fluorescent dye molecules are attached to DNA nanostructures, then detection sensitivity increases, but signal quenching occurs due to molecular interactions
Solution Approach 1:
The patent applies the nested doll principle by embedding fluorescent dye molecules within the three-dimensional structure of the DNA nanostructure core. The DNA helices are arranged in a bundled configuration that nests the dyes in a protected internal environment, shielding them from external quenching agents while maintaining their fluorescent properties for sensitive detection.
Solution Approach 2:
The patent uses composite materials by combining fluorescent dye molecules with DNA nanostructures to create a hybrid detection system. The DNA component provides structural integrity and protection against quenching, while the fluorescent dyes provide detection sensitivity. This composite approach allows the system to achieve both high sensitivity and resistance to signal quenching simultaneously.
3Measurement precision
If conventional GEP methods are used, then detection of mRNA molecules is achieved, but analysis time is lengthy and scalability is limited
Solution Approach 1:
The patent replaces complex mechanical and enzymatic systems with a simplified optical detection system. Instead of using PCR amplification, reverse transcription, and multiple enzymatic steps, the invention uses direct hybridization of DNA nanostructures to mRNA targets followed by fluorescent detection. This substitution of mechanical/enzymatic processes with optical detection dramatically reduces analysis time while maintaining detection precision and enables scalable multiplex analysis.
Solution Approach 2:
The patent applies universality by designing a single DNA nanostructure platform that can detect multiple different mRNA targets simultaneously through different adapter configurations. This multi-functional system eliminates the need for separate detection procedures for each target, thereby improving productivity and scalability while maintaining precise detection of individual mRNA molecules.
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
This approach enables fast, simple, and accurate detection of multiple target structures with reduced false positives, improving the scalability and efficiency of gene expression analysis while maintaining high sensitivity.
Implementation Method 1
each of the 3D DNA nanostructures comprises one or more inwardly disposed fluorescence dye molecules
Implementation Method 2
the shape of the 3D DNA nanostructure and the placement of the marker molecules attached to it... strategic arrangement of dye molecules to prevent interaction and quenching
Data Source
AI summary
The present invention relates to a method and a DNA nanostructure for detecting a target structure. In particular, the present invention relates to a DNA nanostructure, which ensures a preferably linear dependence on the number of marker molecules and the measurement signal regardless of the physical arrangement of a plurality of such DNA nanostructures by virtue of the skilled selection of the shape of the DNA nanostructure and the placement of the marker molecules attached to it. The invention additionally relates to the use of said DNA nanostructures and other nanoreporters, preferably in combination with adapters which bind specifically to target molecules, in a method for quantifying a plurality of target molecules, preferably in a simultaneous manner, using a multiplex method.