Masked Fluorogenic Compounds for Multiplexed Biosensing
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Solution Overview
Problem
Current aptamer technologies are limited in their ability to detect multiple, structurally diverse disease-associated biomarkers, including inorganic molecules and enzymes, due to their high specificity and the need for distinct sequences for each molecular target, making multiplexed biosensing challenging.
Innovation Solution
Development of masked fluorogenic compounds that react with biomarkers to form fluorogenic ligands, which bind to RNA aptamers, enabling fluorescence emission for the detection of various biomarkers, such as hydrogen peroxide, enzymes, and metal ions, using compounds like HBI and its derivatives with specific chemical modifications.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Device complexity
If a single RNA aptamer sequence is used to detect multiple biomarkers, then the complexity of multiplexed biosensing is reduced, but the specificity and binding affinity for each distinct molecular target deteriorates
Solution Approach 1:
The patent introduces small molecule ligands as intermediaries between the RNA aptamer and the diverse biomarkers. The aptamer specifically binds to the small molecule ligand with high affinity, while the ligand is designed to react with or bind to various biomarkers (enzymes, metal ions, reactive oxygen species). This intermediary approach allows a single aptamer sequence to indirectly detect multiple biomarkers while maintaining high specificity through the aptamer-ligand interaction.
Solution Approach 2:
The patent employs chemical modifications of small molecule ligands (such as HBI and its derivatives) to create different versions that can detect different biomarkers. By changing chemical parameters of the ligands (functional groups, substituents), the system maintains the same aptamer binding interface while adapting to different biomarker targets, thus resolving the contradiction between using a single aptamer and detecting multiple targets.
2Measurement precision
If distinct aptamer sequences are selected for each molecular target, then the detection specificity for each biomarker is improved, but the complexity and time required for developing multiplexed biosensors increases
Solution Approach 1:
The patent creates a universal RNA aptamer (such as Spinach, Baby Spinach, Corn, or Broccoli aptamers) that can bind to a class of small molecule ligands. This universal aptamer serves multiple functions by detecting various biomarkers through its interaction with different ligand variants, eliminating the need to develop and select new aptamer sequences for each biomarker target.
Solution Approach 2:
The patent performs preliminary in vitro selection to obtain a universal aptamer sequence that recognizes a common structural feature across multiple ligands. This preliminary action establishes a foundation that can be reused for detecting multiple biomarkers, significantly reducing the time and effort required for subsequent biosensor development compared to selecting individual aptamers for each target.
3Illumination intensity
If conventional fluorogenic probes are used for biomarker detection, then the fluorescence signal is generated, but the ability to detect structurally diverse biomarkers with a single probe is limited
Solution Approach 1:
The patent systematically modifies the chemical parameters of small molecule ligands (such as adding different functional groups, substituents, or side chains to HBI derivatives) to create a library of ligands that can detect various biomarkers. These chemical parameter changes allow the ligands to interact with different biomarkers while maintaining the core fluorogenic structure that binds to the RNA aptamer and generates fluorescence signal.
Solution Approach 2:
The patent creates composite detection systems consisting of three components: the RNA aptamer, the small molecule ligand (such as HBI or its derivatives), and the biomarker. This composite approach combines the high specificity of nucleic acid binding with the chemical versatility of small molecules, enabling the detection of structurally diverse biomarkers including enzymes, metal ions, and reactive oxygen species with a single aptamer-based platform.
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
Enables the detection of multiple biomarkers with a single RNA aptamer sequence, enhancing the ability to diagnose diseases by providing a high-fidelity, adaptable platform for detecting aberrant metabolic pathways and oxidative stress markers.
Implementation Method 1
binding of the fluorogenic ligand with the aptamer leads to fluorescence emission by the fluorogenic ligand
Implementation Method 2
the compound of Formula (II) reacts with a biomarker to provide a compound of Formula (I)
Data Source
AI summary
In one aspect, the present disclosure relates to a masked fluorogenic compound comprising a small molecule protecting group that can be cleaved following a reaction with a biomarker. In some embodiments, cleavage of the small molecule protecting group provides a fluorogenic ligand that binds to an aptamer, leading to fluorescence emission. In another aspect, the present disclosure relates to a method of detecting a disease or a disorder in a subject and/or in a biological sample from the subject.