RNA Aptamer Fluorophore Complexes for Enhanced Sensing
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Solution Overview
Problem
Current RNA aptamers and aptamer-fluorophore complexes are inadequate for enhancing the generation of aptamer-based small molecule sensors and in vitro/in vivo monitoring of RNA molecules, with a need for improved specificity and fluorescence enhancement.
Innovation Solution
Development of nucleic acid molecules that bind specifically to conditionally fluorescent fluorophores, such as DFHBI and DFHBI-1T, to enhance fluorescence upon radiation exposure, and the creation of fusion RNA molecules and detection arrays for monitoring RNA activity, localization, and degradation.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Illumination intensity
If existing RNA aptamers are used to bind fluorophores, then some binding affinity is achieved, but fluorescence enhancement is insufficient for effective sensing
Solution Approach 1:
The patent modifies the RNA aptamer sequence and structural parameters to optimize fluorophore binding affinity and fluorescence enhancement. By changing nucleotide sequences and secondary structure elements, the aptamers achieve superior fluorescence enhancement ratios, transforming the weak binding into a reliable sensing platform.
Solution Approach 2:
The invention creates composite aptamer-fluorophore complexes where the RNA aptamer and fluorophore work synergistically. The composite structure enables the fluorophore to achieve enhanced fluorescence only when bound to the specific aptamer, providing both high signal intensity and selective sensing capability.
2Illumination intensity
If aptamer sequences are optimized for fluorophore binding, then fluorescence enhancement improves, but aptamer stability and cellular compatibility may be compromised
Solution Approach 1:
The patent applies local quality optimization by designing specific structural motifs and sequence elements within the aptamer that are crucial for fluorophore binding, while maintaining other regions for stability. The aptamer structure is divided into functional zones: fluorophore-binding sites with specific nucleotides and stem-loop structures, and stable backbone regions with conserved sequences.
3Measurement precision
If new aptamer sequences are developed for improved binding, then specificity increases, but development time and complexity increase
Solution Approach 1:
The patent employs preliminary computational design and in silico selection of aptamer sequences before experimental validation. By pre-screening potential aptamers through computer algorithms and predicting their binding properties, the development process is accelerated, reducing the time required to identify specific aptamer-fluorophore pairs.
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 new nucleic acid molecules significantly enhance fluorescence signals, enabling more effective monitoring and quantification of RNA molecules in vivo and in vitro, with applications in RNA-based sensors and high-throughput assays, while being non-toxic and cell-permeable.
Implementation Method 1
binding of the nucleic acid molecule to the fluorophore substantially enhances fluorescence of the fluorophore upon exposure to radiation of suitable wavelength
Data Source
AI summary
The present invention relates to novel nucleic acid molecules, called aptamers, that bind specifically to a small molecule fluorophore and thereby enhance the fluorescence signal of the fluorophore upon exposure to radiation of suitable wavelength. Molecular complexes formed between the novel fluorophores, novel nucleic acid molecules, and their target molecules are described, and the use of multivalent aptamer constructs as fluorescent sensors for target molecules of interest are also described.