Silicon containing detectable compounds and uses thereof
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Solution Overview
Problem
The synthesis of red shifted fluorescent dyes is challenging due to the difficulty in building up the carbocyclic framework, which can result in reduced brightness, photostability, and aqueous solubility.
Innovation Solution
Development of silicon-containing detectable compounds, including monovalent nucleotides or nucleosides covalently bound to bioconjugate linkers, which enhance the photostability and aqueous solubility of red shifted fluorescent dyes.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Illumination intensity
If the carbocyclic framework is extended to achieve red shifted fluorescent dyes, then the absorption coefficient increases, but the brightness, photostability and aqueous solubility deteriorate
Solution Approach 1:
The patent changes the chemical parameters of the dye molecule by incorporating silicon atoms and specific functional groups (carboxylic acid, hydroxyl, amino) into the molecular structure. This modifies the electronic properties to maintain high absorption coefficients while improving photostability and aqueous solubility, resolving the contradiction between extended carbocyclic framework benefits and drawbacks
Solution Approach 2:
The invention creates composite molecular structures combining silicon-containing units with fluorescent dye moieties and solubilizing functional groups. This composite approach allows the molecule to simultaneously achieve high absorption, improved photostability, and enhanced aqueous solubility that cannot be obtained by extending carbocyclic frameworks alone
2Illumination intensity
If the carbocyclic framework is extended to achieve red shifted fluorescent dyes, then the absorption coefficient increases, but the aqueous solubility deteriorates
Solution Approach 1:
The patent introduces hydrophilic functional groups (carboxylic acid, hydroxyl, amino) at specific local positions of the molecule to enhance aqueous solubility without compromising the extended carbocyclic framework's absorption properties. This localized modification allows the molecule to maintain high absorption while improving solubility
Solution Approach 2:
By changing the chemical parameters of the dye molecule through silicon incorporation and functional group addition, the patent modifies the molecular properties to simultaneously achieve high absorption coefficients and improved aqueous solubility, resolving the contradiction between framework extension and solubility
3Illumination intensity
If the carbocyclic framework is extended to achieve red shifted fluorescent dyes, then the absorption coefficient increases, but the brightness deteriorates
Solution Approach 1:
The patent modifies the molecular parameters by incorporating silicon atoms and functional groups that enhance quantum yield and reduce non-radiative decay, thereby improving brightness while maintaining high absorption coefficients achieved through framework extension
Solution Approach 2:
The invention creates composite molecular structures that combine high-absorption carbocyclic frameworks with brightness-enhancing silicon-containing units and functional groups, achieving simultaneous improvement in absorption and brightness performance
Data Source
AI summary
Disclosed herein, inter alia, are silicon containing detectable compounds and methods of use thereof. In an aspect is provided a monovalent nucleotide or monovalent nucleoside covalently bound to a monovalent form of a compound described herein (e.g., wherein the R13 moiety of a compound described herein has reacted with a bioconjugate reactive group to form a bioconjugate linker thereby covalently bonding the monovalent compound to the monovalent nucleotide or monovalent nucleoside).