Oligonucleotide Derivative Benzene-Phosphate Backbone Fluorescent Labeling
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Solution Overview
Problem
Existing oligonucleotide derivatives with fluorescent dyes bound to ribose are difficult to synthesize efficiently and have unstable dye clusters, limiting the diversity of detectable wavelengths and fluorescent strength, and lack nuclease resistance.
Innovation Solution
Linking fluorescent dyes to the benzene-phosphate backbone to form stable excimers and exciplexes, enhancing nuclease resistance and achieving diverse fluorescence wavelengths by varying the sequence and arrangement of nucleotide derivative units.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If fluorescent dyes are bound to carbon atoms of ribose on the nucleotide, then fluorescent labels can be formed, but the clusters are difficult to synthesize efficiently and have unstable dye clusters
Solution Approach 1:
The patent changes the binding position parameter of fluorescent dyes from ribose carbon atoms to benzene ring carbon atoms in the nucleotide backbone. This parameter change enables both efficient synthesis through conventional coupling reactions and stable dye clustering through π-π interactions between aromatic rings, resolving the contradiction between synthesis efficiency and cluster stability.
Solution Approach 2:
The invention creates a composite structure where fluorescent dyes are integrated into the aromatic backbone of nucleotides rather than being attached to ribose. This composite approach forms stable excimers and exciplexes through aromatic stacking, achieving both synthetic feasibility and cluster stability simultaneously.
2Illumination intensity
If fluorescent dyes are clustered to increase fluorescent strength, then detection sensitivity improves, but the clustered state is unstable and it is difficult to increase fluorescent wavelengths
Solution Approach 1:
By changing the structural parameter of the nucleotide backbone to include aromatic rings (benzene, pyridine, etc.), the patent enables stable π-π stacking of fluorescent dyes. This structural modification allows formation of stable excimers and exciplexes with enhanced fluorescent strength and red-shifted wavelengths, resolving the contradiction between fluorescent strength and cluster stability.
3Reliability
If conventional oligonucleotide structures are used, then synthesis is straightforward, but nuclease resistance is insufficient for in vivo stability
Solution Approach 1:
The patent modifies the chemical structure parameter of the nucleotide backbone by replacing conventional sugar-phosphate structures with aromatic rings (benzene, pyridine, etc.). This structural change provides inherent nuclease resistance while maintaining synthetic feasibility through conventional coupling reactions, resolving the contradiction between nuclease resistance and structural complexity.
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 solution enables stable and efficient fluorescent labeling with enhanced fluorescent strength and nuclease resistance, allowing for the detection of multiple targets at a single excitation wavelength.
Implementation Method 1
by linking fluorescent dyes to the benzene carbon atoms in the backbone, it is possible to cluster (stack) the dyes effectively and form stable excimers and/or exciplexes
Implementation Method 2
Oligonucleotides are known that are substituted at the base moiety with fluorescent dyes such as pyrene and perylene... fluorescence may be emitted in wavelength bands longer than those of the constituent monomers
Data Source
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AI summary
The disclosures of the Specification provide an oligonucleotide derivative suited to practical use, as well as a fluorescent dye cluster and use therefor. The disclosures of the Specification use a labeling agent comprising a plurality of nucleotide derivative units represented by Formula (1) below: (where, Z represents a nitrogen atom or CH, Y represents an uncondensed aromatic hydrocarbon group or condensed polycyclic hydrocarbon group, X1 represents O, S or Se, and X2 represents SH (or S-), S or Se-, a C1-4 alkyl or a morpholino group.)