Barcode Oligonucleotide Markers for Low-Background Sample Imaging
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Solution Overview
Problem
Background fluorescence in fluorescence imaging, caused by autofluorescence and nonspecific binding of fluorescent markers, reduces the signal-to-noise ratio and compromises image quality, particularly in high-plex applications.
Innovation Solution
A marker system comprising an affinity reagent oligonucleotide with a barcode sequence, a label oligonucleotide with a complementary barcode sequence, and blocking oligonucleotides with partially complementary sequences to reduce nonspecific binding and background fluorescence.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If fluorescent markers are used to analyse biological samples, then the ability to detect and quantify targets is improved, but background fluorescence from autofluorescence and nonspecific binding increases, reducing signal-to-noise ratio
Solution Approach 1:
The patent introduces an oligonucleotide mediator system consisting of a barcode sequence on the affinity reagent, a complementary barcode sequence on the label, and blocking sequences that prevent nonspecific binding. This intermediary nucleic acid system enables specific target detection while blocking background fluorescence signals, thereby improving signal-to-noise ratio without sacrificing detection accuracy
Solution Approach 2:
The patent modifies the chemical parameters of the marker system by incorporating oligonucleotide sequences with specific complementary base pairing properties. The blocking sequences are designed with specific nucleotide compositions and lengths to optimize binding affinity and specificity, changing the chemical interaction parameters to reduce nonspecific binding while maintaining target detection capability
2Adaptability or versatility
If a larger number of fluorescent markers are used for high plex applications, then the ability to analyse multiple analytes is improved, but nonspecific binding and background fluorescence increase, compromising image quality
Solution Approach 1:
The patent segments the marker system into distinct functional components: an affinity reagent with a unique barcode sequence, a label with a complementary barcode sequence, and blocking oligonucleotides. Each component has a specific function, and their modular design allows for systematic combination in high-plex applications while maintaining control over nonspecific binding through individual optimization of each segment
Solution Approach 2:
The oligonucleotide-based blocking system serves multiple functions simultaneously: it blocks nonspecific binding sites, enables specific label- affinity reagent pairing through complementary base pairing, and provides a universal framework that can be applied across multiple different analytes and marker combinations in high-plex applications
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 system enhances image contrast and accuracy by minimizing nonspecific interactions, enabling stable and specific binding of labels to targets, even in samples with multiple analytes.
Implementation Method 1
a label comprising a label oligonucleotide with a complementary barcode sequence at least partially complementary to the barcode sequence of the affinity reagent oligonucleotide, and at least one blocking oligonucleotide with a blocking sequence that is partially complementary to the barcode sequence of the affinity reagent oligonucleotide or to the complementary barcode sequence of the label oligonucleotide
Data Source
AI summary
A marker for analysing a biological sample includes an affinity reagent comprising an affinity reagent oligonucleotide with a barcode sequence, a label comprising a label oligonucleotide with a complementary barcode sequence at least partially complementary to the barcode sequence of the affinity reagent oligonucleotide, and at least one blocking oligonucleotide with a blocking sequence that is partially complementary to the barcode sequence of the affinity reagent oligonucleotide or to the complementary barcode sequence of the label oligonucleotide.