Multiplex Analyte Detection Using Decoding Oligonucleotide Encoding
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Solution Overview
Problem
Existing methods for detecting small quantities of analytes in biological and non-biological samples are inflexible, expensive, complex, time-consuming, and often provide inaccurate results, with low encoding capacities that do not meet modern molecular biology and medicine's requirements.
Innovation Solution
A multiplex method involving at least 20 different sets of analyte-specific probes, each with unique identifier sequences, combined with decoding and signal oligonucleotides, allows for sequential signal-encoding of analytes, decoupling the dependency between analyte-specific and signal oligonucleotides, thereby increasing flexibility and reducing the number of needed signal oligonucleotides.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If directly labeled probe sets are used for detecting analytes, then detection specificity is improved, but the number of differently tagged probe sets increases complexity and cost
Solution Approach 1:
The patent introduces decoding oligonucleotides as intermediaries between analyte-specific probes and signal oligonucleotides. The decoding oligonucleotides contain identifier sequences that recognize specific analyte probes and recruit appropriate signal oligonucleotides, thereby reducing the need for directly labeled complex probe sets while maintaining detection specificity
Solution Approach 2:
The detection system is segmented into separate functional components: analyte-specific probes with unique identifier sequences, decoding oligonucleotides that read these identifiers, and signal oligonucleotides that provide detection signals. This segmentation allows reuse of signal oligonucleotides across multiple analyte types, reducing overall system complexity
2Measurement precision
If multiple detection rounds are performed to increase encoding capacity, then analyte detection accuracy is improved, but processing time increases
Solution Approach 1:
Unique identifier sequences are pre-built into the analyte-specific probe structures during probe design and synthesis. This preliminary encoding allows rapid identification of analytes in subsequent detection rounds without requiring time-consuming probe reconfiguration or multiple sequential hybridization steps
Solution Approach 2:
The patent designs a universal detection platform where the same set of signal oligonucleotides and decoding oligonucleotides can be used across multiple detection rounds for different analytes. The identifier sequences enable the system to universally recognize and respond to various analyte types using a common toolkit, reducing the need for analyte-specific reagents in each detection round
3Adaptability or versatility
If more signal oligonucleotides are used to increase encoding capacity, then multiplexing capability is improved, but cost and system complexity increase
Solution Approach 1:
The patent uses identifier sequences as information carriers that can be copied and recognized by decoding oligonucleotides. Instead of requiring unique signal oligonucleotides for each analyte, the system copies the identifier information from the analyte probes through decoding oligonucleotides to recruit appropriate signal oligonucleotides, enabling multiplexing with a limited set of reusable signal components
Solution Approach 2:
Decoding oligonucleotides serve as mediators that translate the unique identifier sequences on analyte probes into recruitment signals for appropriate signal oligonucleotides. This intermediary layer decouples the relationship between analyte specificity and signal diversity, allowing a small set of signal oligonucleotides to serve multiple analyte types through combinatorial recruitment patterns
4Ease of operation
If conventional detection methods are used, then implementation simplicity is maintained, but flexibility and adaptability to different analytes are reduced
Solution Approach 1:
The patent creates a universal detection platform where a single set of decoding oligonucleotides and signal oligonucleotides can detect multiple different analytes. The analyte-specific probes are designed with standardized unique identifier sequences that are universally recognized by the decoding system, allowing the same detection machinery to adapt to different analyte targets without reconfiguring the core detection components
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 method achieves higher flexibility, lower complexity, reduced costs, faster processing, and improved accuracy by using decoding-oligonucleotides, allowing for more efficient and accurate detection of multiple analytes with fewer detection rounds.
Implementation Method 1
each set of analyte-specific probes comprises at least five (5) analyte-specific probes which specifically interact with different sub-structures of the same analyte
Implementation Method 2
each decoding oligonucleotide comprises: (aa) an identifier connector element (t) comprising a nucleotide sequence which is essentially complementary to at least a section of the unique identifier sequence of the identifier element (T)
Implementation Method 3
each signal oligonucleotide comprising: (aa) a translator connector element (C) comprising a nucleotide sequence which is essentially complementary to at least a section of the nucleotide sequence of a translator element (c)
Data Source
AI summary
The technology provided herein relates to multiplex methods and kits for detecting different analytes in a sample in parallel by sequential signal-encoding of said analytes, as well as in vitro methods for screening, identifying and/or testing a substance and/or drug and in vitro methods for diagnosis of a disease, and an optical multiplexing system.