Encoded Dual-Probe Assays for Sensitive Multiplex Nucleic Acid Detection
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Solution Overview
Problem
Existing assays for detecting nucleic acid targets require high sensitivity and specificity but suffer from low signal levels, necessitating complex and lengthy protocols with high background noise, limiting their performance.
Innovation Solution
The use of encoded dual-probe endonuclease assays that involve binding a dual probe recognition element to the nucleic acid target, forming a cleavable ternary nucleic acid complex, and releasing a recognition element fragment with a code, which is then detected to indicate the presence of the target, allowing for simpler and more sensitive detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If amplification methods (PCR, immunostaining cascades) are used to increase signal level, then detection sensitivity is improved, but protocol complexity and duration increase
Solution Approach 1:
The patent extracts only the essential detection function from complex amplification protocols by using a simplified probe-based system that directly detects target nucleic acids without requiring multiple amplification cycles, thereby reducing protocol complexity while maintaining detection sensitivity
Solution Approach 2:
The patent introduces encoded probes as intermediary elements that carry unique genetic codes serving as surrogates for target analytes. These probes act as mediators between the target and detection system, enabling sensitive detection through code decoding rather than direct signal amplification
2Measurement precision
If amplification methods are used to increase signal level, then detection sensitivity is improved, but background noise increases
Solution Approach 1:
The patent converts the potential harm of background noise into a benefit by using encoded probes with unique genetic codes. The coding system allows differentiation of specific targets from background noise through code matching, transforming the challenge of signal amplification into an advantage for specific detection
Solution Approach 2:
The patent applies local quality by assigning unique genetic codes to specific probes targeting different analytes. This localized coding approach enables specific probes to be distinguished from background noise and non-specific probes, improving signal-to-noise ratio through code-specific detection
3Measurement precision
If encoded probes with unique genetic codes are used as surrogates for target analytes, then detection sensitivity is improved, but assay complexity increases
Solution Approach 1:
The patent uses genetic codes as information copies that represent target analytes. Instead of directly detecting and amplifying target signals, the system creates coded copies (probes) that can be decoded to identify targets, simplifying the detection process while maintaining sensitivity through information-based detection
4Adaptability or versatility
If multiple targets are detected simultaneously using traditional methods, then detection versatility is improved, but signal-to-noise ratio deteriorates
Solution Approach 1:
The patent segments the detection system by assigning unique genetic codes to probes for different target analytes. This segmentation allows multiple targets to be detected simultaneously through code differentiation, maintaining signal-to-noise ratio by distinguishing specific coded signals from background and cross-reactivity
Solution Approach 2:
The patent creates a universal detection platform where encoded probes with different genetic codes can detect multiple target analytes using the same decoding methodology. This multi-functional approach enables simultaneous detection of various targets while maintaining precision through code-specific identification
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
This approach enables easier and more sensitive detection of nucleic acid targets by decoding the released codes, reducing complexity and background noise, and facilitating simultaneous detection of multiple targets in a single platform.
Implementation Method 1
binding a dual probe recognition element to the nucleic acid target, if present, to form a cleavable ternary nucleic acid complex
Implementation Method 2
cleaving the ternary nucleic acid complex, if present, to release a recognition element fragment comprising the mismatch sequence and the code
Data Source
AI summary
Methods are provided for conducting a dual-probe assay on a set of nucleic acid targets, including: combining a set of dual probes with a sample composition potentially comprising a set of nucleic acid targets to form a set of cleavable ternary nucleic acid complexes; releasing from the cleavable ternary nucleic acid complex a set of recognition element fragments; hybridizing each of the set of released recognition element fragments to a coded oligonucleotide probe and using resulting hybridized released recognition elements as primers for copying the coded oligonucleotide probe to produce a sect of target-associated codes, wherein each of the coded oligonucleotide probes comprises a code from a set of codes, each code comprises at least one segment encoding one or more symbols that correspond to a sequence of one or more nucleotides; and performing a detection event to identify a set of detected codes of the target-associated codes.