Multiplex Nucleic Acid Detection Using Mass-Distinguishable Tags
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Solution Overview
Problem
Current nucleic acid detection methods are limited in their ability to efficiently and accurately identify multiple target nucleic acids in a single procedure, particularly in detecting specific nucleic acid modifications and variations.
Innovation Solution
A method involving amplification of target nucleic acids, hybridization with oligonucleotides, extension with capture agents, interaction with a solid phase, and release by competition, followed by detection using mass spectrometry to identify the presence or absence of target nucleic acids based on mass distinguishable tags.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If multiple target nucleic acids are detected using current methods, then the detection capability is limited, but the complexity of the procedure increases
Solution Approach 1:
The detection system is segmented into distinct functional components: mass distinguishable tags for identification, capture agents for immobilization, and solid phase support for separation. This segmentation allows multiple targets to be detected simultaneously through mass spectrometry while maintaining procedural manageability through modular design
Solution Approach 2:
The invention employs universal primers and universal capture agents that can work with multiple different target nucleic acids. The mass distinguishable tags provide a universal detection mechanism through mass spectrometry, allowing the same procedural framework to detect diverse targets without requiring separate optimized protocols for each target
2Measurement precision
If nucleic acid modifications are identified with high precision, then the measurement precision improves, but the detection difficulty increases
Solution Approach 1:
The invention replaces complex mechanical separation and detection systems with mass spectrometry-based detection. Mass spectrometry provides precise measurement of nucleic acid modifications by measuring mass differences, eliminating the need for complex chromatographic separation systems while achieving superior measurement precision
Solution Approach 2:
The invention detects nucleic acid modifications by measuring changes in mass parameters. Mass spectrometry measures the mass-to-charge ratio, allowing detection of subtle modifications such as methylation or other chemical modifications through precise mass differences, transforming the detection parameter from structural to mass-based
3Measurement precision
If mass spectrometry is used for detection, then the sensitivity and specificity improve, but the equipment complexity increases
Solution Approach 1:
The invention introduces mass distinguishable tags and capture agents as intermediaries between the target nucleic acids and the mass spectrometry detector. These intermediaries amplify the detectable signal and enable specific binding, allowing mass spectrometry to detect trace amounts of target with high sensitivity while the tags serve as mediators that simplify the interaction between the complex instrument and the biological samples
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
Enables the simultaneous detection of multiple target nucleic acids with high sensitivity and specificity, allowing for rapid identification of genetic variations and modifications, including single nucleotide polymorphisms, through improved signal-to-noise ratios and efficient release mechanisms.
Implementation Method 1
contacting the amplicons in solution with a set of oligonucleotides under hybridization conditions, where each oligonucleotide in the set includes a hybridization sequence capable of specifically hybridizing to one amplicon
Implementation Method 2
generating extended oligonucleotides that include a capture agent by extending oligonucleotides hybridized to the amplicons by one or more nucleotides
Implementation Method 3
contacting the extended oligonucleotides with a solid phase under conditions in which the capture agent interacts with the solid phase
Implementation Method 4
detecting the extended oligonucleotides released in (e); whereby the presence or absence of each target nucleic acid is determined by the presence or absence of the corresponding extended oligonucleotide
Data Source
AI summary
Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the extended oligonucleotides include a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing the extended oligonucleotide by competition with a competitor; detecting the extended oligonucleotide, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the extended oligonucleotide.