Nucleic Acid Tagged Molecular Interaction Detection
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Solution Overview
Problem
Current methods for detecting molecular interactions in high-throughput formats are limited by the need for immobilization of one interaction partner, which can disrupt interactions and are labor-intensive, especially when investigating vast molecular networks like those in the human genome, where 30,000 proteins can form 4.5*10^8 possible pairs.
Innovation Solution
The method involves tagging molecules of interest with unique nucleic acid moieties that form enhanced combinations upon interaction, allowing for the detection and quantification of all possible interactions within libraries through combinatorial association and microarray analysis, enabling the identification of both partners in a molecular interaction without the need for immobilization.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If one interaction partner is immobilized on a solid phase for detection, then the detection can be performed in high throughput format, but the immobilization can disrupt the molecular interaction and/or alter protein conformation
Solution Approach 1:
The patent introduces nucleic acid tags as intermediary molecules that couple to both interaction partners. These tags mediate the detection process without requiring immobilization of the actual protein molecules, thus preserving interaction integrity while enabling high throughput analysis through nucleic acid-based detection methods
Solution Approach 2:
The patent creates nucleic acid copies or representations of the interaction partners through tagging. Instead of directly analyzing and immobilizing proteins, the system uses nucleic acid tags that serve as proxies, allowing high throughput detection while the actual protein molecules remain in solution and maintain their native conformation and interaction capabilities
2Productivity
If conventional microarray analysis is used to detect molecular interactions, then cost effective high throughput data generation is achieved, but the number of resolvable detectable functions is limited
Solution Approach 1:
The patent segments the information about molecular interactions into separate nucleic acid tags for each interaction partner. Each tag can be independently detected and identified, allowing the system to resolve multiple detectable functions simultaneously by detecting different tag combinations, thereby overcoming the limitation of conventional microarray analysis
Solution Approach 2:
The patent transitions from detecting single detectable functions to detecting combinations of nucleic acid tags from two different molecules. This dimensional expansion allows the system to extract information about multiple interaction partners simultaneously, effectively increasing the number of resolvable detectable functions while maintaining cost effectiveness
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 allows for the efficient detection and quantification of molecular interactions in high-throughput formats, overcoming the limitations of existing methods by enabling the analysis of all possible interactions within or between libraries of molecules, thereby facilitating the identification of affinity and functional interactions.
Implementation Method 1
converting information about protein interactions into nucleic acid-based information, which is highly amenable to analysis with microarrays
Data Source
AI summary
Methods of detecting affinity interactions between at least two molecules of interest are provided. The method comprises: a. forming a plurality of interactors by coupling each molecule of interest with at least one nucleic acid moiety comprising an identification sequence element and at an association element; b. promoting an association between at least two nucleic acid moieties from different interactors to form a plurality of unique associated oligonucleotides, wherein each nucleic acid moiety may form more than one unique associated oligonucleotide, and wherein each unique associated oligonucleotide comprises at least two identification sequence elements derived from the at least two nucleic acid moieties; c. selecting the plurality of unique associated oligonucleotides; and d. subjecting the selected associated oligonucleotides to an analysis that permits detection of the at least two identification sequence elements. Similar methods directed to detecting functional interactions, libraries of interactors employable in the present methods, and kits comprising those libraries are also provided.