Combinatorial Probe Libraries for Microbial Detection
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Solution Overview
Problem
Current detection assays for identifying microbes in samples are limited in their ability to rapidly and accurately determine the presence and identity of multiple microbial targets, especially in clinical, public health, veterinary, and environmental contexts, due to limitations in probe specificity and multiplexing capabilities.
Innovation Solution
The development of a method involving multiple libraries of target-specific probes, where each library is composed of a unique combination of probe sets, allows for simultaneous or sequential hybridization with spatially separated targets, enabling the identification of multiple microbial species or strains by determining which libraries hybridize to specific targets.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If multiple microbial targets are detected using conventional probe assays, then the detection capability is improved, but the number of required probes and assay complexity increase proportionally
Solution Approach 1:
The patent divides the probe library into multiple smaller sublibraries, where each sublibrary contains a unique combination of probe sets. This segmentation allows complex microbial communities to be detected through manageable subsets of probes, reducing assay complexity while maintaining comprehensive detection capability. The combinatorial arrangement of probe sets across sublibraries enables exponential identification capacity without linearly increasing the number of physical probes required.
Solution Approach 2:
The patent introduces a combinatorial dimension to probe organization by arranging probe sets in unique combinations across multiple sublibraries. This dimensional approach transforms the detection system from a linear probe-target relationship into a multidimensional combinatorial code system, where the position and combination of probes across sublibraries encode specific microbial identity information, dramatically increasing detection capacity without proportional increases in physical probe numbers.
2Quantity of substance
If the number of probe libraries is increased to identify more targets, then the number of identifiable targets increases exponentially, but the resource requirements and library management complexity increase
Solution Approach 1:
The patent performs preliminary organization of probe sets into specific combinatorial patterns across sublibraries before the actual detection assay. This pre-arranged combinatorial structure encodes microbial identification information in advance, allowing rapid decoding of target identities during assay execution without requiring complex real-time management or synthesis operations, thus reducing library management complexity while maintaining high target identification capacity.
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 significantly increases the number of identifiable targets, from 15 to 255 or 4095, depending on the number of libraries, offering a substantial advantage over prior art methods by enabling rapid and accurate identification of multiple microbial species or strains in a single assay.
Implementation Method 1
contacting a labeled target-specific probe (e.g., a labeled nucleic acid or labeled antibody) with a sample under conditions suitable for binding of the probe to its target in the sample
Data Source
AI summary
Provided herein is a set of reagents comprising: a plurality of at least three probe libraries, wherein each library of the plurality comprises one or more probe sets that are each specific for a target; and at least one of the libraries comprises a probe set that is present in another of the libraries. The plurality of libraries can be hybridized to spatially separated targets, simultaneously or sequentially. The identity of a spatially separated target can be determined by identifying which combination of the multiple libraries hybridize thereto.