SOMAmer Aptamer Capture for S. aureus Detection
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Solution Overview
Problem
Current methods for detecting microbial contamination in food and water are inefficient and lack specificity, often requiring culture or cell lysis, and are not effective at low cell densities, posing a significant risk to public health.
Innovation Solution
Development of novel slow off-rate modified aptamer (SOMAmer) reagents specific to Staphylococcus aureus proteins, which bind with high affinity and can capture and enrich S. aureus cells from low-density matrices without the need for culture or cell lysis, using SELEX with modified DNA libraries and recombinant or native proteins.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If conventional detection methods are used, then detection can be performed with standard procedures, but detection sensitivity is insufficient at low cell densities
Solution Approach 1:
The patent applies preliminary action by performing aptamer-based enrichment of target microorganisms before detection. The method captures and concentrates low-abundance pathogenic bacteria from complex samples using specific aptamers, thereby pre-concentrating the target analytes to levels detectable by subsequent PCR or other detection methods. This preliminary enrichment step enables detection of pathogens at very low cell densities that would otherwise be undetectable.
Solution Approach 2:
The patent uses aptamers as intermediary molecules that specifically bind to cell surface proteins on pathogenic microorganisms. These aptamers serve as mediators between the target pathogens and the detection system, enabling specific capture and enrichment. The aptamers act as selective intermediaries that bridge the gap between low-abundance targets and detection methods, allowing sensitive detection without requiring direct interaction between the pathogen and detection reagents.
2Reliability
If culture-based methods are used, then microorganism detection can be performed, but the process requires time-consuming culture steps
Solution Approach 1:
The patent replaces the mechanical/biological culture process with a direct molecular detection approach. Instead of relying on time-consuming microbial growth and culture procedures, the method uses aptamer-based capture followed by PCR or other molecular detection techniques. This substitution eliminates the need for extended culture incubation while maintaining or improving detection reliability through specific molecular recognition and amplification.
Solution Approach 2:
The patent performs preliminary enrichment of target microorganisms using aptamers before detection, replacing the need for preliminary culture steps. This preliminary capture and concentration step allows direct proceeding to rapid molecular detection methods, thereby eliminating the time-consuming culture phase while ensuring sufficient target abundance for reliable detection.
3Measurement precision
If cell lysis is required for detection, then intracellular targets can be detected, but the process becomes more complex and time-consuming
Solution Approach 1:
The patent extracts and detects cell surface-associated targets without requiring cell lysis. By targeting proteins and other molecules on the bacterial cell surface, the method obtains sufficient diagnostic information for pathogen identification and detection while avoiding the complex and time-consuming cell disruption steps. This extraction of surface targets preserves cell integrity and simplifies the overall procedure.
4Measurement precision
If standard PCR detection is used, then microorganism DNA can be detected, but PCR inhibitors in the sample reduce detection efficiency
Solution Approach 1:
The patent extracts target microorganisms from complex inhibitory matrices using aptamer-based capture. By specifically binding and isolating pathogens from food, water, or environmental samples, the method removes or separates target cells from PCR inhibitors present in the original sample. This extraction step purifies the target population before detection, eliminating the harmful effect of co-extracted inhibitors on subsequent PCR amplification.
Solution Approach 2:
The patent uses aptamers as intermediary capture agents that selectively bind target microorganisms and facilitate their separation from inhibitory sample matrices. These intermediary molecules enable specific isolation of pathogens while leaving behind PCR inhibitors, thereby mediating the separation of target from interference and enabling successful downstream detection.
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 aptamers significantly enhance the detection of S. aureus cells by several orders of magnitude, allowing for improved limits of detection and efficient removal of PCR inhibitors, enabling effective monitoring of microbial contamination in food and water samples.
Implementation Method 1
the first aptamer is capable of binding to a first cell-surface protein of the microorganism to form a complex
Data Source
AI summary
Described herein are compositions and methods for detecting the presence or absence of a microorganism in a sample comprising contacting the sample with an aptamer capable of binding to a cell-surface protein of the microorganism to form a complex, contacting the mixture with a second aptamer capable of binding to the first cell-surface protein or a second cell-surface protein of the microorganism; and performing an assay to detect the second aptamer, wherein detecting the second aptamer indicates that the microorganism is present in the sample, and wherein not detecting the second aptamer indicates that the microorganism is absent from the sample.