Sequencing-Based Aptamer Screening for High-Throughput Specificity
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Solution Overview
Problem
Existing aptamer screening methods, such as SELEX, have low throughput and high false positive rates due to the inability to simultaneously screen multiple aptamers and targets, and the lack of a positive correlation between binding ability and frequency.
Innovation Solution
A method involving in situ sequencing and screening of aptamer clonal clusters on a solid carrier, allowing simultaneous detection of multiple aptamer libraries and targets, with the binding ability correlating to the copy number, thereby improving accuracy and reducing false positives.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If SELEX method is used to screen nucleic acid aptamers, then specific aptamers can be obtained, but the throughput is low because only one type of target molecule can be screened at a time
Solution Approach 1:
The patent combines multiple target molecules into a single screening reaction system, allowing simultaneous screening of multiple aptamers against different targets. This merging approach increases throughput while maintaining screening specificity through sequential or concurrent detection methods.
Solution Approach 2:
The patent creates a universal screening platform that can handle multiple target types and aptamer libraries simultaneously. The system uses common reagents and protocols that work across different target-aptamer pairs, enabling one system to perform multiple screening functions.
2Adaptability or versatility
If a random oligonucleotide library with high diversity is used, then various aptamers can be obtained, but the false positive rate increases because binding ability does not correlate with binding frequency
Solution Approach 1:
The patent implements feedback mechanisms where binding data from initial screens informs subsequent screening rounds. By using sequencing data and binding frequency information as feedback, the system can identify and eliminate false positives while enriching for true aptamers with correlated binding ability and frequency.
Solution Approach 2:
The patent replaces traditional mechanical separation and analysis methods with sequencing-based detection. This substitution allows for precise identification and quantification of aptamers, enabling accurate distinction between true binders and false positives even in highly diverse libraries.
Data Source
AI summary
Provided is a method for screening for an aptamer by sequencing. The method comprises: performing sequencing on a plurality of candidate aptamers linked to the surface of a solid-phase carrier to obtain sequencing data; contacting the candidate aptamers with a target in a liquid environment, and coupling with the target any candidate aptamer, among the plurality of candidate aptamers, that has selectivity to the target to obtain a conjugate; detecting a signal generated by the conjugate; and on the basis of the sequencing data and the signal, determining an aptamer that has selectivity with respect to the target. Also provided is a method for screening for an aptamer by sequencing, which can reduce the false positive rate occurring in aptamer screening and increase the throughput of specific aptamers outputted per unit time.