Aptamer Molecular Redesign for Higher Specificity and Affinity
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Solution Overview
Problem
Current aptamer technologies face challenges in achieving high specificity and affinity, particularly in complex environments, limiting their practical application and effectiveness in detecting mycotoxins like Ochratoxin A and Aflatoxin B1, which are critical for food safety.
Innovation Solution
A molecular design-guided method using computer rational calculation to modify aptamers by virtual screening, saturation mutation, and base substitution, followed by experimental verification, to enhance their binding specificity and affinity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If SELEX technology is used to screen aptamers, then binding affinity is improved, but specificity deteriorates because aptamers may bind to non-homologous targets
Solution Approach 1:
The patent applies preliminary action by performing counter-SELEX screening against multiple target analogs and homologs before final aptamer selection. This pre-screening process eliminates aptamers that bind to non-specific targets, ensuring high specificity is achieved before the aptamers are used for their intended purpose.
Solution Approach 2:
The patent employs parameter changes by systematically varying selection conditions in counter-SELEX experiments, including different stringency levels, temperatures, and competitor concentrations. These parameter adjustments allow optimization of both affinity and specificity by selecting aptamers that maintain binding under varied conditions while rejecting off-target binders.
2Manufacturing precision
If counter SELEX is used to improve specificity by excluding oligonucleotides that bind to target analogs, then specificity for homologous targets is improved, but the ability to characterize specificity for non-homologous targets deteriorates
Solution Approach 1:
The patent implements universality by designing a comprehensive counter-SELEX strategy that screens against multiple types of target analogs simultaneously, including homologs, isomers, and structurally related compounds. This multi-functional screening approach creates aptamers with broad specificity profiles that can be characterized against diverse target types, not just homologous targets.
Solution Approach 2:
The patent applies preliminary action by performing extensive counter-SELEX screening against a panel of target analogs before final aptamer selection. This pre-characterization process establishes the aptamer's specificity profile across multiple target types, enabling subsequent use against non-homologous targets with confidence.
3Manufacturing precision
If large-scale experimental screening is performed to characterize aptamer specificity, then comprehensive specificity data is obtained, but time consumption and workload increase
Solution Approach 1:
The patent applies preliminary action by using in silico molecular docking and virtual screening to pre-evaluate aptamer binding to multiple target analogs before performing wet-lab experiments. This computational pre-screening filters out aptamers with poor specificity profiles, reducing the number of candidates requiring experimental validation and significantly decreasing overall screening time and workload.
Solution Approach 2:
The patent replaces mechanical experimental screening with computational methods by using molecular docking simulations, free energy calculations, and machine learning models to predict aptamer specificity. This substitution of computational mechanics for physical experimentation dramatically reduces time and resource requirements while maintaining or improving assessment accuracy.
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 modified aptamers demonstrate significantly improved binding specificity and affinity, facilitating rapid and sensitive detection of mycotoxins, thereby enhancing food safety and enabling practical applications.
Implementation Method 1
Important features of aptamers proposed by researchers include specificity and affinity originated from the electrostatic interaction and hydrophobic interaction
Implementation Method 2
Important features of aptamers proposed by researchers include specificity and affinity originated from the electrostatic interaction and hydrophobic interaction
Data Source
AI summary
The invention relates to the technical field of bioengineering and provides a method for improving the specificity and affinity of an aptamer. The method includes: S1, screening a target of an aptamer from a compound information database by virtual computing; S2, verifying the screening result in Step S1 through experiments; S3, performing virtual saturation mutation on a site of the aptamer, and screening out a mutation site of the aptamer; S4, performing base substitution to the mutation site of the aptamer; and S5, detecting the binding parameter of the aptamer after base substitution with the target screened in Step S1, and selecting an aptamer with improved specificity and affinity after base substitution. An efficient molecular design-guided method is developed by computer rational calculation, to improve the specificity and binding affinity of the aptamer by directional modification. The present invention is of great significance for the practical application of aptamers.