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Targeted Selection of Aptamer Complementary Elements toward Rapid Development of Aptamer Transducers
Tim Hachigian1, Drew Lysne1, Elton Graugnard1
1Micron School of Materials Science and Engineering, Boise State University, 1910 University Dr., Boise, Idaho 83725, United States.
The Journal of Physical Chemistry. B
|May 16, 2023
Summary
This study enhances aptamer transducers (ATs) by modifying aptamer complementary elements (ACEs) to optimize biosensing performance. Modified ATs show moderate correlation between predicted and actual performance, guiding future high-throughput biosensor development.
Area of Science:
- Biotechnology
- Molecular Biology
- Analytical Chemistry
Background:
- Aptamer transducers (ATs) offer versatile biosensing capabilities for medical and environmental applications.
- Previous work introduced a customizable AT for diverse output domains and reporter networks.
Purpose of the Study:
- To investigate the kinetic behavior and performance of novel ATs by modifying the aptamer complementary element (ACE).
- To explore the ligand-binding landscape of duplexed aptamers using a novel ACE selection technique.
Main Methods:
- Constructed modified ATs with varying ACE length, start site position, and single mismatch positions.
- Tracked kinetic responses using fluorescence reporters and derived a kinetic model.
- Extracted reaction constant (k1) and effective dissociation constant (Kd,eff) to calculate a relative performance metric (k1/Kd,eff).
Main Results:
- Evaluated kinetic responses and performance of modified ATs based on ACE modifications.
- Calculated k1 and Kd,eff, revealing insights into adenosine AT dynamics.
- Found moderate correlation between predicted performance (ACE scan method) and actual AT performance.
Conclusions:
- Modified ATs demonstrate a moderate correlation between predicted and observed performance, validating the ACE selection method.
- The study provides insights into duplexed aptamer domain dynamics.
- Suggests a high-throughput approach for developing more sensitive ATs.
