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Updated: Apr 14, 2026
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Phthalic Acid Ester-Binding DNA Aptamer Selection, Characterization, and Application to an Electrochemical Aptasensor
Published on: March 21, 2018
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Energy-based method for designing aptamers to target phosphatidylserine.
Fatima Alharbi1, Hamed Alsulami1, Suliman AlOmar2
1Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia.
Methodsx
|April 13, 2026
Summary
A new computational method, the screened Coulomb interaction approach (SCIA), designs aptamers by calculating binding energies. This approach ensures target specificity for developing novel aptamer-based therapeutics and diagnostics, including for phosphatidylserine targets.
Area of Science:
- Biomolecular Engineering
- Computational Chemistry
- Drug Discovery
Background:
- Existing aptamer design methods do not account for binding energetics during development.
- A need exists for computational tools to predict aptamer-target interactions accurately.
Purpose of the Study:
- To introduce a novel, energy-based aptamer design platform.
- To develop a method for calculating drug-target binding energies (DTBEs) and association/dissociation processes.
- To design specific aptamers for phosphatidylserine (PS) using the new platform.
Main Methods:
- Utilized a screened Coulomb interaction (SCI) formalism to model charge distributions in aptamer-target complexes.
- Employed a seed-and-grow approach for aptamer construction, optimizing SCIs.
- Calculated DTBEs for aptamers and aptamer building blocks (ABBs) interacting with target molecules.
- Selected aptamer length based on DTBE trends towards equilibrium in biological environments.
Main Results:
- Developed the screened Coulomb interaction approach (SCIA) for aptamer design.
- Successfully designed nucleic acid aptamers with specific binding to phosphatidylserine (PS).
- Demonstrated the platform's capability to discover aptamers for both lipid and protein targets.
- Created aptamer-based therapeutic and diagnostic templates for PS-related diseases.
Conclusions:
- The SCIA platform enables the rational design of target-specific aptamers by incorporating binding energetics.
- This method significantly advances aptamer discovery for therapeutic and diagnostic applications.
- SCIA provides a robust framework for developing aptamer-based drugs targeting specific biomarkers like PS.
