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Refinement and Truncation of DNA Aptamers Based on Molecular Dynamics Simulations: Computational Protocol and
Ana Díaz-Fernández1,2, Carmen S Ciudad1, Natalia Díaz1
1Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería, 8, 33006 Oviedo, Asturias, Spain.
Journal of Chemical Information and Modeling
|April 14, 2025
Summary
This study introduces a molecular dynamics protocol to determine DNA aptamer 3D structures, enabling rational design of shorter, high-affinity aptamers for improved diagnostic and therapeutic applications.
Area of Science:
- Biochemistry
- Molecular Biology
- Biotechnology
Background:
- Aptamers are valuable tools in diagnostics and drug delivery, but conventional selection yields overly long sequences.
- Optimizing aptamer length for binding affinity often involves inefficient trial-and-error methods.
Purpose of the Study:
- To develop a general strategy for determining DNA aptamer 3D structures.
- To rationally design shorter aptamers with preserved or enhanced binding affinities.
- To elucidate the role of structural elements like poly thymine spacers.
Main Methods:
- A semiautomated molecular dynamics protocol was employed to predict aptamer 3D structures.
- Truncated aptamers were designed based on predicted structures of known peptide/protein ligands.
- Energetic scoring of molecular dynamics trajectories was used to differentiate secondary structures.
Main Results:
- Truncated aptamers, 20-35% shorter than originals, exhibited similar or improved binding affinities.
- The protocol successfully guided rational design and optimization of aptamer candidates.
- The study provided insights into the energetic contributions of poly thymine spacers.
Conclusions:
- The developed 3D structure generation protocol accelerates aptamer optimization.
- This approach leads to the development of more efficient analytical reagents and therapeutic agents.
- Rational design based on structural insights enhances aptamer functionality.
