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GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning
Paolo Climaco1, Noelle M Mitchell2, Matthew Tyler3
1Institut für Numerische Simulation, University of Bonn, Bonn, 53115, NRW, Germany.
Mathematical Biosciences
|June 29, 2025
Summary
We developed GMfold, a Python tool for rapid DNA aptamer secondary structure prediction. This high-throughput method aids in analyzing large aptamer pools from SELEX, advancing biosensor and therapeutic development.
Area of Science:
- Biotechnology
- Computational Biology
- Molecular Biology
Background:
- Aptamers are DNA molecules that bind targets with high affinity.
- Predicting DNA secondary structures is crucial for understanding aptamer function.
- Existing tools like mfold are not suitable for high-throughput analysis of large aptamer pools.
Purpose of the Study:
- To develop a high-throughput computational method for predicting DNA aptamer secondary structures.
- To enable real-time analysis of thousands of DNA sequences for aptamer selection.
- To facilitate machine-learning integration into aptamer discovery and design.
Main Methods:
- Developed GMfold, a Python code for high-throughput aptamer secondary structure determination.
- Utilized subgraph matching methods to group aptamer candidates by structural similarity.
- Improved the SeqFold open-source code by incorporating subgraph matching concepts.
- Represented secondary structures as lowest-energy bipartite subgraph matchings.
Main Results:
- GMfold enables high-throughput prediction of DNA secondary structures.
- The new methods allow comparison of thousands of DNA sequences based on secondary structures.
- The approach is effective for analyzing large sequence pools generated by SELEX.
Conclusions:
- GMfold and improved SeqFold provide efficient tools for aptamer secondary structure analysis.
- These computational advancements support machine-learning-informed aptamer selection.
- This work is foundational for developing improved aptamer-based biosensors and therapeutics.
