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Searching the Sequence Space for Potent Aptamers Using SELEX in Silico
Qingtong Zhou1, Xiaole Xia1,2, Zhaofeng Luo
1Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States.
Journal of Chemical Theory and Computation
|December 9, 2015
Summary
We developed SELEX in silico, a computational method for discovering aptamers. This approach accelerates the identification of high-affinity aptamers, as demonstrated by the successful isolation of theophylline-binding aptamers.
Area of Science:
- Biotechnology
- Computational Biology
- Molecular Biology
Background:
- Systematic evolution of ligands by exponential enrichment (SELEX) is the standard for aptamer discovery.
- Current SELEX methods face challenges in thoroughly exploring sequence space and identifying potent aptamers.
Purpose of the Study:
- To introduce SELEX in silico, a computational strategy for enhanced aptamer discovery.
- To address limitations in aptamer library design, sequence enrichment, and identification.
Main Methods:
- SELEX in silico involves two main steps: secondary structure-based sequence screening and molecular dynamics simulation-based virtual screening.
- The method screens a vast sequence space (4^13) for potential aptamer candidates.
Main Results:
- Six potent theophylline-binding aptamers were identified using SELEX in silico.
- Experimental validation confirmed high affinity binding (Kd: 0.16–0.52 μM), comparable to existing aptamers.
Conclusions:
- SELEX in silico offers a practical computational solution for aptamer discovery and optimization.
- This method significantly enhances the efficiency and scope of aptamer identification.
