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Performing SELEX experiments in silico
J A J Wondergem1, H Schiessel1, M Tompitak1
1Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands.
The Journal of Chemical Physics
|November 10, 2017
Summary
Computational tools can now emulate DNA sequence selection experiments, offering insights into protein-DNA interactions and enabling studies of challenging DNA structures like rings.
Area of Science:
- Computational biology
- Biophysics
- Molecular dynamics
Background:
- DNA elasticity is sequence-dependent, influencing protein-DNA complex formation and DNA structural preferences.
- Systematic Evolution of Ligands by EXponential enrichment (SELEX) experiments identify DNA sequence preferences for entities like nucleosomes and DNA rings.
Purpose of the Study:
- To demonstrate the emulation of SELEX experiments using computational and theoretical tools.
- To enhance understanding of simulation parameters (temperature, selection pressure) and model predictions.
- To enable in silico studies of experimentally challenging DNA systems.
Main Methods:
- Utilized recently developed computational and theoretical tools for in silico emulation of sequence selection experiments.
- Employed a rigid base-pair model to predict DNA sequence preferences.
- Simulated DNA rings and other potentially high-cost DNA structures.
Main Results:
- Achieved agreement between the rigid base-pair model's predictions and experimental results for DNA rings.
- Identified discrepancies between model predictions and experimental data, highlighting open research questions.
- Successfully applied SELEX methodology in silico to systems difficult to study experimentally, such as short or overwound DNA rings.
Conclusions:
- In silico emulation of SELEX experiments provides valuable insights into DNA sequence preferences and biophysical models.
- Computational approaches facilitate the study of DNA systems that are experimentally inaccessible or costly.
- This methodology advances our understanding of DNA-protein interactions and DNA structural dynamics.
