SELEXION. Systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear...

Area of Science:

• Biochemistry
• Molecular Biology
• Computational Biology

Background:

• Novel technologies for isolating biologically active nucleic acid molecules involve iterative selection and polymerase chain reaction (PCR) amplification.
• Experimental conditions significantly influence the outcome of these enrichment processes.

Purpose of the Study:

• To predict the impact of variations in experimental conditions on nucleic acid enrichment.
• To develop strategies and guidelines for enhancing the effectiveness of nucleic acid enrichment.
• To optimize conditions for maximum enrichment and recovery of rare, well-binding molecules.

Main Methods:

• Mathematical analysis and computer simulation of nucleic acid enrichment processes.
• Reconstruction tests to validate a mathematical model based on equilibrium binding.
• Extensive simulation across a range of conditions to predict enrichment levels.

Main Results:

• A mathematical model based on equilibrium binding accurately explains high enrichment levels achieved in laboratory settings.
• Predicted enrichment levels vary significantly with different experimental conditions.
• Optimal protein and nucleic acid concentrations were determined for maximizing enrichment and recovery of rare molecules.

Conclusions:

• Mathematical modeling and simulation are effective tools for understanding and optimizing nucleic acid enrichment.
• The developed strategies and guidelines are broadly applicable to DNA, RNA, and peptide ligand enrichment.
• An interactive simulation program has been created for non-linear optimization of enrichment processes.