Controlling uncertainty in aptamer selection

Abstract

The search for high-affinity aptamers for targets such as proteins, small molecules, or cancer cells remains a formidable endeavor. Systematic Evolution of Ligands by EXponential Enrichment (SELEX) offers an iterative process to discover these aptamers through evolutionary selection of high-affinity candidates from a highly diverse random pool. This randomness dictates an unknown population distribution of fitness parameters, encoded by the binding affinities, toward SELEX targets. Adding to this uncertainty, repeating SELEX under identical conditions may lead to variable outcomes. These uncertainties pose a challenge when tuning selection pressures to isolate high-affinity ligands. Here, we present a stochastic hybrid model that describes the evolutionary selection of aptamers to explore the impact of these unknowns. To our surprise, we find that even single copies of high-affinity ligands in a pool of billions can strongly influence population dynamics, yet their survival is highly dependent on chance. We perform Monte Carlo simulations to explore the impact of environmental parameters, such as the target concentration, on selection efficiency in SELEX and identify strategies to control these uncertainties to ultimately improve the outcome and speed of this time-and resource-intensive process.aptamer | SELEX | evolutionary dynamics | stochastic process | hybrid model

A statistical framework for analyzing deep mutational scanning data

“…The behavior of a variant v in a simulated binding experiment (e.g. phage display, yeast display) can be described in terms of the displaying entity’s likelihood of being selected in a given round [ 39 , 46 ]. This likelihood is related to the binding affinity of each variant, and, by extension, the binding probability of an individual protein molecule under the experimental conditions.…”

Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers

“…In contrast, comparing sequence frequencies between replicate trajectories after three rounds showed a multimodal distribution for many populations, wherein different subsets of sequences either enrich, remain neutral, or deplete ( Figures S4 B–S4H and S5 B–S5H). These minor variations between replicate trajectories likely reflect stochastic variations in sample handling 25 and highlight the potential value in providing multiple, independent evolutionary opportunities for a given sequence to enrich or deplete. As expected, distributions were widened more dramatically when comparing different selection rounds or selections against different targets ( Figures S6 and S7 ).…”

Aptamer Bioinformatics

“…Spill et al developed a model that simulates Capture-SELEX and includes non-covalent ligand–substrate immobilization [ 15 ]. Aptamer–target binding was represented using a hybrid approach whereby an equilibrium constant is combined with a stochastic probability model.…”