Traditional SELEX (Systematic Evolution of Ligands by EXponential enrichment) is a method to select high-affinity, specific nucleic acid aptamers from a vast random library (10¹³-10¹⁵ sequences). The bottleneck has always been the final cloning and Sanger sequencing of only a few dozen candidates, which often misses rare, high-performance aptamers. NGS-assisted SELEX integrates Next-Generation Sequencing at multiple rounds of the SELEX process. This provides a massive, data-rich view of the entire evolutionary landscape, enabling intelligent selection and identification of the best aptamers. Typical Workflow of an NGS-Assisted SELEX Service A professional service provider will manage this entire pipeline: Project Design & Library Synthesis: Collaboration to define target (protein, small molecule, cell), counter-selection requirements, and library design (random region length, fixed primers for NGS). Parallel SELEX Execution: Performing the iterative selection process (binding, partitioning, amplification) across multiple rounds (usually 8-12). Key NGS Integration Points: Initial Library Analysis: Sequencing the naive library to confirm diversity and complexity. Monitoring Rounds (e.g., Rounds 3, 6, 9): Taking small samples from intermediate rounds for NGS. This is the critical advantage. It tracks: Sequence Enrichment: Which families are becoming more abundant. Diversity Collapse: When to stop selection before losing good candidates. Informed Decision-Making: Data guides adjustments in selection stringency for subsequent rounds. Final Round Deep Sequencing: Comprehensive NGS of…
What is Classical SELEX? SELEX is an iterative, in vitro selection process used to isolate single-stranded DNA or RNA molecules (aptamers) that bind with high affinity and specificity to a target (e.g., a protein, small molecule, cell, or virus). The "classical" method refers to the original, well-established protocol involving: Incubation: A vast, random-sequence nucleic acid library (10^14 - 10^15 different sequences) is exposed to the target. Partitioning: Unbound sequences are washed away; bound sequences are retained. Elution: The bound sequences are recovered. Amplification: The recovered sequences are amplified by PCR (for DNA) or RT-PCR (for RNA). Repetition: This cycle (typically 8-15 rounds) is repeated, enriching the pool for the strongest binders. Components of a Classical SELEX Service A full-service provider typically manages the entire pipeline: 1. Project Design & Consultation Target Characterization: Discussing the target's properties (purity, stability, availability). Selection Strategy: Deciding on immobilization method (e.g., target immobilized on beads, or "counter-SELEX" to eliminate binders to the immobilization matrix or similar non-target molecules). Library Design: Choosing DNA or RNA, length of the random region (typically 20-60 nt), and fixed primer regions. 2. The SELEX Process Execution Library Synthesis: Chemical synthesis of the initial random library. Cycle Management: Performing the repetitive rounds of binding, washing, elution, and amplification under optimized buffer and stringency…
