Core Concept of NGS-SELEX Traditional SELEX uses a few rounds of selection and cloning/Sanger sequencing of a handful of clones. NGS-SELEX performs deep sequencing (millions to billions of reads) at every selection round. This allows you to: Track the entire evolution of the oligonucleotide pool in real-time. Identify enriched sequences and families early. Perform sophisticated bioinformatics analysis to find winners, not just rely on final round abundance. Dramatically reduce the number of selection rounds needed (often 3-6 rounds instead of 8-15). Standard Service Workflow A full-service provider would typically offer the following pipeline: 1. Project Design & Library Synthesis Consultation: Target properties (protein, small molecule, cell), desired aptamer properties (Kd, specificity, buffer conditions). Library Design: Standard (40-60 nt random region) or custom (doped libraries, modified nucleotides like 2'-F, 2'-OMe, SOMAmers). Primer & Library Synthesis: Providing the initial, highly diverse DNA or RNA library (10^14 - 10^15 unique sequences). 2. SELEX Selection Immobilization: Immobilizing the target (on beads, column, plate) or using solution-based techniques (capture-SELEX, toggle-SELEX). Counter-Selection: Including steps to remove binders to immobilization matrix or off-targets. Stringency Control: Increasing selection pressure over rounds (e.g., reduced target concentration, increased wash stringency). Amplification: Careful PCR (with optimization to minimize bias) to regenerate the pool for the next round. 3. NGS & Core Bioinformatics Sample Preparation: Preparing sequencing…
CELL-SELEX (Cell-Based Systematic Evolution of Ligands by EXponential enrichment) is a selection strategy used to discover nucleic-acid aptamers—short single-stranded DNA or RNA molecules that fold into shapes capable of binding cellular targets with high affinity and specificity. What makes CELL-SELEX AND BIOMARKER DISCOVERY such a powerful pairing is that cell-SELEX can enrich binders against native cell-surface features (often membrane proteins, glycoproteins, lipids, or complex epitopes) without needing to know the target in advance. This is especially valuable in biomarker discovery, where the “best” marker may be unknown, heterogeneous, or highly dependent on the cellular context. 1) What CELL-SELEX Is (and Why It Matters for Biomarkers) Traditional SELEX often starts with a purified target (e.g., a recombinant protein). In cell-SELEX, the “target” is a living cell population that represents a phenotype you care about—such as a disease subtype, drug-resistant cells, activated immune cells, or a specific differentiation stage. The selection process enriches aptamers that bind those cells while removing sequences that bind irrelevant or shared features. Why this matters for biomarkers: Native conformation is preserved. Cell-surface proteins keep their natural folding, post-translational modifications, and membrane context—features that can be lost in purified preparations. Unbiased discovery. You can discover binding…
