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…
Small molecules are some of the most valuable—and most difficult—targets in molecular recognition. They include metabolites, drugs, toxins, cofactors, and signaling compounds that often weigh only a few hundred Daltons. Developing expertise in aptamers to small molecules means mastering a set of selection and validation strategies that differ substantially from protein-target aptamer work, because small molecules offer fewer contact points, weaker “handles” for separation, and more ways to generate false positives. This article explains how small-molecule aptamers are discovered, why selection is uniquely challenging, how advanced SELEX variants improve success rates, and what “good” looks like when you engineer an aptamer into a sensor, assay, or therapeutic concept. 1) What makes small-molecule aptamers special? Aptamers are single-stranded DNA or RNA sequences that fold into 3D shapes able to bind a target through non-covalent interactions—hydrogen bonding, π–π stacking, electrostatics, and shape complementarity. For proteins, large surfaces provide many contacts, so binding can be robust even when the selection workflow is imperfect. Small molecules are different: Tiny binding interface: fewer interaction opportunities means affinity can be harder to evolve and easier to mis-measure. Separation is tricky: in classic SELEX you often immobilize the target; immobilization can change the target’s presentation…
What “SELEX Aptamer Selection” Means SELEX stands for Systematic Evolution of Ligands by Exponential Enrichment. In plain terms, SELEX aptamer selectionis an iterative laboratory workflow that starts with a huge pool of random DNA or RNA sequences and repeatedly enriches the fraction that binds a chosen target with high affinity and specificity. The “winners” are called aptamers—single-stranded nucleic acids that fold into 3D shapes capable of target recognition, often compared to “chemical antibodies,” but made by selection and synthesis rather than immune systems. Core Concept: Darwinian Evolution in a Test Tube SELEX is essentially variation + selection + amplification: Variation: Begin with a randomized oligonucleotide library (often ~10^13–10^16 unique sequences). Selection: Expose the library to the target; keep sequences that bind. Amplification: PCR (or RT-PCR for RNA workflows) amplifies binders to create the next-round pool. Increasing stringency: Each round tightens conditions (less target, harsher washes, more competitors), enriching the best binders over multiple cycles. Most conventional SELEX workflows run multiple rounds (often roughly 6–15) before candidates are sequenced and characterized. The Classic SELEX Workflow (Step-by-Step, With the “Why”) 1) Library design (the “starting universe”) A typical library contains: A random region (e.g., N30–N60) that can…