What is an Aptamer Screening Service? It is a contract-based service where a specialized laboratory uses Systematic Evolution of Ligands by EXponential enrichment (SELEX) to discover single-stranded DNA or RNA molecules (aptamers) that bind with high affinity and specificity to your target molecule (e.g., a protein, an antibody's constant region, or a cell-surface receptor). Core Service Components A full-service provider typically offers an end-to-end pipeline: 1. Project Design & Target Preparation Consultation: Defining the goal (e.g., detection, inhibition, delivery). Target Characterization: Ensuring the target (purified protein, antibody, receptor-expressing cells) is properly formatted and validated. Negative Selection/Counter-SELEX: Designing the screening to avoid binders to similar, non-target structures (e.g., the Fc region of a different antibody isotype, a common cell surface protein). 2. Library & Selection (The Core SELEX Process) Library Design: Using a diverse random oligonucleotide library (typically 10^14 - 10^15 unique sequences). Selection Method: The choice of method is critical and depends on the target: Protein SELEX: For purified, soluble targets immobilized on beads or in solution. Cell-SELEX: For membrane receptors in their native conformation on live cells. Excellent for discovering aptamers to unknown receptor complexes. Capture-SELEX/Toggle-SELEX: For difficult-to-immobilize targets or to increase stringency. In Vivo SELEX: For discovering aptamers that home to specific tissues in vivo. Iterative Rounds: Typically 8-15 rounds of…
What is Counter-SELEX? First, a quick recap of SELEX (Systematic Evolution of Ligands by EXponential Enrichment): SELEX is an iterative process to isolate specific DNA or RNA aptamers from a vast random library (10^14 - 10^15 sequences) that bind tightly to a target molecule (e.g., a protein, small molecule, cell). Counter-SELEX is a powerful refinement to this process. Its core purpose is to improve specificity by negative selection. How it works: During or between rounds of positive selection (binding to the desired target), the oligonucleotide pool is exposed to one or more counter-targets. The Goal: Sequences that bind to these counter-targets are deliberately removed or depleted from the pool. Only sequences that bind specifically to the desired target and not to the closely related counter-targets are carried forward. Common Counter-Targets: Structural analogs: For a small-molecule drug, you might use its inactive metabolite or a similar drug from the same class. Protein isoforms or family members: To develop an aptamer for a specific kinase, you'd use other kinases from the same family as counter-targets. Immobilization matrix: If the target is immobilized on beads, pre-incubating the library with "blank" beads removes matrix binders. Related cell types: For a cell-specific aptamer (e.g., cancer vs. healthy), the healthy cells are used as the counter-target. What Does a…
What is Whole-cell SELEX? Whole-cell SELEX (Systematic Evolution of Ligands by EXponential enrichment) is a technique used to discover aptamers (single-stranded DNA or RNA molecules) that bind specifically to a target living cell. Unlike traditional SELEX that uses a purified protein target, whole-cell SELEX presents the target in its native, complex cellular environment. This allows for the selection of aptamers against: Native cell-surface proteins in their proper folding and post-translational modifications. Complex targets like transmembrane receptors in their natural lipid environment. Unknown surface biomarkers without prior knowledge of the cell's molecular makeup. Specific cell states (e.g., activated, cancerous, infected) based on differences in surface expression. The Core Process: How Whole-cell SELEX Works A professional service will manage this complex, iterative pipeline: Library & Design: Starting with a vast, random synthetic oligonucleotide library (10^14 - 10^15 unique sequences). Positive Selection: Incubating the library with the target cells (e.g., cancer cells, stem cells, bacteria). Aptamers that bind to any surface structure are retained. Counter-Selection (Critical Step): The bound pool is then exposed to non-target or control cells (e.g., healthy cells, a different cell line). Sequences that bind to these are discarded. This step is crucial for generating specificity. Elution & Amplification: Aptamers specifically bound to the target cells are recovered, amplified by PCR…
