Core Concept & Purpose The goal is to subtract sequences that bind to: The immobilization matrix/surface (e.g., streptavidin beads, nitrocellulose filters, chip surface). Closely related molecules or structural analogs (e.g., to ensure an aptamer for drug A doesn't bind metabolite B). Components of the selection buffer or the cellular milieu where the aptamer will be used (e.g., serum proteins for therapeutic aptamers). By pre-incubating the DNA library with these "negative targets" before exposure to the desired target, non-specific binders are captured and discarded. Only the unbound, "cleaned" library proceeds to the positive selection round. Key Features of a Professional Negative SELEX Service Strategic Design: Experts design the optimal order, frequency, and stringency of negative vs. positive selection rounds. Relevant Negative Targets: The service advises on and sources the most critical counter-targets (e.g., using the exact resin from positive selection for matrix subtraction, or sourcing specific protein analogs). Dedicated Rounds: Entire selection rounds may be dedicated to negative selection against a key interferent. Pre-SELEX Depletion: Often, the initial naive library is pre-depleted against the matrix to remove common surface binders from the start. Typical Integration into a Service Workflow Within a broader SELEX project (e.g., Protein-SELEX), a Negative SELEX step is woven in as follows: Pre-Clearance (Round 0): The initial DNA library is…
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…
