Core Principle & Typical Service Workflow A professional service for Conventional SELEX typically follows this established, iterative cycle (8-15 rounds), as visualized below: Key Service Characteristics Target Immobilization: The target molecule is fixed to a solid support (e.g., magnetic beads, column resin, nitrocellulose membrane). Positive Selection: The library is passed over the immobilized target. Sequences with some binding affinity are retained, while others are washed away. Stringency Control: The service provider systematically increases selection pressure across rounds (e.g., by reducing target concentration, increasing wash stringency, adding counter-targets in Negative SELEX steps) to drive the evolution of high-affinity, specific binders. Monitoring: Enrichment is tracked via quantitative PCR, and final pools are analyzed by Next-Generation Sequencing (NGS) to identify convergent sequence families. Common Applications for this Service This classic approach is ideal for: Proteins that are stable and can be immobilized without losing native conformation (e.g., antibodies, enzymes, recombinant tags). Large molecules or complexes (e.g., viruses, whole cells—though Cell-SELEX is now more common for cells). Establishing proof-of-concept for a new target class where simpler, robust methodology is preferred. Deliverables Similar to other SELEX services, clients receive: A final report detailing the selection process and conditions. A list of top-ranked aptamer sequences with affinity (Kd) and specificity data. Aliquots of synthesized, validated…
What is Small Molecule SELEX? SELEX is an iterative in vitro selection process that sifts through a vast random library of nucleic acid sequences (typically 10^13 - 10^15 different molecules) to find the few that bind tightly and specifically to a target. The Challenge with Small Molecules: Low epitope density: Small molecules offer limited surface area for binding, making it hard to find high-affinity aptamers. Immobilization required: They must be attached to a solid support (beads, chip, column) for partitioning, which can mask potential binding sites or introduce non-specific interactions. Negative Selection is Crucial: To avoid selecting aptamers that bind to the immobilization matrix instead of the target. Standard Service Workflow (What the Provider Does): Project Design & Target Immobilization: Consultation: The provider works with you to understand the target's chemistry, desired affinity, and application (e.g., biosensor, therapeutic inhibitor, diagnostic). Conjugation: They chemically conjugate your small molecule to an appropriate carrier (e.g., beads, magnetic particles, agarose resin, or a surface like a chip). This is a critical, proprietary step for many providers. The SELEX Cycle (Repeated 8-15 rounds): Incubation: The vast oligonucleotide library is incubated with the immobilized target. Partitioning: Unbound sequences are washed away. Sequences bound to the target (and unfortunately, sometimes to the matrix) are retained. Elution: Bound…
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…
The unique secondary and tertiary structures of aptamers provide the specificity to detect even small structural changes in the target molecule, including the presence or absence of methyl or hydroxyl groups or differences in enantiomeric configurations. Aptamers that bind specific targets are identified through a process known as Systematic Evolution of Ligands by Exponential enrichment (SELEX) in which binding molecules are selected from a large and diverse library of nucleic acids (either DNAs or RNAs). In this process, the nucleic acid library is incubated with the target molecule. Non-binding nucleic acids are then washed away, leaving behind only the molecules that have a capacity to bind to the target molecule. The nucleic acids that are not washed away are then used to create a new library of nucleic acids that is enriched for the subset that binds the desired target. Repeating this selection-cycle on each subsequent library with increasing stringency of binding (e.g. lower concentration of target), ensures that nucleic acids that bind to the target with both high specificity and high affinity are enriched. Aptamers are short, single-stranded oligonucleotides (DNA or RNA) that bind to specific target molecules with high affinity and specificity. They are often called "chemical antibodies."…
