1. What is SELEX? SELEX stands for Systematic Evolution of Ligands by EXponential enrichment. It is a laboratory technique used to identify aptamers—short single-stranded DNA or RNA sequences that can bind specifically to a target molecule (proteins, small molecules, cells, or even viruses). Aptamers act similarly to antibodies but are synthetic, highly stable, and can be chemically modified. 2. Principle of SELEX The SELEX process is based on iterative rounds of selection and amplification: Library Preparation Start with a large randomized pool of oligonucleotides (typically 10^13–10^15 unique sequences). Each sequence is a potential aptamer candidate. Binding (Target Incubation) Incubate the library with the target molecule. Only sequences that can bind the target will stay attached; non-binders are washed away. Partitioning (Separation of Binders and Non-binders) Physically separate bound sequences from unbound sequences. Techniques depend on the target (magnetic beads, affinity columns, etc.). Elution Bound sequences are eluted (released) from the target. Amplification The eluted sequences are amplified using PCR (for DNA aptamers) or RT-PCR (for RNA aptamers). This generates an enriched pool for the next round. Iterative Rounds Steps 2–5 are repeated for 8–15 rounds to gradually enrich sequences with high affinity and specificity for the target. Sequence Identification After…
Aptamer Screening via HT-SELEX (High-Throughput Systematic Evolution of Ligands by Exponential Enrichment) is the modern, powerful method for discovering aptamers. Let's break down what this service entails, its process, advantages, and key considerations. What is an Aptamer? First, a quick reminder: Aptamers are single-stranded DNA or RNA oligonucleotides that bind to a specific target molecule (proteins, small molecules, cells, viruses) with high affinity and specificity, analogous to antibodies. They are often called "chemical antibodies." What is HT-SELEX? Traditional SELEX is iterative and low-throughput. HT-SELEX supercharges this process by integrating: Next-Generation Sequencing (NGS): To analyze the entire aptamer pool at each round. Advanced Bioinformatics: To identify binding motifs and track enrichment. Automation: Using robotics for partitioning (e.g., magnetic beads, microfluidics) to increase throughput and reproducibility. This results in a faster, more efficient, and data-driven screening process. Standard HT-SELEX Service Workflow A typical service provider will follow these steps: 1. Project Design & Library Synthesis Target Preparation: You provide the target (recombinant protein, small molecule conjugate, whole cell, etc.). Its purity and stability are critical. Library Design: A randomized oligonucleotide library is synthesized (typically 10^14 - 10^15 unique sequences). Libraries can be DNA, RNA, or modified nucleotides (e.g., SOMAmers) for enhanced stability and affinity. 2. The Selection Rounds (Cycles of…
What is Magnetic Bead SELEX? SELEX (Systematic Evolution of Ligands by EXponential Enrichment) is the gold-standard process for discovering aptamers—single-stranded DNA or RNA molecules that bind to a specific target with high affinity and specificity, similar to antibodies. Magnetic Bead SELEX is a widely used variant where the target molecule is immobilized on magnetic beads. This format offers significant advantages in automation, handling, and efficiency. Why Choose a Magnetic Bead SELEX Service? Developing aptamers in-house is time-consuming, requires specialized expertise, and involves significant optimization. A professional service provides: Expertise & Experience: Knowledge of library design, PCR optimization, and counter-selection strategies. Specialized Equipment: Access to automated magnetic separation systems, NGS, and bioinformatics. Time & Cost Efficiency: Faster turnaround (typically 2-4 months) than setting up a new lab. Higher Success Rate: Proven protocols to avoid common pitfalls like PCR bias or selection of non-specific binders. Typical Workflow of a Magnetic Bead SELEX Service Phase 1: Project Design & Target Preparation Consultation: You define the target (e.g., a protein, small molecule, cell), desired affinity (Kd), and application (diagnostics, therapeutics, sensors). Target Immobilization: The service provider chemically conjugates your target to the surface of magnetic beads (e.g., streptavidin-biotin, NHS-amine coupling). A "negative selection" bead (without target) is also prepared to remove…
What is Whole-tissue Section SELEX? It's an advanced Systematic Evolution of Ligands by EXponential enrichment (SELEX) technique where the selection target is not a purified protein or single cell type, but an intact, pathological tissue section (e.g., a slice of a human tumor biopsy on a glass slide). The core idea is to select DNA or RNA aptamers that bind specifically to the molecular landscape of diseased tissue, while simultaneously negating binding to adjacent healthy tissue from the same patient. The Standard SELEX vs. Whole-Tissue Section SELEX Feature Standard SELEX Whole-Tissue Section SELEX Target Purified protein, single cell type, or simple mixture. Complex, native tissue architecture with millions of molecular targets in their natural context. Goal Find an aptamer for a known, pre-defined target. Discover aptamers for unknown, disease-specific biomarkers without prior target identification. Context Target is isolated, may have altered conformation. Targets are in their native state, with intact post-translational modifications, protein complexes, and tissue microenvironments. Counter-Selection Against a buffer or a simple non-target (e.g., BSA). Against a serial section of adjacent healthy tissue from the same patient, ensuring disease specificity. Why Is This a Powerful Service? Target-Agnostic Discovery: You don't need to know the biomarker in advance. The process "lets the tissue decide" what the best molecular targets are.…
Aptamers are single-stranded oligonucleotides that fold into defined architectures and bind to targets such as proteins. In binding proteins they often inhibit protein–protein interactions and thereby may elicit therapeutic effects such as antagonism. Aptamers are discovered using SELEX (systematic evolution of ligands by exponential enrichment), a directed in vitro evolution technique in which large libraries of degenerate oligonucleotides are iteratively and alternately partitioned for target binding. They are then amplified enzymatically until functional sequences are identified by the sequencing of cloned individuals. For most therapeutic purposes, aptamers are truncated to reduce synthesis costs, modified at the sugars and capped at their termini to increase nuclease resistance, and conjugated to polyethylene glycol or another entity to reduce renal filtration rates. The first aptamer approved for a therapeutic application was pegaptanib sodium (Macugen; Pfizer/Eyetech), which was approved in 2004 by the US Food and Drug Administration for macular degeneration. Eight other aptamers are currently undergoing clinical evaluation for various haematology, oncology, ocular and inflammatory indications. Aptamers are ultimately chemically synthesized in a readily scalable process in which specific conjugation points are introduced with defined stereochemistry. Unlike some protein therapeutics, aptamers do not elicit antibodies, and because aptamers generally contain sugars modified at their 2′-positions,…
What is an Aptamer? An aptamer is a short, single-stranded oligonucleotide (DNA or RNA) or peptide that binds to a specific target molecule (e.g., proteins, small molecules, cells, viruses) with high affinity and specificity. Often called "chemical antibodies," they offer advantages like stability, low-cost synthesis, and minimal batch-to-batch variation. The Core Process: SELEX The standard method for aptamer selection is SELEX (Systematic Evolution of Ligands by EXponential enrichment). Basic SELEX Workflow: Library Synthesis: Create a vast random-sequence oligonucleotide library (typically 10¹³ - 10¹⁵ unique sequences) flanked by constant primer regions for PCR amplification. Incubation: The library is incubated with the target molecule under controlled conditions (buffer, temperature, time). Partitioning: Bound sequences are separated from unbound ones. This is the most critical step and varies based on target (e.g., filtration, affinity columns, magnetic bead separation). Elution: Bound aptamers are recovered from the target (e.g., by denaturation or competitive elution). Amplification: The recovered pool is amplified by PCR (for DNA) or RT-PCR (for RNA) to create an enriched library for the next round. Iteration: Steps 2-5 are repeated (typically 8-15 rounds) to progressively enrich for sequences with the highest affinity and specificity. Cloning & Sequencing: The final enriched pool is cloned and sequenced to identify individual aptamer candidates. Key Variants of…
