“High-throughput aptamer screening” is a method used to rapidly identify aptamers—short single-stranded DNA or RNA molecules—that can bind specifically to a target molecule, such as a protein, small molecule, or even whole cells. Let’s break this down in detail: 1. What Are Aptamers? Aptamers are oligonucleotides (DNA or RNA) that fold into specific three-dimensional shapes allowing them to bind with high affinity and specificity to their targets. They function similarly to antibodies but are synthetic, smaller, more stable, and can be chemically modified. 2. High-Throughput Screening (HTS) in Aptamer Discovery Traditional aptamer discovery uses SELEX (Systematic Evolution of Ligands by Exponential Enrichment), which involves multiple iterative rounds of binding, separation, and amplification. High-throughput aptamer screening accelerates this process by using automation and large-scale technologies to simultaneously test thousands to millions of sequences against the target. 3. Key Techniques in High-Throughput Aptamer Screening Microarray-Based Screening Thousands of aptamer candidates are immobilized on a chip. The target (protein, small molecule, or cell) is fluorescently labeled and applied. Aptamers that bind the target emit signals detected by imaging. Next-Generation Sequencing (NGS)-Coupled SELEX After each SELEX round, sequences are analyzed via NGS. Sequence enrichment patterns reveal high-affinity aptamer candidates without the need for extensive…
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…
What is SELEX and What are Aptamers? Aptamers: Often called "chemical antibodies," they are short, single-stranded DNA or RNA oligonucleotides that fold into specific 3D shapes to bind with high affinity and specificity to a target molecule (e.g., a viral protein, whole bacterium, or parasite surface marker). SELEX (Systematic Evolution of Ligands by EXponential enrichment): This is the iterative combinatorial chemistry process used to discover aptamers from a vast random library (10^14-10^15 unique sequences). It involves repeated cycles of: 1) Binding the library to the target, 2) Separating bound from unbound sequences, 3) Amplifying the bound sequences, and 4) Starting a new, enriched cycle. Core Components of a Pathogen SELEX Service A professional service will typically manage the entire pipeline: 1. Project Design & Target Preparation: Consultation: Defining the precise target (e.g., whole inactivated SARS-CoV-2, Salmonella outer membrane protein, Plasmodium lysate). Counter-SELEX: A critical step for pathogen specificity. The process is run against related non-targets (e.g., host cells, non-pathogenic bacterial strains) to filter out cross-reactive aptamers, ensuring the final aptamers distinguish between pathogen and non-pathogen. 2. The SELEX Execution: Performing multiple (usually 8-15) rounds of the selection process under optimized conditions (buffer, temperature, washing stringency). 3. Next-Generation Sequencing (NGS) & Bioinformatics: After the final rounds, the enriched pool is sequenced using NGS. Bioinformatic analysis identifies sequence…
What is a Metal Ion-Targeted Aptamer Screening Service? It is a contract research service where a specialized laboratory uses an in vitro selection process (most commonly SELEX - Systematic Evolution of Ligands by EXponential Enrichment) to identify single-stranded DNA or RNA oligonucleotides (aptamers) that bind with high affinity and specificity to a specific metal ion (e.g., Pb²⁺, Hg²⁺, UO₂²⁺, As³⁺, Cd²⁺). Unlike aptamers for proteins, metal ion aptamers often rely on the ion's unique coordination chemistry to induce a specific fold or structural switch in the oligonucleotide. Core Service Workflow (The Screening Process) A typical service provider would follow these steps: Design & Library Synthesis: Creation of a vast random-sequence oligonucleotide library (10¹⁴ - 10¹⁵ different sequences). Target Preparation: The target (e.g., Pb²⁺) is often presented in a specific buffer system that controls charge, pH, and the presence of competing ions to drive selection for the desired specificity. Selection Rounds (SELEX Cycle): Binding: Incubate the library with the target metal ion. Partition: Separate metal-bound sequences from unbound ones. This is the most critical and challenging step for small ions. Techniques include: Immobilization: Cheating the ion to a solid support (beads). Capture-SELEX: Using a complementary strand or an auxiliary molecule. Size-based separation: If binding induces a conformational change (e.g., dimerization). Amplification: PCR (for…
1. What Are Aptamers? Aptamers are short, single-stranded DNA or RNA oligonucleotides (typically 20-80 bases) that fold into specific 3D structures, allowing them to bind to target molecules (like hormones) with high affinity and specificity, similar to antibodies. They are often called "chemical antibodies." 2. Why Target Hormones with Aptamers? Hormones are critical signaling molecules (e.g., insulin, cortisol, thyroid hormones, estradiol, adrenaline). Aptamers against them offer unique advantages: High Specificity: Can distinguish between structurally similar hormones (e.g., T3 vs. T4). Synthetic & Reproducible: Produced chemically with minimal batch-to-batch variation. Stability: More thermally stable than antibodies. Modifiability: Can be easily labeled with fluorescent dyes, quenchers, or nanoparticles for detection. Low Immunogenicity: Ideal for in vivo diagnostic or therapeutic applications. 3. Core Components of the Screening Service A full-service provider would typically offer the following pipeline: a. Design & Library Construction: Use of a vast random oligonucleotide library (10^14 - 10^15 unique sequences). Customization of library design based on hormone properties (small molecule vs. peptide/protein). b. SELEX Process (The Core Screening): This is an iterative, in vitro selection process. Incubation: The library is exposed to the target hormone (immobilized or in solution). Partitioning: Unbound sequences are washed away; bound sequences (aptamer candidates) are retained. Elution & Amplification: Bound sequences are eluted and amplified by PCR…
What is an Aptamer? First, a quick definition: Aptamers are short, single-stranded DNA or RNA oligonucleotides that bind to a specific target molecule (like proteins, toxins, cells) with high affinity and specificity. They are often called "chemical antibodies" but offer advantages like easier synthesis, higher stability, and lower cost. What is Toxin-Targeted Aptamer Screening? This service involves the in vitro selection and development of custom aptamers designed to bind specifically to a toxic substance. The core technology is called SELEX (Systematic Evolution of Ligands by EXponential enrichment). The process screens vast random libraries (10^14 - 10^15 different sequences) against the toxin to isolate the few sequences that bind tightly and specifically. Key Steps in the Service Pipeline Project Consultation & Target Definition: Clarify the toxin (e.g., mycotoxins like Aflatoxin B1, marine toxins like Saxitoxin, bacterial toxins like Botulinum, environmental toxins like heavy metals). Define the desired application (Detection/Biosensing, Neutralization, Capture/Purification). Specify the sample matrix (food extract, blood serum, environmental water). Library Design & SELEX Strategy: Design of a naive single-stranded DNA or RNA library. Choosing the appropriate SELEX variant: Negative Selection/Counter-SELEX: To exclude sequences that bind to similar non-toxin molecules or the assay matrix (crucial for specificity). Capture-SELEX: For small toxins that can't be immobilized. Cell-SELEX: If the…
Core Technology: SELEX The foundation of all these services is the SELEX process, an in vitro method to select aptamers from a vast random library (typically 10^13 - 10^15 unique sequences). The library is incubated with the target, unbound sequences are washed away, and bound sequences are eluted and amplified by PCR (for DNA) or RT-PCR (for RNA). This cycle is repeated 8-15 times to enrich for the tightest binders. Services for Protein Targets This is the most common application, as aptamers are often touted as "chemical antibodies." 1. Standard Protein SELEX: Target: Purified, recombinant proteins (e.g., cytokines, receptors, enzymes, viral capsids). Key Considerations: Protein Purity & Conformation: Critical for success. Services often require >90% purity and verification of native folding. Immobilization: The protein is usually immobilized on beads (e.g., streptavidin/biotin, Ni-NTA/His-tag) to facilitate partitioning. Some services offer solution-phase SELEX to avoid conformation changes. Counter-Selection: To ensure specificity, libraries are pre-incubated with related proteins or the immobilization matrix to subtract non-specific binders. 2. Specialized SELEX for Complex Proteins: Membrane Protein SELEX: For receptors and channels. Requires special handling (e.g., use of nanodiscs, detergent micelles, or whole cells overexpressing the target). Post-Translationally Modified Protein SELEX: For targets where phosphorylation, glycosylation, etc., are essential for function. 3. Cell-SELEX (for Cell-Surface…
What is an Aptamer? An aptamer is a short, single-stranded DNA or RNA oligonucleotide that folds into a specific 3D structure, allowing it to bind to a target molecule (like a cytokine) with high affinity and specificity, akin to a monoclonal antibody. Why Target Cytokines with Aptamers? Cytokines are key signaling proteins in immune and inflammatory responses. Dysregulation is implicated in diseases like: Autoimmune disorders: Rheumatoid arthritis, psoriasis, inflammatory bowel disease. Cancer: Tumor microenvironment signaling. Cytokine Storms: Severe COVID-19, sepsis. Neurological diseases. Aptamers offer advantages over traditional antibody-based therapies: High Specificity: Can distinguish between closely related cytokine isoforms or conformational states. Controlled Synthesis: Chemically produced, no batch-to-batch variation. Modifiability: Easily conjugated with drugs, fluorophores, or nanoparticles. Low Immunogenicity: Less likely to cause an immune response. Stability: Generally more stable than proteins. The Aptamer Screening Service Workflow (SELEX) A professional service will manage the entire SELEX (Systematic Evolution of Ligands by EXponential Enrichment) process. Here’s a typical pipeline: Phase 1: Project Design & Target Preparation Consultation: Define the goal—neutralization, detection, or delivery. Target Selection: Which cytokine? (e.g., TNF-α, IL-6, IL-1β, IFN-γ). Requires a high-purity, bioactive protein. Services often help with recombinant expression/purification if needed. Library Design: A vast random-sequence oligonucleotide library (10^14-10^15 unique sequences) is the starting point. Libraries can be DNA, RNA, or contain modified…
1. Core Concept: What is Capture-SELEX? Capture-SELEX (Systematic Evolution of Ligands by EXponential Enrichment) is an advanced selection technique used to discover single-stranded DNA or RNA aptamers that bind to a specific target molecule. The key innovation is that the target molecule is immobilized (or "captured") on a solid support via a short, known oligonucleotide sequence that is part of the initial random library. This makes it exceptionally powerful for selecting aptamers against small molecules or targets without natural immobilization sites. 2. The Key Differentiator: How It Differs from Classical SELEX Classical SELEX: The target itself is immobilized directly on a surface (e.g., a bead or plate). This can sometimes lead to aptamers that bind to the surface or the immobilized region of the target, which may not function well in solution. Capture-SELEX: The library itself is immobilized via a complementary "capture sequence." Only sequences that bind to the free, unmodified target in solution undergo a conformational change that releases them from the capture strand for collection. 3. Step-by-Step Process of a Capture-SELEX Service A service provider will typically manage this entire pipeline: Step 1: Project Design & Library Synthesis You define the target (e.g., a small molecule, protein, cell). The service designs a custom single-stranded DNA (ssDNA) library: [5' Fixed Primer Sequence - RANDOM Region…
What is CE-SELEX? SELEX (Systematic Evolution of Ligands by EXponential Enrichment) is the standard process for aptamer development. It involves iterative rounds of selection and amplification to enrich nucleic acid sequences that bind tightly to a target molecule. Traditional SELEX often uses immobilization of the target on beads or filters, which can be slow (8-15 rounds) and may introduce bias by selecting for sequences that bind to the immobilization matrix itself. CE-SELEX uses Capillary Electrophoresis as the separation mechanism. The key principle is that when an aptamer binds to its target, it forms a complex with a different charge-to-size ratio, causing it to migrate at a different time (shifted peak) in the capillary compared to the unbound nucleic acid library. This complex can be isolated and collected with exquisite precision. Core Advantages of a CE-SELEX Screening Service A service provider offering CE-SELEX delivers significant benefits: Extreme Speed and Efficiency: Often requires only 2-4 rounds of selection to obtain high-affinity aptamers (nanomolar to picomolar Kd), compared to many more rounds in traditional SELEX. This translates to weeks or months of time saved. Solution-Phase Selection: The target is free in solution, eliminating immobilization bias. This allows for selection against targets in their native conformation and enables selection for small molecules and…
