“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 Capture-SELEX? Unlike traditional SELEX where the target is immobilized, Capture-SELEX immobilizes the initial DNA library itself via a short complementary "capture" sequence. The key target molecule is free in solution. Binding occurs when an aptamer candidate in the library binds to the target, causing a structural change that releases it from the immobilization surface. This approach offers distinct advantages: Ideal for small molecules and proteins: Especially targets that are difficult to immobilize without affecting their structure. Minimizes non-specific binding: Selection pressure is purely for target-induced structure formation/release. Enriches for structure-switching aptamers: Resulting aptamers often undergo conformational change upon binding, making them excellent for biosensor development. Typical Capture-SELEX Screening Service Workflow A professional service provider will manage this complex, iterative process from start to finish. Here’s what you can expect: Phase 1: Project Design & Library Preparation Consultation & Target Specification: Defining target properties, desired affinity (Kd), specificity (against which counter-targets), and buffer conditions. Customized Library Design: Designing a single-stranded DNA library (10^14 - 10^15 unique sequences) with: A central random region (e.g., 30-50 nucleotides). Fixed primer regions for PCR amplification. A capture sequence region complementary to an immobilized oligonucleotide. Immobilization Matrix Preparation: Coupling the complementary "capture" oligonucleotides to a solid support (e.g., magnetic beads, chromatography resin). Phase 2: The Iterative Selection (SELEX) Cycles…
What is Filter Membrane Binding SELEX? SELEX (Systematic Evolution of Ligands by EXponential enrichment) is the standard method for discovering high-affinity, specific nucleic acid aptamers. The Filter Membrane Binding variant is one of the most classic and robust SELEX techniques. Core Principle: It leverages a nitrocellulose or mixed cellulose ester filter membrane, which irreversibly binds proteins and other macromolecules but allows short, unbound single-stranded DNA or RNA oligonucleotides to pass through. The Selection Mechanism: During each selection round, the target molecule (e.g., a protein) is immobilized on the filter. An immense library of random oligonucleotides (10^13 - 10^15 unique sequences) is applied. Only sequences that bind to the target are retained on the filter with it. Unbound sequences are washed away. The bound aptamer candidates are then eluted, amplified by PCR (or RT-PCR for RNA), and used as the enriched library for the next round. Key Features of the Service A professional service will typically offer: Target Flexibility: Optimal for purified proteins (recombinant or native), protein complexes, viruses, and even some small molecules if conjugated to a carrier protein. Counter-SELEX: A critical step to ensure specificity. The enriched library is passed through a filter bound to non-target molecules (e.g., related proteins, cell lysates, immobilization matrix) to subtract cross-reactive binders. High-Throughput…
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 Stem Cell Aptamer Screening Service? It is a contract research service where a specialized lab uses Systematic Evolution of Ligands by EXponential Enrichment (SELEX) to discover and develop DNA or RNA aptamers that bind with high affinity and specificity to a target of your choice related to stem cells. Aptamers are often called "chemical antibodies." They are short, single-stranded oligonucleotides that fold into unique 3D shapes, allowing them to bind to targets like proteins, small molecules, or even whole cells. Core Targets for Stem Cell Applications The service can be tailored to screen for aptamers against: Specific Cell Surface Markers: (e.g., CD34, CD133, SSEA-4, TRA-1-60) for identification and isolation. Whole Live Stem Cells: To get aptamers that recognize the unique molecular signature of a specific stem cell type (e.g., mesenchymal stem cells, cancer stem cells, pluripotent stem cells). Differentiation State-Specific Targets: To distinguish between pluripotent, progenitor, and fully differentiated cells. Specific Stem Cell-Derived Products: (e.g., exosomes, vesicles). Typical Workflow of the Service A professional service provider will guide you through these stages: Phase Description Your Input 1. Project Design Defining the target (specific protein, cell line, primary cells), counter-selection cells (to ensure specificity), and desired aptamer properties (e.g., Kd, nuclease resistance). Provide target cells, control cells, and…
What is a Bacterial Aptamer Screening Service? It is a specialized contract research service where a provider uses Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to discover and develop single-stranded DNA or RNA aptamers that bind with high affinity and specificity to a bacterial target. The target can be: Whole bacterial cells (e.g., E. coli O157:H7, Salmonella typhimurium). Specific bacterial components (e.g., surface proteins like pili, flagella, capsular polysaccharides, secreted toxins). Key virulence factors (e.g., endotoxins like LPS). The resulting aptamers are powerful recognition elements for diagnostics, therapeutics, and research. Core Steps in the Service Pipeline A typical full-service offering includes: 1. Project Design & Target Preparation: Consultation: Defining the goal (e.g., detection of a specific strain, therapeutic neutralization). Target Choice: Deciding between whole cells (for broad detection) or purified components (for precise targeting). Counter-SELEX: Using related non-target cells (e.g., non-pathogenic strain) to eliminate cross-reactive aptamers and ensure specificity. 2. Library Synthesis & SELEX Process: Library Design: Using a random-sequence oligonucleotide library (typically ~10^14 different molecules). Selection Rounds (8-15 cycles): Iteratively incubating the library with the target, washing away unbound sequences, eluting the bound ones, and amplifying them via PCR (for DNA) or RT-PCR (for RNA). Monitoring: Using quantitative PCR or flow cytometry to track enrichment progress. 3. Next-Generation Sequencing (NGS) & Bioinformatics:…
Core Concept: Aptamers vs. Antibodies Aptamers are often called "chemical antibodies." Their key advantages for cancer targeting include: Small size: Better tissue penetration. In vitro synthesis: Highly reproducible, no batch-to-batch variation. Ease of modification: Can be chemically tagged with dyes, drugs, or nanoparticles. Low immunogenicity. Target Range: Can bind to proteins, carbohydrates, lipids, or even complex molecular patterns on a whole cell's surface. The Screening Service Workflow (Cell-SELEX) A typical service follows these steps: 1. Project Design & Target Selection Client Input: You define the target (e.g., "Aptamers for metastatic triple-negative breast cancer cell line MDA-MB-231"). Counter-Selection: Crucial step. To ensure specificity, the service provider will also use a control cell line (e.g., normal breast epithelial cells or a less aggressive cancer type) to remove aptamers that bind to common, non-target molecules. Library Design: The provider uses a vast random oligonucleotide library (e.g., 10^14 different sequences). 2. The SELEX Process This is an iterative, multi-round biochemical "fishing" experiment: Incubation: The library is exposed to the target cancer cells. Washing: Weakly or unbound sequences are washed away. Elution: Bound aptamers are recovered (e.g., by heating or trypsinizing cells). Amplification: Recovered aptamers are amplified by PCR (for DNA) or RT-PCR (for RNA). Stringency Increase: In each subsequent round, conditions become stricter (more washing, shorter incubation, addition…
What is the Core Service? The service provider uses an iterative, in vitro selection process called SELEX (Systematic Evolution of Ligands by EXponential Enrichment) to screen vast random oligonucleotide libraries (10^14 - 10^15 unique sequences) against your target protein. The output is a set of characterized aptamer sequences that bind to the viral capsid. Standardized Screening Workflow A professional service will manage this entire pipeline: 1. Project Design & Target Preparation: Target Discussion: Defining the specific capsid protein (e.g., HIV-1 CA, HBV core, SARS-CoV-2 N), its form (full-length, domain, assembled capsid/nucleocapsid), and purity. Target Immobilization: The protein is often immobilized on a solid support (beads, plate) to facilitate separation of bound/unbound sequences. Some services offer solution-phase or capillary electrophoresis (CE-SELEX) methods for higher stringency. 2. SELEX Selection Rounds (Cycles 5-15): Incubation: The oligonucleotide library is incubated with the target. Partitioning: Unbound sequences are washed away; bound sequences are retained. Elution: Bound aptamers are eluted (e.g., by heating, denaturing agents). Amplification: Eluted aptamers are amplified by PCR (for DNA) or RT-PCR (for RNA). Purification: The amplified pool is purified for the next selection round. Counter-Selection: To ensure specificity, the pool is often passed through a negative control (e.g., irrelevant protein, cell lysate) to remove non-specific binders. 3. Sequencing & Identification: High-Throughput…
What is an Antibody Aptamer Screening Service? It is a specialized contract research service where a biotechnology company uses SELEX (Systematic Evolution of Ligands by EXponential Enrichment) or advanced variations of it to discover and develop aptamers that bind with high affinity and specificity to a target antibody. Antibody: A large, Y-shaped protein produced by the immune system to identify and neutralize pathogens. Aptamer: A short, single-stranded DNA or RNA oligonucleotide (or a modified derivative) that folds into a specific 3D structure, enabling it to bind to a target molecule with antibody-like specificity. Often called "chemical antibodies." The goal of the service is to provide clients with synthetic, recombinant-like binding molecules as alternatives or complements to traditional monoclonal antibodies. Why Screen for Aptamers Against Antibodies? Aptamers offer distinct advantages, making them attractive for various applications: Anti-Drug Antibody (ADA) Detection: Develop aptamer-based assays to detect and quantify ADAs in clinical trials for biotherapeutics. Diagnostic Tools: Create aptamer sensors (aptasensors) to detect specific antibody biomarkers for diseases (e.g., autoantibodies in autoimmune disorders). Therapeutic Neutralization: Discover aptamers that can bind and neutralize pathological antibodies (e.g., in autoimmune diseases like lupus or myasthenia gravis). Purification & Pull-Down: Use aptamers as ligands in chromatography or in assays to capture and isolate specific antibodies from complex…
