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? Aptamers are single-stranded DNA or RNA oligonucleotides that fold into specific 3D shapes, enabling them to bind to target molecules (proteins, small molecules, cells, viruses) with high affinity and specificity, similar to antibodies. They are often called "chemical antibodies." Why Use Aptamer Screening Services in Drug Discovery? Efficiency: Outsourcing to experts with specialized platforms (SELEX) accelerates discovery. Cost-Effectiveness: Avoids capital investment in complex SELEX and NGS infrastructure. Expertise: Leverages specialized knowledge in oligonucleotide chemistry, bioinformatics, and target biology. Focus: Allows internal teams to concentrate on downstream therapeutic development. Core Components of an Aptamer Screening Service A full-service provider typically offers an end-to-end pipeline: 1. Project Design & Target Preparation Consultation: Defining the target (recombinant protein, cell surface marker, whole cell), desired affinity (nM-pM), and specificity (e.g., against homologs). Counter-SELEX Strategy: Planning to eliminate binders to non-desired epitopes or related targets to ensure high specificity. 2. In Vitro Selection (SELEX) The core technology is SELEX (Systematic Evolution of Ligands by EXponential enrichment). Advanced variants are used for complex targets: Protein-SELEX: For purified recombinant proteins. Cell-SELEX: For membrane proteins in their native conformation on live cells; identifies aptamers for diseased vs. healthy cells. Tissue-SELEX: For even more complex biological environments. Capture-SELEX: For small molecules that are difficult to immobilize. High-Throughput SELEX (HT-SELEX): Uses NGS early…
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…
What is an Aptamer? An aptamer is a short, single-stranded DNA or RNA oligonucleotide that binds to a specific target molecule (like a protein) with high affinity and specificity. They are often called "chemical antibodies" but offer advantages like smaller size, chemical stability, and in-vitro generation. The Core Service: SELEX (Systematic Evolution of Ligands by EXponential Enrichment) The standard method for aptamer screening is SELEX. A specialized service will manage this entire iterative, high-complexity process for you. General SELEX Workflow: Target Preparation & Immobilization: Your service provider will prepare your purified protein. It is often immobilized on a solid support (beads, column, plate) to separate bound from unbound sequences. Incubation with Library: A vast, random synthetic oligonucleotide library (10^13 - 10^15 unique sequences) is incubated with the target. Partitioning: Weak or non-binding sequences are washed away. Tightly bound aptamers are retained. Elution & Amplification: The bound sequences are eluted and amplified by PCR (for DNA) or RT-PCR (for RNA). Stringency & Counter-SELEX: Subsequent rounds introduce increased washing stringency and incubation with non-target molecules (e.g., similar proteins, immobilization matrix) to filter out non-specific binders. This is crucial for specificity. Cloning & Sequencing: After 8-15 rounds, the enriched pool is cloned and sequenced to identify individual candidate aptamers. Characterization &…
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 Protein SELEX? SELEX (Systematic Evolution of Ligands by EXponential Enrichment) is an iterative, in vitro process used to discover aptamers—single-stranded DNA or RNA molecules that bind to a specific target (like a protein) with high affinity and specificity. Protein SELEX specifically refers to using a purified protein as the target to isolate aptamers against it. These aptamers are often called "chemical antibodies" due to their similar binding function. Core Workflow of a Protein SELEX Service A professional service will manage this entire complex process, typically involving the following stages: 1. Project Design & Consultation Target Characterization: Discussing the target protein's properties (size, purity, stability, domains, post-translational modifications). Selection Strategy: Choosing the right SELEX variant (e.g., Nitrocellulose filter, Magnetic bead, Capillary Electrophoresis, or Cell-SELEX for membrane proteins). Defining counter-selection steps to avoid binders to unwanted tags or impurities. Library Design: Using a standard or custom random oligonucleotide library (e.g., 40-60 random nucleotides flanked by primer sites). 2. The SELEX Cycle (Repeated 8-15 Rounds) mermaid graph TD A[Start: ssDNA/RNA Library<br>~10^15 unique sequences] --> B{Incubation with<br>Target Protein}; B --> C[Partition: Separate<br>Bound from Unbound Sequences]; C --> D[Elution: Recover<br>Bound Sequences]; D --> E[Amplification:<br>PCR (DNA) or RT-PCR (RNA)]; E --> F[Purification:<br>Regenerate ssDNA/RNA for next round]; F --> G{Enrichment<br>Sufficient?}; G -- No…
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…
What is Solution-Phase SELEX? SELEX (Systematic Evolution of Ligands by EXponential Enrichment) is the iterative process used to discover aptamers—single-stranded DNA or RNA molecules that bind to a specific target with high affinity and specificity. Solution-Phase SELEX refers to performing the selection process with the target molecule free in solution, rather than immobilized on a solid surface (like beads or a column). This often involves a partitioning step that separates bound from unbound sequences using a method like filtration, capillary electrophoresis, or magnetic bead capture of the target. Key Advantages of Solution-Phase SELEX Preservation of Native Target Conformation: The target is in its natural, free state in solution. This is crucial for complex targets like membrane proteins, which can denature or present epitopes unnaturally when immobilized. Access to All Binding Sites: All surfaces of the target are available for aptamer binding, increasing the diversity of potential aptamers discovered. Avoidance of Non-Specific Binding to Solid Support: Reduces background noise from library sequences sticking to the immobilization matrix (e.g., sepharose beads, plastic wells), leading to cleaner selections. Better for Small Molecules and Peptides: Ideal for targets that are difficult to immobilize without blocking their functional groups. Mimics Physiological Conditions: More closely replicates how the aptamer will interact with its target in real-world applications…
What is Classical SELEX? SELEX is an iterative, in vitro selection process used to isolate single-stranded DNA or RNA molecules (aptamers) that bind with high affinity and specificity to a target (e.g., a protein, small molecule, cell, or virus). The "classical" method refers to the original, well-established protocol involving: Incubation: A vast, random-sequence nucleic acid library (10^14 - 10^15 different sequences) is exposed to the target. Partitioning: Unbound sequences are washed away; bound sequences are retained. Elution: The bound sequences are recovered. Amplification: The recovered sequences are amplified by PCR (for DNA) or RT-PCR (for RNA). Repetition: This cycle (typically 8-15 rounds) is repeated, enriching the pool for the strongest binders. Components of a Classical SELEX Service A full-service provider typically manages the entire pipeline: 1. Project Design & Consultation Target Characterization: Discussing the target's properties (purity, stability, availability). Selection Strategy: Deciding on immobilization method (e.g., target immobilized on beads, or "counter-SELEX" to eliminate binders to the immobilization matrix or similar non-target molecules). Library Design: Choosing DNA or RNA, length of the random region (typically 20-60 nt), and fixed primer regions. 2. The SELEX Process Execution Library Synthesis: Chemical synthesis of the initial random library. Cycle Management: Performing the repetitive rounds of binding, washing, elution, and amplification under optimized buffer and stringency…
What are Aptamers? Aptamers are short, single-stranded DNA or RNA oligonucleotides (typically 20-80 nucleotides) that fold into specific three-dimensional shapes, enabling them to bind to target molecules with high affinity and specificity. They are often called "chemical antibodies." The process of creating them is called SELEX (Systematic Evolution of Ligands by EXponential enrichment), which iteratively selects aptamers from vast random-sequence libraries against a desired target (e.g., a protein, small molecule, or even a whole cell). Key Advantages of Aptamers as Therapeutics Compared to traditional protein-based biologics like antibodies, aptamers offer several compelling benefits: High Specificity & Affinity: Can distinguish between closely related targets (e.g., different protein isoforms). Small Size: Typically 8-25 kDa, much smaller than antibodies (~150 kDa). This can improve tissue penetration. Full Chemical Synthesis: Produced in vitro via chemical synthesis, eliminating batch-to-batch variability and the need for biological systems (cells or animals). This makes manufacturing scalable and consistent. Low Immunogenicity: Being nucleic acids, they are generally less likely to trigger immune reactions than foreign proteins. Excellent Stability: DNA aptamers, in particular, are thermally stable and can be stored easily. Stability in biological fluids can be engineered. Ease of Modification: Can be chemically modified to enhance stability (e.g., resist nucleases), prolong half-life (e.g., PEGylation), or add functional groups…
