Customized Aptamer Selection refers to a tailored process of identifying and developing aptamers—short, single-stranded DNA or RNA molecules—that specifically bind to a target molecule (proteins, small molecules, cells, or pathogens) according to a client’s specific requirements. Unlike standard aptamer screening, it focuses on individualized targets, binding conditions, and functional needs. Key Features: Target Specificity: Aptamers are selected for high affinity and specificity to a particular target. Flexible Design: Can be designed for proteins, peptides, small molecules, ions, or whole cells. Binding Conditions Customization: pH, temperature, ionic strength, or buffer system can be tailored. Functional Application: Aptamers can be developed for diagnostics, therapeutics, biosensors, or research. High-Throughput & Efficiency: Advanced techniques allow rapid screening for optimal aptamers. Typical Workflow: Target Analysis: Understanding target structure and function. Library Preparation: Generate a diverse pool of oligonucleotides. SELEX (Systematic Evolution of Ligands by EXponential enrichment): Iterative selection process to enrich high-affinity aptamers. Binding Affinity Testing: Determine Kd (dissociation constant) and specificity. Sequence Optimization & Modification: Chemical modifications for stability or functionalization. Delivery of Customized Aptamer: Ready for research, diagnostics, or therapeutic use. Common Applications: Diagnostics: Biosensors for disease markers. Therapeutics: Targeted drug delivery. Research Tools: Protein purification or molecular imaging. Environmental Monitoring: Detection of…
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 Whole Cell-SELEX? SELEX (Systematic Evolution of Ligands by EXponential enrichment) is a technique used to develop aptamers—single-stranded DNA or RNA oligonucleotides that bind to a specific target molecule with high affinity and specificity, akin to antibodies. Whole Cell-SELEX is a variant where the target is not a purified protein, but an entire living cell. This is crucial for discovering aptamers against: Native cell-surface proteins in their natural conformation and modification state. Complex membrane protein complexes. Disease-specific cell markers (e.g., on cancer cells, pathogens) without prior knowledge of the specific molecular target. Specific cell types in a heterogeneous mixture (e.g., cancer stem cells within a tumor). A service provider performs this technically demanding and iterative process on behalf of researchers or companies. The Core Process of a Whole Cell-SELEX Service A typical service workflow involves close collaboration with the client: 1. Project Design & Consultation Defining Targets: Client specifies the positive selection cell (e.g., human glioblastoma cells) and the critical negative/counter selection cell (e.g., normal astrocytes or a related cell line). This is key to generating selective aptamers. Library Design: The service provider uses a vast (10^14 - 10^15 sequences) random oligonucleotide library. 2. The SELEX Cycle (Iterative Rounds) This is the core experimental phase performed by the service provider: Incubation: The library is incubated…
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…
What is an Aptamer? First, a quick reminder: Aptamers are short, single-stranded DNA or RNA oligonucleotides that bind to a specific target with high affinity and specificity. They are often called "chemical antibodies." The Core Service: SELEX (The Screening Process) The service revolves around executing a SELEX (Systematic Evolution of Ligands by EXponential enrichment) campaign. This is an iterative, in-vitro combinatorial chemistry process that screens a vast random library (10^14 - 10^15 unique sequences) to find the few that bind your target. A standard SELEX workflow includes: Library Design & Synthesis: Creating the initial random oligonucleotide pool. Incubation: The library is exposed to the target. Partitioning: Bound sequences are separated from unbound ones (the most critical step, varying by target type). Amplification: The bound sequences are amplified (usually by PCR for DNA, RT-PCR for RNA). Counter-Selection (Negative Selection): To increase specificity, the pool is exposed to non-target surfaces (e.g., immobilization matrix, related proteins) to remove non-specific binders. Repetition: Steps 2-5 are repeated for 8-15 rounds until a high-affinity pool is enriched. Cloning & Sequencing: The final pool is cloned, and individual aptamer sequences are identified via Next-Generation Sequencing (NGS). Bioinformatics & Analysis: NGS data is analyzed to identify candidate sequences, often clustered into families based on sequence/structure motifs. Characterization: Top candidates…
What is Live Cell SELEX? Traditional SELEX uses purified target proteins. Live Cell SELEX uses intact, living cells in their native state. This is crucial because: It selects for aptamers that bind to targets in their natural conformation and post-translational modifications (e.g., glycosylation). It inherently selects for cell-specificity (e.g., cancer cell vs. healthy cell) without needing to know the exact molecular target upfront. It can discover aptamers against unknown or membrane-bound targets that are difficult to purify. Core Workflow of a Typical Service A full-service provider will manage the entire pipeline: 1. Project Design & Consultation Target Cell Line Definition: Defining the "positive" cell line (e.g., patient-derived cancer cells, activated immune cells). Counter-Selection Strategy: Choosing the "negative" cell line(s) (e.g., healthy counterpart, isogenic control) to eliminate non-specific binders. Library Design: Recommending or customizing the starting random oligonucleotide library (length, modifications like 2'-F pyrimidines for RNA aptamers for stability). 2. The Selection Phase (The Iterative SELEX Cycles) Incubation: The random library is incubated with the counter-selection cells. Unbound/non-specific sequences are collected. Positive Selection: The pre-cleared library is incubated with the target cells. Cells are washed stringently. Recovery: Cell-bound aptamers are recovered (e.g., by cell lysis, heat elution, or protease treatment). Amplification: Recovered sequences are amplified by PCR (for DNA) or RT-PCR (for…
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…
