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 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.…
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…
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…
Aptamer Capture-SELEX Service refers to a specialized, outsourced process where a company or academic core facility performs the entire Capture-SELEX procedure to develop DNA or RNA aptamers for a client's specific target molecule. This is a crucial service for researchers and companies who need high-affinity, specific aptamers but lack the specialized equipment, expertise, or time to run the SELEX process in-house. Let's break down what this service entails. 1. What is Capture-SELEX? First, understand the standard SELEX (Systematic Evolution of Ligands by EXponential enrichment). It's an iterative process to select aptamers from a vast random oligonucleotide library (10^14 - 10^15 different sequences). Capture-SELEX is a specific variant designed primarily for small molecules or targets that are difficult to immobilize directly on a solid support without affecting their structure/function. The Key Difference: Instead of immobilizing the target itself, a short, complementary "capture strand" is immobilized on beads or a surface. The initial ssDNA library is designed with a region complementary to this capture strand. The target is free in solution. How it Works: The library is bound to the surface via the capture strand. The target molecule is introduced in solution. Only library sequences that fold into a structure capable of binding the target will undergo a conformational change. This binding event often weakens or…
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 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…
Aptamers are short single-stranded DNA or RNA molecules that fold into 3D shapes capable of binding specific targets (proteins, small molecules, cells) with high affinity and selectivity. The classic way to discover them is SELEX(Systematic Evolution of Ligands by EXponential enrichment): iterative rounds of binding, partitioning, amplification, and re-selection. What changed the field is high-throughput sequencing (HT-SELEX)—sequencing pools after each round—turning SELEX into a data-rich optimization problem where bioinformatics is no longer optional but central to identifying true binders, understanding enrichment dynamics, and avoiding artifacts. This article explains how bioinformatics for aptamer selection works end-to-end, what signals to extract from sequencing data, how to connect sequence to structure and function, and where modern machine learning fits—without relying on external case studies or outbound links. 1) Why Bioinformatics Matters in Aptamer Selection Traditional SELEX often ends with testing a handful of sequences from late rounds. HT-SELEX changes the game by giving you: Population-level visibility: you can track millions of sequences across rounds, not just a few clones. Early discovery: promising families can emerge before the pool looks “clean,” enabling earlier decision-making and fewer wet-lab rounds when combined with modeling. Artifact detection: PCR bias, sequencing errors, and “sticky” motifs can…
