Core Concept of NGS-SELEX Traditional SELEX uses a few rounds of selection and cloning/Sanger sequencing of a handful of clones. NGS-SELEX performs deep sequencing (millions to billions of reads) at every selection round. This allows you to: Track the entire evolution of the oligonucleotide pool in real-time. Identify enriched sequences and families early. Perform sophisticated bioinformatics analysis to find winners, not just rely on final round abundance. Dramatically reduce the number of selection rounds needed (often 3-6 rounds instead of 8-15). Standard Service Workflow A full-service provider would typically offer the following pipeline: 1. Project Design & Library Synthesis Consultation: Target properties (protein, small molecule, cell), desired aptamer properties (Kd, specificity, buffer conditions). Library Design: Standard (40-60 nt random region) or custom (doped libraries, modified nucleotides like 2'-F, 2'-OMe, SOMAmers). Primer & Library Synthesis: Providing the initial, highly diverse DNA or RNA library (10^14 - 10^15 unique sequences). 2. SELEX Selection Immobilization: Immobilizing the target (on beads, column, plate) or using solution-based techniques (capture-SELEX, toggle-SELEX). Counter-Selection: Including steps to remove binders to immobilization matrix or off-targets. Stringency Control: Increasing selection pressure over rounds (e.g., reduced target concentration, increased wash stringency). Amplification: Careful PCR (with optimization to minimize bias) to regenerate the pool for the next round. 3. NGS & Core Bioinformatics Sample Preparation: Preparing sequencing…
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…
Aptamers and antibodies are both molecular recognition tools—they bind targets with high specificity and affinity—but they come from very different histories. Antibodies emerged from immunology and serum therapy, while aptamers grew out of in vitro evolution and nucleic-acid chemistry. Understanding their origins helps explain why they behave differently in diagnostics, research, and therapeutics. 1) What Antibodies Are—and Why Their History Matters Antibodies are proteins produced by the immune system that recognize antigens. Their “history” is tightly linked to the birth of modern immunology: early observations that blood serum could protect against infection eventually led to the concept of specific “anti-bodies” as functional components of immunity. Over the 20th century, progress in structural biology and molecular genetics clarified how antibodies achieve both diversity and specificity, culminating in technologies that made antibodies reliable lab and industrial tools. Key turning point: monoclonal antibodies A major leap occurred in the 1970s with the development of methods to produce monoclonal antibodies—antibodies of single, defined specificity that could be generated reproducibly and at scale. This transformed antibodies from biological curiosities into standardized reagents for diagnostics and targeted therapy. 2) What Aptamers Are—and How They Were Discovered Aptamers are short, single-stranded nucleic…
“Aptamer fields” can be understood as the interconnected research and application areas where aptamers—short, single-stranded DNA or RNA molecules—are designed and used as highly selective binding agents (often described as “chemical antibodies”) for targets ranging from proteins and small molecules to whole cells. This article explains what defines the aptamer fields, how aptamers are created, where they’re used, and what technical trends are shaping the space. 1) What Are Aptamers (and Why They Matter in Aptamer Fields)? Aptamers are typically ~20–100 nucleotides long and fold into 3D structures that bind specific targets with high affinity and specificity. Unlike antibodies (biological proteins), aptamers are nucleic acids, which affects how they are discovered, synthesized, modified, and integrated into devices. Key reasons aptamers have become a “field” rather than a niche tool: Programmability: sequence-controlled design and chemical modification Manufacturability: scalable synthesis routes compared with biological production Versatility: diagnostics, biosensing, therapeutics, imaging, and research reagents 2) The Core Engine: SELEX and How Aptamers Are Discovered Most aptamers are generated using SELEX (Systematic Evolution of Ligands by EXponential enrichment), an iterative in-vitro selection process that enriches sequences that bind a chosen target. In common workflows, a large random library is…
CUSTOM APTAMER DISCOVERY & DEVELOPMENT is the process of creating target-specific single-stranded DNA or RNA aptamers—short nucleic acids that fold into 3D shapes capable of binding proteins, small molecules, cells, vesicles, or other targets with antibody-like selectivity. Most custom programs rely on SELEX (Systematic Evolution of Ligands by EXponential enrichment), then refine “hits” into robust, application-ready binders through sequencing-driven analysis and post-selection optimization. 1) What Aptamers Are (and Why They’re Used) Aptamers are typically ~15–90 nucleotides long and can be engineered to bind targets across a wide size range (from small molecules to whole cells). They’re attractive because they are chemically synthesized (batch-to-batch consistency), can be readily labeled (fluorophores, biotin, etc.), and are generally thermally stable and re-foldable—features that often simplify assay development and manufacturing. Common aptamer use cases Diagnostics & biosensors (capture probes, signal transducers, point-of-care formats) Targeted delivery & therapeutics research (cell-directed binding, payload delivery concepts) Affinity purification & analytical workflows (pull-downs, enrichment, separations) 2) The Core Workflow in Custom Aptamer Discovery A custom program is best thought of as a pipeline with four linked decisions: target format → selection strategy → analytics → optimization. Step A — Target Definition and “Bindability” Planning…
What “SELEX Aptamer Selection” Means SELEX stands for Systematic Evolution of Ligands by Exponential Enrichment. In plain terms, SELEX aptamer selectionis an iterative laboratory workflow that starts with a huge pool of random DNA or RNA sequences and repeatedly enriches the fraction that binds a chosen target with high affinity and specificity. The “winners” are called aptamers—single-stranded nucleic acids that fold into 3D shapes capable of target recognition, often compared to “chemical antibodies,” but made by selection and synthesis rather than immune systems. Core Concept: Darwinian Evolution in a Test Tube SELEX is essentially variation + selection + amplification: Variation: Begin with a randomized oligonucleotide library (often ~10^13–10^16 unique sequences). Selection: Expose the library to the target; keep sequences that bind. Amplification: PCR (or RT-PCR for RNA workflows) amplifies binders to create the next-round pool. Increasing stringency: Each round tightens conditions (less target, harsher washes, more competitors), enriching the best binders over multiple cycles. Most conventional SELEX workflows run multiple rounds (often roughly 6–15) before candidates are sequenced and characterized. The Classic SELEX Workflow (Step-by-Step, With the “Why”) 1) Library design (the “starting universe”) A typical library contains: A random region (e.g., N30–N60) that can…
Aptamers are short, single-stranded nucleic acid molecules (DNA or RNA) that fold into specific 3D shapes and bind targets with high affinity and selectivity—often compared to how antibodies recognize antigens, but built from nucleic acids rather than proteins. Unlike a “generic DNA strand,” an aptamer’s function comes from structure: loops, stems, bulges, pseudoknots, and other motifs that create a binding surface matching a target’s geometry and chemistry. Targets can include proteins, peptides, small molecules, ions, and even whole cells (depending on the selection strategy). Why Aptamers Matter (and How They Differ From Antibodies) Aptamers are often described as “chemical antibodies,” but the differences are exactly why they’re valuable. Key advantages frequently highlighted Low immunogenicity (reduced risk of provoking immune responses) High stability and the ability to refold after denaturation in many cases Easy chemical synthesis (batch consistency, scalable manufacturing) Straightforward modification (labels, linkers, immobilization handles) Trade-offs you should know Nuclease sensitivity (especially RNA aptamers) can be a limitation in biological fluids unless stabilized. Selection bias can occur during discovery (e.g., PCR bias), meaning “best in the tube” isn’t always “best in reality.” Very high affinity does not automatically guarantee best real-world specificity; selection conditions matter. …
