Key Characteristics and Working Principles of Aptamers 1. What is an Aptamer? An aptamer is a short, single-stranded oligonucleotide (DNA or RNA) obtained through in vitro selection, capable of binding to a specific target with high affinity and high specificity. Its name derives from the Latin "aptus" (meaning "to fit") and the Greek "meros" (meaning "part"). It can be regarded as a chemical antibody, but its essence is nucleic acid rather than protein. 2. Key Characteristics Compared to traditional antibodies, aptamers possess a series of outstanding advantages: High Affinity and High Specificity Can bind tightly to targets with dissociation constants (Kd) in the nanomolar (nM) or even picomolar (pM) range, similar to antibodies. Capable of distinguishing between targets with subtle differences, e.g., distinguishing phosphorylated from non-phosphorylated states of the same protein, recognizing minor conformational changes in proteins, or differentiating structurally similar molecules (like caffeine and theophylline). Extremely Broad Target Range Targets are not limited to immunogenic substances. From ions, small molecules, drugs, and toxins to proteins, viruses, bacteria, cells, and even entire tissues, aptamers can potentially be selected for almost any target. Chemical Synthesis and Modification Can be produced on a large scale, at low cost, and with high purity in vitro via solid-phase synthesis, ensuring minimal batch-to-batch variation.…
An aptamer is a short, single-stranded DNA or RNA sequence that is synthesized artificially. It can fold into a specific three-dimensional structure (such as a hairpin, bulge, G-quadruplex, etc.), enabling it to bind to a target molecule with high specificity and high affinity. You can think of it as a "chemical antibody," but its essence is not protein—it is nucleic acid. Key Characteristics and Advantages (Compared to Traditional Antibodies) Characteristic Aptamer Traditional Antibody Nature Single-stranded DNA or RNA (nucleic acid) Protein Production Chemical synthesis in vitro, controllable process, minimal batch-to-batch variation Biological production in vivo (using animal cells), potential batch-to-batch variation Stability Very high. Heat-resistant, can be stored long-term at room temperature, can undergo repeated denaturation and renaturation without losing activity Relatively low. Usually requires low-temperature storage, prone to denaturation and loss of activity Immunogenicity Generally low or none, unlikely to cause an immune response May cause an immune response (especially heterologous antibodies) Modification & Labeling Very easy. Can precisely incorporate fluorescent groups, chemical modifications, linkers, etc., during synthesis More difficult, modifications may affect binding capability Target Range Very broad. From ions and small molecules to proteins, whole cells, viruses, and even bacteria Primarily targets immunogenic biomacromolecules Molecular Size Small (typically 5-15 kDa), strong tissue penetration Large (~150…
Technical Document: Aptamer Screening – Principles, Applications, and Advances Document Version: 1.0 Date: October 26, 2023 Subject: Overview of the methodologies and diverse applications of aptamer screening technologies. 1.0 Executive Summary Aptamer screening, primarily through the Systematic Evolution of Ligands by EXponential enrichment (SELEX) process, is a high-throughput in vitro technology for identifying single-stranded DNA or RNA oligonucleotides (aptamers) with high affinity and specificity for a target molecule. This document outlines the core principles of aptamer screening and its transformative applications across diagnostics, therapeutics, biotechnology, and environmental monitoring. Aptamers, often termed "chemical antibodies," offer advantages such as in vitro synthesis, low immunogenicity, and ease of modification, making them powerful tools in molecular recognition. 2.0 Introduction to Aptamer Screening Aptamers are short, synthetic oligonucleotides that fold into defined three-dimensional structures, enabling them to bind to targets ranging from small ions and organic molecules to proteins, cells, and even whole organisms. The process of discovering these binding sequences is called aptamer screening. The gold standard method is SELEX, a repetitive cycle of: Incubation: A vast, random oligonucleotide library (10^14–10^15 sequences) is exposed to the target. Partitioning: Target-bound sequences are separated from unbound ones. Amplification: The bound sequences are amplified via PCR (for DNA) or RT-PCR (for RNA). Conditioning: The enriched pool is prepared for the next selection…
Aptamer Screening Methods Introduction Aptamers are single-stranded DNA or RNA oligonucleotides that bind to specific target molecules with high affinity and specificity. The Systematic Evolution of Ligands by EXponential enrichment (SELEX) process is the primary method for aptamer development. The choice of screening strategy depends critically on the nature of the target—its size, structure, chemical properties, and available functional groups for immobilization. This document outlines established and emerging SELEX methodologies tailored for different target classes: small molecules, proteins, and whole cells. 1. Screening Methods for Small Molecule Compounds Small molecule targets (MW < 1000 Da, e.g., toxins, antibiotics, hormones) present unique challenges due to their simple structure, limited binding sites, low affinity for nucleic acids, and difficulty in separation from unbound sequences. Screening strategies often require immobilization of the target or the library, with optimized separation techniques. 1.1. Agarose Affinity Chromatography SELEX Principle: The small molecule target is covalently coupled to cross-linked agarose beads packed into a chromatography column. A nucleic acid library is passed through; bound sequences are retained and later eluted for amplification. Process: Typically requires 3–18 selection rounds. Applications: Early and successful selection of aptamers for dyes, ATP, S-adenosylhomocysteine, L-arginine, coenzyme A, kanamycin, and benzylpenicillin. Advantages: Mature, reliable technology. Limitations: Requires large…
In recent years, various screening methods have been developed to generate aptamers more reliably and efficiently. These include Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and its various derivative techniques, such as magnetic bead SELEX, capture SELEX, graphene oxide SELEX, cell-SELEX, capillary electrophoresis SELEX, and atomic force microscopy SELEX. This review summarizes these methods and analyzes the key characteristics, advantages, and limitations of each SELEX approach (see Table 1). The wide application of aptamers has driven the continuous development of SELEX technology. Over recent decades, numerous new methods for screening aptamers have emerged, significantly reducing the screening time from weeks to just hours. Table 1. Advantages and disadvantages of SELEX method currently used. Method Key Aspects Advantages Disadvantages Target small molecule compounds Agarose affinity chromatography SELEX The aptamers that can bind to the target can be isolated by fixing the small molecular target with agarose affinity chromatography column The most traditional aptamer screening method with the longest application time Low separation efficiency, requires relatively large amounts of elution materials MB-SELEX SsDNA or target was fixed with magnetic beads, and the bound sequence was separated from the unbound sequence by magnetic field. Avoid changes in the inherent structure of the target…
has an experienced team of technical staff to provide aptamer screening services for different targets ranging from purified proteins to whole cells and tissues. We are committed to providing our customers aptamer screening services for protein with high-quality and high affinity aptamers. Aptamers are an excellent alternative or complement to monoclonal antibodies, with high immunogenicity and low production costs. Aptamers have several clear advantages over antibodies due to their smaller size and nucleic acid properties, which can improve their clinical applicability and industrial applicability. Fig 1. Important advantages of aptamer over antibody [1]. Numerous in vitro screens have shown that the screened aptamers can specifically bind any target, including ions, nucleotides, peptides, large glycoproteins, viral particles, cells, etc., and even tissues and organs in animals can be used as targets for aptamer screening. However, different targets have different affinity for aptamers, for example, small molecule targets have weaker affinity for aptamers. At present, aptamer screening is still mainly focused on the protein field. Aptamer Screening for Purified Protein The protein-targeted aptamer is usually a short oligonucleotide sequence or short polypeptide obtained by in vitro screening, which can bind to the corresponding ligand with high affinity and strong specificity. And the biomedical community provides a new…
Integrated high-throughput antibody characterization to advance drug discovery research Surface Plasmon Resonance (SPR) is a powerful analytical technology for analyzing and characterizing antibodies. SPR measures the antibody-antigen binding kinetics and performs epitope binning and mapping. Benefits of SPR antibody characterization using the Carterra LSA: High-throughput: Kinetically screen and rank up to 1,152 mAbs and 384 clones at one time in parallel. Low sample usage: Only <200µl of each interactant is required. Rapid data analysis: Powerful software tools enable large data sets to be rapidly fitted, visualized, and automatically validated against several data quality parameters. Detailed data mining: Interrogate mAb panels via interactive on-rate, off-rate, affinity, and iso-affinity plots. Data integration: Combine binning and kinetics screening data for comprehensive monoclonal antibody mAb evaluation. Let's Discuss Your Experiment Antibody screening and kinetics services The Carterra LSA enables high-throughput screening of up to 384 antibodies simultaneously. Click on the image below to see the full results from a single capture kinetics assay where a monovalent target (analyte) was titrated over 384 antibodies, each captured onto individual spots of a 384-array. Each panel represents the global kinetic analysis on a single spot; all 384 spots were analyzed in parallel (some spots are excluded) Screening…
APTAMER SCREENING SERVICE: Aptamer Development Nucleic acid aptamers are short single-stranded oligonucleotides (ssDNA or ssRNA) that can selectively bind to a specific target with high affinity. A large number of aptamers have been developed to recognize various targets including small molecules, protein and entire cells. Aptamers have been widely used in both basic research and clinical purposes. The standard process used to screen aptamers is known as systematic evolution of ligands by exponential enrichment (SELEX). This process includes multiple rounds of incubation, separation, elution, amplification, and single-strand oligonucleotide purification and sequencing. kmdbioscience has established an optimized platform for aptamer screening. We can select DNA aptamers against purified protein samples as well as small chemical molecules. We have successfully developed several aptamers with Kd affinity ranging from 0.1 ~ 10 nM. In most cases, more than one aptamer can be achieved through multiple rounds of selection. If the customer needs, we can provide all the aptamers obtained from the screening. Let kmdbioscience assists you to promote progress in your aptamer-related research.
Technical Highlights of the Aptamer Development Process Aptamer development is centered around the SELEX (Systematic Evolution of Ligands by EXponential enrichment) process. Its key technological highlights can be summarized in the following stages: 1. Library Design & Synthesis Vast Diversity: Creation of a synthetic random-sequence oligonucleotide library (typically 10^14 - 10^15 different sequences) flanked by fixed primer regions. Chemical Modification: Incorporation of modified nucleotides (e.g., 2'-F, 2'-O-Me) to enhance nuclease resistance and binding affinity post-selection. 2. Target-Specific Selection (The Core of SELEX) Incubation: The library is incubated with the immobilized or soluble target molecule (protein, small molecule, cell, etc.). Partitioning: Efficient separation of target-bound sequences from unbound ones using methods like filtration, affinity chromatography, or capillary electrophoresis. Counter-Selection: A critical step to subtract sequences that bind to non-target components (e.g., immobilization matrix or related off-targets), drastically improving specificity. 3. Amplification & Iteration PCR/RT-PCR: Recovery and exponential amplification of the bound sequences to generate an enriched pool for the next selection round. Stringency Control: Gradual increase in selection pressure (e.g., reduced target concentration, shorter incubation time, stringent washes) over successive rounds (typically 8-15 rounds) to drive the evolution of high-affinity, specific binders. 4. Cloning, Sequencing & Characterization Clone Isolation: Post-SELEX, the enriched pool is cloned, and individual sequences are identified. Bioinformatics…
Core Concept: SELEX The synthesis of aptamers is not a direct chemical construction from a blueprint, but rather a selection and amplification process from a vast random library. The primary method is called SELEX (Systematic Evolution of Ligands by EXponential enrichment). The Technical Process: A Step-by-Step Breakdown The entire process can be divided into three major phases: Library Design & Synthesis, Selection (SELEX), and Post-SELEX Optimization & Production. Phase 1: Library Design and Chemical Synthesis This is the starting raw material. Design: A single-stranded DNA (ssDNA) or RNA library is designed with a central randomized region (typically 20-60 nucleotides) flanked by constant primer regions. Random Region: Provides the vast sequence diversity (e.g., 40 random positions = 4⁴⁰ ~ 1.2x10²⁴ possible sequences). Constant Regions: Essential for PCR amplification during later steps. Chemical Synthesis: The DNA library is synthesized using solid-phase phosphoramidite chemistry (the same as for oligonucleotide drugs and primers). Machines introduce nucleotides one-by-one in a controlled cycle (Deprotection, Coupling, Capping, Oxidation). For RNA libraries, transcription from a DNA template is used, or they are synthesized directly with 2'-OH protecting groups. Phase 2: The SELEX Cycle (Iterative Selection & Amplification) This is the iterative engine that finds the needle (high-affinity aptamers) in the haystack (random library). For ssDNA SELEX: Key Technical Steps in Detail: Incubation: The synthetic library…
