What Are Aptamers? Aptamers (from the Latin aptus = "to fit," and Greek meros = "part") are short, single-stranded oligonucleotides (DNA or RNA) that fold into specific 3D shapes, allowing them to bind to a target molecule with high affinity and specificity. They are often called "chemical antibodies" due to their similar function, but they are made of nucleic acids, not proteins. DNA Aptamers Composition: Deoxyribonucleic acid. Structure: Typically more rigid and stable than RNA due to the absence of the 2'-hydroxyl group, which makes it less prone to hydrolysis. Key Features: High Stability: Very resistant to degradation, especially compared to RNA. They are the more robust choice for diagnostic applications outside of controlled environments. Ease of Synthesis: DNA is chemically simpler and cheaper to synthesize and modify at large scales. Simpler Folding: DNA libraries can have less structural diversity than RNA, which may limit the complexity of binding pockets they can form. Common Applications: Biosensors, diagnostic assays, as inhibitors in therapeutics. RNA Aptamers Composition: Ribonucleic acid. Structure: The presence of the 2'-hydroxyl group allows for greater structural diversity and more complex folding (e.g., pseudoknots, tight loops). This often enables higher-affinity binding. Key Features: Structural Complexity: Can form a wider variety of intricate 3D shapes, leading to potentially higher specificity and affinity for challenging targets. Lower…
Aptamers: Structure and Function Definition and Overview Aptamers are short, single-stranded oligonucleotides (DNA or RNA) or peptides that bind to specific target molecules with high affinity and specificity. They are often termed "chemical antibodies" due to their target-binding capabilities, but are entirely synthetic and produced via an in vitro selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Structure of Aptamers 1. Primary Structure Composition: Made of nucleotides (DNA: dA, dT, dG, dC; RNA: A, U, G, C) typically 20-80 bases in length. Sequence: The unique sequence of bases determines the specific three-dimensional shape and thus the binding functionality. 2. Secondary Structure Driven by intramolecular base pairing and stacking, aptamers fold into specific, stable motifs: Stem-loops (Hairpins): Common structural element providing a recognition pocket. G-quadruplexes: Formed by guanine-rich sequences; planar stacks of G-tetrads stabilized by cations (e.g., K⁺). Pseudoknots: Complex structures with nested base-pairing. Bulges and Internal Loops: Provide flexibility and specific interaction points. 3. Tertiary Structure The overall three-dimensional fold, resulting from the arrangement of secondary motifs. This unique 3D shape creates binding pockets, clefts, or surfaces that recognize and bind to the target via: Complementary Shape (Lock-and-Key & Induced Fit): The aptamer folds to match the target's surface topology. Non-Covalent Interactions: Electrostatic interactions, hydrogen bonding, van der Waals forces, and…
Core Principle: SELEX SELEX is an iterative, in vitro process that screens vast random nucleic acid libraries (10^14 - 10^15 sequences) to isolate high-affinity, specific aptamers against a target. Key Screening Methodologies for Liver Cancer The choice of target is paramount and dictates the screening strategy. 1. Cell-SELEX (Whole-Cell SELEX) This is the most common method for discovering aptamers that bind to native cell surface biomarkers without prior knowledge of their identity. Target Cells: Human liver cancer cell lines (e.g., HepG2, SMMC-7721, Huh7, PLC/PRF/5). Counter-Selection Cells: Crucial for specificity. Typically use: Normal human hepatocyte cell lines (e.g., LO2, THLE-3). Non-malignant liver cells or immortalized hepatocytes. Sometimes other cancer cell lines (e.g., from lung, colon) to avoid cross-reactivity. Process: Incubate the ssDNA or RNA library with target liver cancer cells. Wash away unbound sequences. Elute bound sequences (e.g., by heating, trypsinization, or cell lysis). Amplify eluted sequences (PCR for DNA, RT-PCR for RNA). Incubate the enriched pool with counter-selection cells. Sequences that bind are discarded; the unbound pool proceeds. Repeat cycles (usually 8-20 rounds) until a highly enriched pool is obtained. Clone and sequence the final pool for individual aptamer identification. Advantage: Identifies aptamers to unknown, natively folded, and post-translationally modified membrane proteins. 2. Tissue-SELEX…
Screening of Aptamers and Their Potential Application in Targeted Diagnosis and Therapy of Liver Cancer Introduction to Aptamers Aptamers are short, single-stranded DNA or RNA oligonucleotides (typically 20-100 nucleotides) that bind to specific target molecules with high affinity and specificity, similar to antibodies. They are often called "chemical antibodies" but offer advantages including: Ease of synthesis and modification Low immunogenicity Enhanced tissue penetration Thermal stability Lower production costs Screening Methods for Liver Cancer-Specific Aptamers 1. SELEX Technology Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is the primary method for aptamer selection: Key adaptations for liver cancer: Cell-SELEX: Using live hepatoma cells (e.g., HepG2, Huh7) as targets Tissue-SELEX: Employing liver cancer tissue specimens In vivo SELEX: Direct screening within animal models Automated SELEX: High-throughput screening platforms 2. Target-Specific SELEX Variations Protein-based SELEX: Against liver cancer biomarkers (AFP, GPC3, etc.) Whole-cell SELEX: For cell surface epitope targeting Toggle SELEX: For cross-reactivity across different liver cancer cell types Applications in Liver Cancer Diagnosis 1. Imaging and Detection Molecular Imaging: Radiolabeled aptamers for PET/CT imaging Fluorescent Aptamers: For intraoperative guidance and tumor margin identification MRI Contrast Agents: Aptamer-conjugated nanoparticles for enhanced imaging 2. Biosensor Development Electrochemical Sensors: For detecting circulating tumor cells Colorimetric Assays: Point-of-care testing for…
Of course. Aptamers, often called "chemical antibodies," are single-stranded DNA or RNA oligonucleotides that bind to specific target molecules (proteins, small molecules, cells, etc.) with high affinity and specificity. Their unique properties—ease of synthesis, stability, low immunogenicity, and small size—make them powerful tools across numerous fields. Here is a comprehensive overview of the key applications of aptamers, categorized by field: 1. Therapeutics & Medicine Aptamers are developed as targeted drugs, often competing with monoclonal antibodies. Targeted Cancer Therapy: Aptamers can deliver toxic drugs, siRNAs, or radioisotopes directly to cancer cells by binding to overexpressed surface markers (e.g., nucleolin, PSMA). This minimizes damage to healthy tissues. Antidotes and Antagonists: The only FDA-approved aptamer to date, Pegaptanib (Macugen), is used for age-related macular degeneration (AMD). It binds and inhibits VEGF-165, a protein promoting abnormal blood vessel growth. Antiviral and Antimicrobial Agents: Aptamers can block viral entry (e.g., against HIV gp120, SARS-CoV-2 spike protein) or inhibit essential bacterial proteins, offering potential alternatives to traditional antibiotics. Anti-inflammatory and Autoimmune Diseases: Aptamers can neutralize inflammatory cytokines (e.g., TNF-α, IL-6) implicated in diseases like rheumatoid arthritis or psoriasis. Targeted Drug Delivery Systems: Aptamers conjugated to nanoparticles or liposomes create "smart" delivery vehicles that release their cargo only at the disease site. 2.…
The Core Principle of SELEX Think of SELEX as artificial selection or directed evolution for molecules. You start with a massive, diverse library of random nucleic acid sequences (typically 10^14 to 10^15 different molecules) and iteratively select for the tiny fraction that binds tightly to your target molecule. The Standard SELEX Process (Step-by-Step) The process is cyclical, typically requiring 5-15 rounds to enrich high-affinity binders. 1. Library Design & Synthesis: A synthetic library is created where each molecule has constant primer regions (for PCR amplification) flanking a central randomized region (20-60 nucleotides long). This creates a "pool of possibility" often called a combinatorial library. 2. Incubation (Binding): The library is incubated with the target molecule (e.g., a protein, small molecule, cell, or even a whole pathogen). Conditions (buffer, temperature, ionic strength) are controlled to favor specific binding. 3. Partitioning (Separation): This is the most critical step. The bound sequences (potential aptamers) must be efficiently separated from the unbound ones. Common methods: immobilizing the target on a column/beads, filtration through nitrocellulose filters (which trap protein-bound RNA/DNA), or capillary electrophoresis. 4. Elution (Recovery): The bound sequences are recovered, often by denaturing the complex (e.g., heating, changing pH, or using denaturants). 5. Amplification: The recovered sequences are amplified using PCR (for DNA aptamers) or Reverse Transcription-PCR (for…
1. Synthetic & Chemical Origin Fully In Vitro Production: Unlike biological antibodies produced in living cells (mice, rabbits, CHO cells), Adaptamers are synthesized chemically in a controlled laboratory setting. Precise Chemical Structure: Their composition, structure, and modifications are defined at the atomic level, leading to perfect batch-to-batch consistency. No Biological System Required: Production is independent of cell culture, fermentation, or animal use, making it more scalable and ethically straightforward. 2. Adaptive & Engineered Binding "Adapta-" Implies Engineering: The name suggests the molecule is engineered or evolved in vitro (like aptamers via SELEX) to bind with high affinity and specificity to a chosen target—proteins, small molecules, cells, etc. Tailor-Made: Their binding sites are not constrained by biological immune system mechanisms. They can be designed against targets that are poorly immunogenic, toxic, or highly conserved. 3. Core Molecular Scaffold (Likely Nucleotide or Peptide-Based) While unspecified, the most probable backbones are: Nucleic Acid-Based (like advanced aptamers): Composed of DNA or RNA, but heavily chemically modified (e.g., with 2'-fluoro, 2'-O-methyl, locked nucleic acids (LNA), or entirely synthetic bases) to confer nuclease resistance and enhanced stability. Peptide-Based (like peptidomimetics or constrained peptides): Composed of non-natural amino acids or cyclic structures for rigidity and protease resistance. Hybrid or Other Polymer: Could be a fusion of chemistries (e.g., oligonucleotide with a peptide-like side chain) for…
What are Aptamers? Aptamers are single-stranded DNA or RNA molecules obtained through in vitro selection techniques (such as SELEX) from synthetic, randomized nucleic acid libraries. They can bind to target molecules (such as proteins, small molecules, cells, etc.) with high affinity and specificity through unique three-dimensional structures, earning them the titles "chemical antibodies" or "nucleic acid antibodies." Key Characteristics Chemical Nature Mostly single-stranded DNA or RNA, producible via chemical synthesis, offering good stability and ease of modification or labeling. Binding Mechanism Form hydrogen bonds, electrostatic interactions, etc., through spatial conformations (e.g., hairpins, pockets, bulges) to recognize targets with atomic-level precision. High Affinity & Specificity Capable of distinguishing structurally similar molecules (e.g., caffeine vs. theophylline), with dissociation constants (Kd) reaching nanomolar (nM) or even picomolar (pM) levels. Strong Stability Resistant to high temperatures, reversible denaturation, and less susceptible to damage in acidic/basic environments (especially DNA aptamers), making them suitable for complex applications. Advantages Compared to Antibodies Feature Aptamers Antibodies (Traditional Protein Antibodies) Production Time In vitro selection (weeks), chemical synthesis, high batch consistency Animal immunization or cell culture (months), significant batch variability Stability Heat-resistant, easy storage, transportable at room temperature Prone to denaturation, requires cold storage Modification Flexibility Easy labeling with fluorescent dyes, isotopes, etc. Modifications may affect structure Immunogenicity…
Aptamers are nucleic acid sequences that specifically bind with target molecules and are vital to applications such as biosensing, drug development, disease diagnostics, etc. The traditional selection procedure of aptamers is based on the Systematic Evolution of Ligands by an Exponential Enrichment (SELEX) process, which relies on repeating cycles of screening and amplification. With the rapid development of aptamer applications, RNA and XNA aptamers draw more attention than before. But their selection is troublesome due to the necessary reverse transcription and transcription process (RNA) or low efficiency and accuracy of enzymes for amplification (XNA). In light of this, we review the recent advances in aptamer selection methods and give an outlook on future development in a non-SELEX approach, which simplifies the procedure and reduces the experimental costs. We first provide an overview of the traditional SELEX methods mostly designed for screening DNA aptamers to introduce the common tools and methods. Then a section on the current screening methods for RNA and XNA is prepared to demonstrate the efforts put into screening these aptamers and the current difficulties. We further predict that the future trend of aptamer selection lies in non-SELEX methods that do not require nucleic acid amplification. We divide…
KMD Bioscience offers comprehensive aptamer discovery services that cover the full workflow—from nucleic acid aptamer design and synthesis, to multi-target SELEX screening, to final affinity and specificity validation. With advanced laboratory platforms and experienced scientists, we provide reliable and efficient one-stop aptamer solutions for diagnostics, therapeutics, biosensors and research applications. Nucleic Acid Aptamer Introduction Aptamers are single-stranded nucleic acid molecules (DNA or RNA) that fold into stable three-dimensional structures capable of binding specific targets with high affinity. Compared with antibodies, aptamers offer several advantages, including small molecular size, low immunogenicity, chemical synthesis, batch consistency and flexible modification. They can bind diverse targets such as proteins, peptides, cells, small molecules and ions, making them valuable tools in biotechnology and analytical applications. DNA Aptamer: DNA aptamers are aptamers composed of deoxyribonucleic acid (DNA). They usually have a double helix structure and are composed of four bases (adenine A, thymine T, guanine G, cytosine C) connected by phosphodiester bonds. They are single-stranded oligonucleotide sequences, typically with 56-120 bases, that bind the target sequence efficiently by recognizing specific spatial structures. DNA aptamers are widely used in biological analysis, biomedicine, and other fields because of their stability and easy chemical modification. RNA Aptamers: RNA aptamers are aptamers…
