Structure and function of aptamers
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Structure and function of aptamers

Date：2026-01-04

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 stacking interactions.

4. Key Structural Features

  • Small Size: Typically 8-15 kDa (much smaller than antibodies ~150 kDa).

  • High Stability: DNA aptamers are chemically stable; RNA aptamers can be susceptible to nucleases unless modified (e.g., 2′-fluoro, 2′-O-methyl).

  • Synthetic and Tunable: Can be chemically modified for enhanced stability, affinity, or to add functional groups (fluorophores, drugs, nanoparticles).

Function of Aptamers: The Binding Mechanism

The core function is high-affinity, specific target recognition and binding.

1. Targets

Aptamers can be generated against a vast array of targets:

  • Small Molecules: Ions, toxins, drugs, metabolites (e.g., theophylline, ATP).

  • Proteins: Cell surface receptors, cytokines, enzymes, antibodies.

  • Whole Cells: Pathogens (bacteria, viruses), cancer cells (cell-SELEX).

  • Complex Structures: Tissues, prions.

2. Binding Characteristics

  • High Affinity: Dissociation constants (Kd) in the pico- to nanomolar range, comparable to antibodies.

  • High Specificity: Can discriminate between closely related molecules (e.g., discriminate theophylline from caffeine by a single methyl group).

  • Binding Reversibility: Binding is typically reversible under denaturing conditions, allowing for regeneration/reuse in sensors.

Functional Applications (Derived from Their Structure-Function Relationship)

1. Diagnostics and Biosensing

  • Aptasensors: Their binding induces a conformational change (“signal-on” or “signal-off”), detectable electrochemically, optically, or via mass.

  • Example: Detection of thrombin using a G-quadruplex aptamer.

2. Therapeutics

  • Antagonists: Block the active site of a protein (e.g., receptor, enzyme). Pegaptanib (Macugen®) is an FDA-approved RNA aptamer that inhibits VEGF to treat age-related macular degeneration.

  • Agonists: Activate a target receptor.

  • Delivery Vehicles: Conjugated to drugs, siRNAs, or nanoparticles for targeted delivery to specific cells (e.g., cancer cells).

3. Research and Biotechnology

  • Affinity Reagents: Used in place of antibodies in techniques like ELISA, flow cytometry, and chromatography.

  • Cell Isolation and Imaging: Fluorescently labeled aptamers can identify and sort specific cell types.

Advantages vs. Antibodies

Feature Aptamers Antibodies
Production In vitro (SELEX), chemical synthesis; no animals/cells. In vivo (animal immune system); biological production.
Size Small (~1-2 nm). Large (~10-15 nm).
Stability Thermally reversible; robust storage. Sensitive to heat/pH; require cold chain.
Modifiability Easy chemical modification at precise sites. Complex conjugation, often heterogeneous.
Batch-to-Batch Variation Minimal (synthetic). Can be significant (biological).
Targets Toxins, non-immunogenic targets. Primarily immunogenic proteins.
Immunogenicity Generally low (especially with modifications). Can elicit immune response.

Summary and Key Takeaway

Aptamers are structured, functional oligonucleotides whose unique 3D conformation, dictated by their sequence, allows for precise molecular recognition. Their synthetic nature, small size, stability, and versatility make them powerful tools bridging biotechnology, medicine, and diagnostics. While not a complete replacement for antibodies, they offer distinct advantages for many applications where antibodies are limited. The field continues to grow with advances in SELEX technology, novel modifications, and innovative therapeutic and diagnostic designs.