Aptamer Screening Service-Protein-Specific Selection

What is an Aptamer?

An aptamer is a short, single-stranded DNA or RNA oligonucleotide that binds to a specific target molecule (like a protein) with high affinity and specificity. They are often called “chemical antibodies” but offer advantages like smaller size, chemical stability, and in-vitro generation.

The Core Service: SELEX (Systematic Evolution of Ligands by EXponential Enrichment)

The standard method for aptamer screening is SELEX. A specialized service will manage this entire iterative, high-complexity process for you.

General SELEX Workflow:

1. Target Preparation & Immobilization: Your service provider will prepare your purified protein. It is often immobilized on a solid support (beads, column, plate) to separate bound from unbound sequences.

2. Incubation with Library: A vast, random synthetic oligonucleotide library (10^13 – 10^15 unique sequences) is incubated with the target.

3. Partitioning: Weak or non-binding sequences are washed away. Tightly bound aptamers are retained.

4. Elution & Amplification: The bound sequences are eluted and amplified by PCR (for DNA) or RT-PCR (for RNA).

5. Stringency & Counter-SELEX: Subsequent rounds introduce increased washing stringency and incubation with non-target molecules (e.g., similar proteins, immobilization matrix) to filter out non-specific binders. This is crucial for specificity.

6. Cloning & Sequencing: After 8-15 rounds, the enriched pool is cloned and sequenced to identify individual candidate aptamers.

7. Characterization & Validation: Top candidates are synthesized, and their binding affinity (Kd), specificity, and optimal conditions are characterized (e.g., via SPR, BLI, ELISA).

Key Features of a Professional Aptamer Screening Service

• Customized SELEX Variants: They employ advanced SELEX methods tailored to your target and application:

  • Cell-SELEX: For targeting membrane proteins in their native conformation on live cells.

  • Capture-SELEX: Uses an immobilized oligonucleotide library; ideal for small molecules or targets hard to immobilize.

  • CE-SELEX: Uses capillary electrophoresis for superior partitioning efficiency, often yielding higher-affinity aptamers faster.

  • In-Solution SELEX: Keeps the target native without immobilization.

• Counter-SELEX Design: Expertise in selecting appropriate negative targets (e.g., homologous proteins, serum components) is critical to ensure your aptamer doesn’t cross-react.

• Next-Generation Sequencing (NGS) & Bioinformatics: Modern services use NGS to analyze pools from multiple rounds. Bioinformatics tools identify enriched families, consensus structures, and predict binding motifs, speeding up discovery.

• Post-SELEX Modifications: They offer chemical modifications (2′-F, 2′-O-methyl ribose, LNA, phosphate backbone) to enhance nuclease resistance and serum stability for in vivo applications.

• Full Characterization Package: Beyond sequencing, they provide data on affinity, specificity, stoichiometry, and functional assays.

Why Use a Service vs. In-House Development?

• Expertise & Experience: Avoid the steep learning curve of SELEX optimization.

• Specialized Equipment: Access to SPR/BLI, NGS, HPLC synthesizers, and more.

• Time & Cost Efficiency: A dedicated team can complete screening in 3-6 months, often faster than setting up a new lab.

• Higher Success Rate: Experience with difficult targets (e.g., hydrophobic proteins, non-immunogenic targets).

Typical Deliverables

1. Final Report: Detailed methodology, characterization data (Kd, IC50, specificity profile), and sequence information.

2. Aptamer Sequences: 3-5 validated, high-affinity aptamer sequences specific to your target protein.

3. Samples: Lyophilized aptamer(s) in nanomole to micromole quantities.

4. Recommendations: For optimal buffer conditions, storage, and potential applications.

Applications of the Resulting Protein-Specific Aptamers

• Diagnostics: As capture/detection agents in biosensors (e.g., electrochemical, optical), lateral flow assays, and ELISA replacements.

• Therapeutics: As antagonists to block protein-protein interactions (e.g., VEGF, TNF-α) or as targeted delivery vehicles (aptamer-drug conjugates).

• Research Tools: For protein detection, purification (affinity chromatography), and cellular imaging.

• Biotechnology: As affinity ligands in affinity columns or in microfluidic devices.

What to Provide to the Service Provider

• High-Purity Target Protein: >90% purity, with information on formulation buffer, tags, and concentration. A homogenous sample is key.

• Clear Objectives: Desired affinity range (nM, pM), required specificity (e.g., “must not bind to human serum albumin or protein X family”), and intended application (diagnostic, therapeutic, in vitro use).

• Negative Targets: For counter-SELEX (e.g., related proteins, cell lysates, serum).

• Timeline & Budget: Standard projects range from $30,000 to $100,000+ depending on complexity, SELEX method, and depth of characterization.

Leading Service Providers (Illustrative)

• Aptamer Group Companies: BasePair Biotechnologies, Aptamer Sciences, AptaDiscovery.

• Large CROs: Many contract research organizations now have dedicated aptamer discovery divisions.

• Academic Core Facilities: Some universities offer fee-for-service SELEX.

By partnering with a specialized aptamer screening service, you can efficiently obtain high-quality, protein-specific aptamers to accelerate your research or product development pipeline.