Protein-Targeted Aptamer Screening Service

What is an Aptamer?

An aptamer is a short, single-stranded oligonucleotide (DNA or RNA) that folds into a unique 3D structure, allowing it to bind to a specific target molecule (like a protein) with similar specificity to an antibody. They are often called “chemical antibodies.”

Why Use a Screening Service Instead of In-House Development?

• Expertise & Equipment: The screening process (SELEX) requires specialized skills, robotics, and next-generation sequencing (NGS) infrastructure.

• Time & Cost Efficiency: Outsourcing can be faster and more cost-effective than setting up a new, complex pipeline.

• Higher Success Rate: Experienced providers have optimized protocols for difficult targets (e.g., membrane proteins, toxic proteins).

The Core Process: SELEX

The standard method is SELEX (Systematic Evolution of Ligands by EXponential Enrichment). A professional service will offer advanced variants of this process.

A Typical Service Workflow:

1. Project Consultation & Design:

   • Target Characterization: Discussion about your protein (purified? membrane-bound? post-translational modifications?).

   • Selection Strategy: Choosing the best SELEX method (e.g., Capillary Electrophoresis-SELEX (CE-SELEX) for very high affinity, Cell-SELEX for cell-surface targets, Toggle-SELEX for cross-species specificity).

   • Counter-Selection: Designing the process to avoid binding to non-target proteins (e.g., carrier proteins, related isoforms).

2. Library Synthesis & Preparation:

   • Creation of a vast random oligonucleotide library (typically 10¹³ – 10¹⁵ unique sequences).

3. The Selection Rounds (Cycles of SELEX):

   • Binding: Incubating the library with the target protein.

   • Partitioning: Separating protein-bound sequences from unbound ones (using filters, beads, or capillary electrophoresis).

   • Amplification: PCR (for DNA) or RT-PCR (for RNA) of the bound sequences to create an enriched library for the next round.

   • Stringency Increase: Gradually increasing selection pressure (e.g., reduced incubation time, increased wash stringency, counter-selection) over 8-15 rounds to favor the strongest binders.

4. High-Throughput Sequencing & Bioinformatics:

   • NGS: Sequencing the enriched pools from the final rounds.

   • Bioinformatics Analysis: Identifying enriched sequence families, consensus motifs, and predicting secondary structures. This is a key value-add of professional services.

5. Candidate Aptamer Synthesis & Characterization:

   • Synthesis: Chemically synthesizing the top 10-50 candidate aptamers (often with modifications like 2′-F for RNA to enhance stability).

   • Primary Screening: Testing binding affinity (e.g., via Surface Plasmon Resonance (SPR), Bio-Layer Interferometry (BLI), or ELISA-like assays) and specificity.

   • Lead Aptamer Identification: Selecting 1-3 lead aptamers with the best Kd (dissociation constant, often nM to pM range) and specificity.

6. Validation & Reporting:

   • Functional Validation: Testing in your intended application format (e.g., flow cytometry, immunohistochemistry, sandwich assay, inhibition assay).

   • Final Report: Delivery of sequences, binding data, structural analysis, and protocols.

Key Technologies Used by Top Providers

• NGS Platforms (Illumina): For deep sequencing of selection pools.

• High-Throughput SPR or BLI: For rapid, label-free kinetic analysis of hundreds of candidates.

• Microfluidic or CE-SELEX: For extremely efficient partitioning, leading to fewer selection rounds and higher affinity aptamers.

• Advanced Oligo Synthesis: Ability to incorporate modified nucleotides (2′-F, 2′-O-Me, LNA) for enhanced nuclease resistance and stability.

Applications of the Resulting Aptamers

• Diagnostics: Biosensors, point-of-care tests, ELISA replacements (aptamer-based assays called “ELONA”).

• Therapeutics: Antagonists, agonists, or targeted delivery vehicles (e.g., aptamer-drug conjugates).

• Research Tools: Protein detection, purification (aptamer-affinity columns), imaging, and cell sorting.

• Biotechnology: Quality control, process monitoring.

What to Look for in a Service Provider

1. Proven Expertise & Portfolio: Ask for case studies or publications related to your target class.

2. Technology Platform: Do they offer modern, efficient SELEX variants (CE-SELEX, M-SELEX)?

3. Depth of Analysis: Do they go beyond sequencing to provide structural prediction and in-depth bioinformatics?

4. Characterization Capabilities: Ensure they have SPR/BLI for reliable affinity measurement.

5. Customization & Collaboration: Will they tailor the process to your specific needs and end-application?

6. Intellectual Property (IP) Clarity: Understand who owns the resulting aptamer sequences. This is a critical contractual point.

Typical Project Timeline & Cost

• Timeline: 4 to 6 months from project initiation to delivery of validated lead aptamers.

• Cost: Highly variable, typically ranging from $30,000 to $100,000+ USD, depending on target complexity, stringency, depth of characterization, and IP terms.

Leading Companies in the Field (Examples)

• Aptamer Group (UK)

• AptaDiscovery (France)

• Aptagen, LLC (US)

• Base Pair Biotechnologies (US)

• TriLink BioTechnologies (Aptamer Development Services) (US)

• Many academic labs and specialized biotech CROs also offer these services.

In summary, a Protein-Targeted Aptamer Screening Service provides an end-to-end solution to transform your target protein into high-affinity, specific aptamer reagents, leveraging expert knowledge and sophisticated technology to de-risk and accelerate your project. When engaging a provider, clear communication about your target, desired application, and IP expectations is paramount.