Whole Cell-SELEX Aptamer Screening Service

What is Whole Cell-SELEX?

SELEX (Systematic Evolution of Ligands by EXponential enrichment) is a technique used to develop aptamers—single-stranded DNA or RNA oligonucleotides that bind to a specific target molecule with high affinity and specificity, akin to antibodies.

Whole Cell-SELEX is a variant where the target is not a purified protein, but an entire living cell. This is crucial for discovering aptamers against:

• Native cell-surface proteins in their natural conformation and modification state.

• Complex membrane protein complexes.

• Disease-specific cell markers (e.g., on cancer cells, pathogens) without prior knowledge of the specific molecular target.

• Specific cell types in a heterogeneous mixture (e.g., cancer stem cells within a tumor).

A service provider performs this technically demanding and iterative process on behalf of researchers or companies.

The Core Process of a Whole Cell-SELEX Service

A typical service workflow involves close collaboration with the client:

1. Project Design & Consultation

• Defining Targets: Client specifies the positive selection cell (e.g., human glioblastoma cells) and the critical negative/counter selection cell (e.g., normal astrocytes or a related cell line). This is key to generating selective aptamers.

• Library Design: The service provider uses a vast (10^14 – 10^15 sequences) random oligonucleotide library.

2. The SELEX Cycle (Iterative Rounds)
This is the core experimental phase performed by the service provider:

• Incubation: The library is incubated with the negative selection cells. Unbound sequences are collected to remove binders to common surface features.

• Positive Selection: The pre-cleared library is incubated with target cells.

• Washing: Weakly or non-specifically bound sequences are washed away.

• Elution: Cell-bound aptamers are recovered (e.g., by heating, trypsinization, or cell lysis).

• Amplification: Eluted aptamers are amplified by PCR (for DNA-SELEX) or RT-PCR (for RNA-SELEX).

• Purification: The amplified pool is purified for the next round.

• Monitoring: Binding enrichment is tracked after several rounds using flow cytometry or qPCR.

8-20 rounds are typically required to enrich for high-affinity, specific aptamers.

3. Post-SELEX Analysis & Delivery

• Cloning & Sequencing: The final enriched pool is cloned, and individual aptamers are sequenced.

• Bioinformatics: Sequences are analyzed for homology to cluster into families and identify consensus motifs.

• Characterization of Candidates: The service often includes basic characterization of top candidate aptamers:

  • Binding Affinity (Kd): Determined via flow cytometry.

  • Specificity: Tested against control cell lines.

  • Confocal Microscopy: To confirm cell surface binding.

• Final Report & Delivery: Client receives a detailed report, sequence data, and characterized aptamer candidates.

Advantages of Using a Whole Cell-SELEX Service

• Expertise & Efficiency: Access to specialized skills and optimized protocols, saving months of labor and troubleshooting.

• No Target Identification Needed: Ideal for discovering biomarkers or targeting cells with unknown surfaceome changes.

• Native Conformation Targets: Aptamers are selected against proteins as they naturally exist on the cell.

• Turnkey Solution: From design to characterized candidates, allowing researchers to focus on downstream applications.

• Reduced Infrastructure Cost: Avoids capital investment in specialized equipment (e.g., high-throughput sequencers, FACS).

Typical Service Deliverables

A complete service package usually includes:

1. A finalized, project-specific SELEX protocol.

2. The final enriched aptamer pool.

3. Sequences and clustering analysis of 50-200 individual aptamer clones.

4. 3-10 lead candidate aptamer sequences.

5. In vitro binding data (Kd and specificity) for the lead candidates.

6. A comprehensive project report.

Key Considerations When Choosing a Service Provider

• Experience & Track Record: Look for published work or case studies in your field (e.g., oncology, immunology).

• Cell Line Expertise: Ensure they can handle your specific cell types (adherent, suspension, primary cells, etc.).

• Counter-Selection Strategy: Their approach to negative selection is critical for specificity.

• Characterization Depth: Clarify what level of binding validation (Kd, specificity, microscopy) is included.

• Intellectual Property (IP) Terms: Clearly define ownership of the discovered aptamer sequences. This is crucial.

• Timeline & Cost: A full service can take 3-6 months and cost anywhere from $30,000 to $100,000+, depending on scope and characterization.

Potential Limitations to Discuss

• Unknown Target: The specific protein target of the aptamer remains unidentified after SELEX (requires separate target identification efforts like protein pull-down/MS).

• Complexity: Working with whole cells introduces variables like cell viability, receptor internalization, and batch-to-batch variation.

• Service vs. In-House: For labs planning extensive aptamer development, building in-house capacity might be more cost-effective long-term.

Applications of the Resulting Aptamers

The aptamers generated from this service can be used for:

• Diagnostics: As detection probes in flow cytometry, imaging, or biosensors.

• Targeted Drug Delivery: Conjugated to nanoparticles, drugs, or siRNAs.

• Cell Isolation: For magnetic or fluorescence-activated cell sorting (FACS).

• Therapeutics: As antagonistic or agonistic agents (e.g., Macugen® for AMD).

• Basic Research: As tools to study cell surface biology and protein function.

By outsourcing to a specialized Whole Cell-SELEX Aptamer Screening Service, researchers can rapidly acquire powerful molecular tools for cell-specific targeting, accelerating their diagnostic and therapeutic development pipelines.