Aptamer Live Cell SELEX Service

What is Live Cell SELEX?

Traditional SELEX uses purified target proteins. Live Cell SELEX uses intact, living cells in their native state. This is crucial because:

• It selects for aptamers that bind to targets in their natural conformation and post-translational modifications (e.g., glycosylation).

• It inherently selects for cell-specificity (e.g., cancer cell vs. healthy cell) without needing to know the exact molecular target upfront.

• It can discover aptamers against unknown or membrane-bound targets that are difficult to purify.

Core Workflow of a Typical Service

A full-service provider will manage the entire pipeline:

1. Project Design & Consultation

• Target Cell Line Definition: Defining the “positive” cell line (e.g., patient-derived cancer cells, activated immune cells).

• Counter-Selection Strategy: Choosing the “negative” cell line(s) (e.g., healthy counterpart, isogenic control) to eliminate non-specific binders.

• Library Design: Recommending or customizing the starting random oligonucleotide library (length, modifications like 2′-F pyrimidines for RNA aptamers for stability).

2. The Selection Phase (The Iterative SELEX Cycles)

• Incubation: The random library is incubated with the counter-selection cells. Unbound/non-specific sequences are collected.

• Positive Selection: The pre-cleared library is incubated with the target cells. Cells are washed stringently.

• Recovery: Cell-bound aptamers are recovered (e.g., by cell lysis, heat elution, or protease treatment).

• Amplification: Recovered sequences are amplified by PCR (for DNA) or RT-PCR (for RNA).

• Single-Strand Generation: The double-stranded product is converted back to a single-stranded library for the next round.

• Monitoring: The service monitors enrichment, typically using flow cytometry with a labeled library pool, to decide when to stop (usually 8-15 rounds).

3. Next-Generation Sequencing (NGS) & Bioinformatics

• The final enriched pool is sequenced using high-throughput NGS.

• Bioinformatics Analysis:

  • Clustering to identify sequence families.

  • Identification of consensus motifs and structures.

  • Ranking of candidate sequences based on copy number and fold-enrichment.

4. Candidate Validation

• Services typically include the synthesis and initial testing of the top candidate aptamers (e.g., 5-10 sequences).

• Validation assays often include:

  • Flow Cytometry: Confirming binding to target cells and lack of binding to control cells.

  • Confocal Microscopy: Visualizing cellular binding and internalization.

  • Affinity Measurement: Determining dissociation constant (Kd) via flow cytometry or other methods.

  • Specificity Assessment: Testing against a panel of related cell lines.

5. Delivery & Reporting

• Final report with all data.

• Sequences of validated aptamer candidates.

• Proprietary aptamers delivered to the client, often with recommendations for further development (truncation, modification, conjugation).

Key Applications of Aptamers Selected via This Service

• Targeted Therapeutics: Cell-specific drug delivery, aptamer-drug conjugates.

• Diagnostics: Identifying rare cells (CTCs, circulating tumor cells) or pathogens.

• Cell-Specific Imaging Agents: For surgery or in vivo imaging.

• Biomarker Discovery: The aptamer itself can be used to pull down and identify its unknown target protein.

• Basic Research: As a tool to study cell surface biology and protein function in situ.

Advantages of Using a Service vs. In-House

• Expertise & Experience: Access to specialized scientists who troubleshoot SELEX daily.

• Speed: Dramatically reduces time from months to weeks.

• Infrastructure: No need to invest in NGS, sophisticated flow cytometers, or large-scale oligonucleotide synthesis.

• Higher Success Rate: Experienced providers optimize conditions (buffer, temperature, shear forces) to avoid common pitfalls.

Considerations When Choosing a Provider

• Experience with Live Cells: Do they have a proven track record with your cell type (e.g., primary cells, suspension cells)?

• Counter-Selection Rigor: Their strategy for ensuring specificity is critical.

• Depth of Bioinformatics: Ability to analyze complex NGS data is paramount.

• Validation Package: What specific assays are included? Is affinity measurement included?

• Intellectual Property (IP): Clearly understand who owns the resulting aptamer sequences.

• Turnaround Time & Cost: Typically a multi-month project costing tens of thousands of USD.

Leading Providers (Examples)

While many companies offer SELEX, specialized live cell SELEX services are offered by:

• Aptamer Group

• AptaGen

• Base Pair Biotechnologies

• AMSBIO (Aptamer Solutions)

• Several academic core facilities also offer fee-for-service SELEX.

In summary, an Aptamer Live Cell SELEX Service is an end-to-end solution that transforms a complex, technically demanding discovery process into a contract research project. It empowers researchers to rapidly obtain functional, cell-specific aptamers as tools for diagnostics, therapeutics, and fundamental biological research.