Aptamer Screening Service-Whole-cell SELEX

What is Whole-cell SELEX?

Whole-cell SELEX (Systematic Evolution of Ligands by EXponential enrichment) is a technique used to discover aptamers (single-stranded DNA or RNA molecules) that bind specifically to a target living cell.

Unlike traditional SELEX that uses a purified protein target, whole-cell SELEX presents the target in its native, complex cellular environment. This allows for the selection of aptamers against:

• Native cell-surface proteins in their proper folding and post-translational modifications.

• Complex targets like transmembrane receptors in their natural lipid environment.

• Unknown surface biomarkers without prior knowledge of the cell’s molecular makeup.

• Specific cell states (e.g., activated, cancerous, infected) based on differences in surface expression.

The Core Process: How Whole-cell SELEX Works

A professional service will manage this complex, iterative pipeline:

1. Library & Design: Starting with a vast, random synthetic oligonucleotide library (10^14 – 10^15 unique sequences).

2. Positive Selection: Incubating the library with the target cells (e.g., cancer cells, stem cells, bacteria). Aptamers that bind to any surface structure are retained.

3. Counter-Selection (Critical Step): The bound pool is then exposed to non-target or control cells (e.g., healthy cells, a different cell line). Sequences that bind to these are discarded. This step is crucial for generating specificity.

4. Elution & Amplification: Aptamers specifically bound to the target cells are recovered, amplified by PCR (for DNA) or RT-PCR (for RNA), and prepared for the next round.

5. Iteration: Steps 2-4 are repeated (typically 8-15 rounds) to enrich the pool for high-affinity, specific binders.

6. Cloning & Sequencing: The final enriched pool is cloned, and individual aptamer sequences are identified via next-generation sequencing (NGS).

7. Characterization: Candidate aptamers are synthesized and validated for binding affinity (Kd), specificity, and function (e.g., blocking internalization, imaging).

Key Components of a Professional Service

When you contract a whole-cell SELEX service, look for providers that offer:

• Project Consultation: Expert guidance on cell line selection, counter-selection strategy, and desired aptamer properties (e.g., for imaging, delivery, inhibition).

• Strict Cell Culture & QC: Maintaining consistent, viable, and phenotypically stable target and control cells throughout the lengthy process.

• Advanced Selection Strategies: Techniques like FACS-SELEX (using Fluorescence-Activated Cell Sorting) or Microfluidics-based SELEX for superior precision and efficiency.

• Bioinformatics & NGS Analysis: Using computational tools to analyze sequencing data, identify consensus families, and predict secondary structures.

• Full Validation Suite: Providing binding assays (flow cytometry, confocal microscopy), affinity measurements (SPR, BLI), and stability/functional tests.

Applications of the Resulting Aptamers

Aptamers discovered via whole-cell SELEX are powerful tools for:

• Diagnostics: Detecting circulating tumor cells (CTCs), specific pathogens, or cell biomarkers.

• Targeted Drug Delivery: Conjugating aptamers to nanoparticles, drugs, or siRNAs to home in on specific cell types.

• Molecular Imaging: Using fluorescent or radiolabeled aptamers for in vivo or ex vivo imaging of tumors or diseased tissues.

• Cell Isolation & Research: As affinity reagents for purifying specific cell populations (e.g., stem cells).

• Therapeutics: As antagonists to block receptor function directly.

Advantages & Challenges

Choosing a Service Provider: Key Questions to Ask

1. What is your experience with our specific cell type?

2. What counter-selection strategy do you recommend and why?

3. Do you offer FACS-SELEX or other advanced selection methods?

4. What depth of NGS sequencing and bioinformatic analysis is included?

5. What level of validation (Kd, specificity, application testing) is part of the package?

6. What is the typical project timeline and cost structure?

In summary, a Whole-cell SELEX Aptamer Screening Service provides an end-to-end solution to discover high-affinity nucleic acid ligands against complex cellular targets. It bypasses the need for purified proteins and leverages the native cell surface to generate reagents with significant potential in biomedicine, diagnostics, and basic research. The success of the project hinges on the provider’s experimental design, especially in counter-selection, and their analytical capabilities.