Viral Capsid Protein Aptamer Screening Service

What is the Core Service?

The service provider uses an iterative, in vitro selection process called SELEX (Systematic Evolution of Ligands by EXponential Enrichment) to screen vast random oligonucleotide libraries (10^14 – 10^15 unique sequences) against your target protein. The output is a set of characterized aptamer sequences that bind to the viral capsid.

Standardized Screening Workflow

A professional service will manage this entire pipeline:

1. Project Design & Target Preparation:

• Target Discussion: Defining the specific capsid protein (e.g., HIV-1 CA, HBV core, SARS-CoV-2 N), its form (full-length, domain, assembled capsid/nucleocapsid), and purity.

• Target Immobilization: The protein is often immobilized on a solid support (beads, plate) to facilitate separation of bound/unbound sequences. Some services offer solution-phase or capillary electrophoresis (CE-SELEX) methods for higher stringency.

2. SELEX Selection Rounds (Cycles 5-15):

• Incubation: The oligonucleotide library is incubated with the target.

• Partitioning: Unbound sequences are washed away; bound sequences are retained.

• Elution: Bound aptamers are eluted (e.g., by heating, denaturing agents).

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

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

• Counter-Selection: To ensure specificity, the pool is often passed through a negative control (e.g., irrelevant protein, cell lysate) to remove non-specific binders.

3. Sequencing & Identification:

• High-Throughput Sequencing (NGS): The final enriched pool is sequenced using Next-Generation Sequencing.

• Bioinformatics Analysis: Clustering analysis identifies sequence families, consensus motifs, and predicts secondary structures. The most promising candidates (e.g., most abundant, forming stable structures) are selected for synthesis.

4. Characterization & Validation (Tiered Service):

• Primary Binding Assay: Confirm binding via ELONA (Enzyme-Linked Oligonucleotide Assay) or SPR (Surface Plasmon Resonance)/BLI (Bio-Layer Interferometry) to determine dissociation constant (Kd, typically nM to pM range).

• Specificity Testing: Against related viral proteins or host proteins.

• Functional Analysis (Advanced):

  • Inhibition of capsid assembly/disassembly.

  • Blocking of viral entry or replication in cell-based assays.

  • Epitope mapping (identifying the binding site on the capsid).

Key Applications of the Resulting Aptamers

The aptamers discovered through this service can be used for:

• Therapeutic Development: As antagonists to inhibit viral capsid function (assembly, uncoating, nuclear import).

• Diagnostic Tools: As capture/detection elements in biosensors (e.g., electrochemical, optical) for rapid viral detection.

• Targeted Delivery: Conjugating aptamers to drug-loaded nanoparticles for specific delivery to virus-infected cells.

• Basic Research: As probes to study capsid protein dynamics, localization, and protein-protein interactions.

Advantages of Using a Service vs. In-House

• Expertise & Experience: Access to specialized SELEX protocols and troubleshooting knowledge.

• Advanced Technology: Use of NGS and sophisticated bioinformatics pipelines for efficient candidate identification.

• Time & Cost Efficiency: Avoids capital investment in large libraries, NGS, and SPR/BLI instruments.

• Customization: Ability to perform challenging selections (e.g., against intact viral particles, under specific buffer conditions).

What to Look for in a Service Provider

1. Proven Experience: Ask for case studies or publications related to viral targets.

2. Technology Platform: Do they offer CE-SELEX, Cell-SELEX, or Toggle-SELEX (for cross-reactivity)? These can yield higher-quality aptamers.

3. Characterization Depth: Clarify what level of binding kinetics (Kd), specificity, and functional data is included in the base package.

4. Target Flexibility: Can they handle your specific protein format (recombinant, from serum, on virions)?

5. Intellectual Property (IP) Clarity: Ensure contracts clearly define ownership of the discovered aptamer sequences.

6. Timeline & Deliverables: A typical full service from selection to validated leads takes 3 to 6 months. Deliverables should include sequences, structures, and comprehensive binding data.

Potential Service Providers (Examples)

While many companies offer aptamer discovery, those with explicit experience in virology include:

• Aptamer Group

• Aptagen, LLC

• Base Pair Biotechnologies

• AMSBIO (offers partnered services)

• Creative Biogene

• Academic Core Facilities: Many universities with aptamer expertise offer fee-for-service screening (e.g., labs at University of Florida, Carnegie Mellon, etc.).

Conclusion

A Viral Capsid Protein Aptamer Screening Service provides a turnkey solution to generate high-affinity molecular recognition tools against a critical viral target. By outsourcing this technically demanding and iterative process, researchers can accelerate their projects in virology, therapeutics, and diagnostics, gaining valuable aptamer leads with defined binding and functional properties.

Next Step: When contacting a provider, be prepared to discuss your specific viral capsid target, desired aptamer format (DNA/RNA/chemically modified), and intended application to get an accurate quote and project plan.