Subtractive SELEX Services

Unlock High-Affinity Probes with Subtractive SELEX Services at KMD Bioscience

At KMD Bioscience, we specialize in transforming the intricate science of molecular selection into powerful, practical solutions. Our Subtractive SELEX (Systematic Evolution of Ligands by EXponential Enrichment) Services are designed to isolate high-specificity, high-affinity aptamers—single-stranded DNA or RNA molecules—against your most challenging targets. In a landscape crowded with biological noise, our subtractive approach ensures you capture the precise molecular keys you need.

What is Subtractive SELEX?

Traditional SELEX is a powerful iterative process that selects aptamers from vast random-sequence libraries by binding to a target molecule. However, when the target is complex (like a specific cell type, a post-translationally modified protein, or a rare epitope on a common protein), background binding to similar or related structures can dominate, yielding non-specific aptamers.

Subtractive SELEX introduces a critical purification step. Before or during selection against the desired target, the nucleic acid library is pre-incubated with non-target or counter-target structures (e.g., a non-target cell line, a non-modified protein, or a common protein domain). Sequences that bind to these undesired structures are actively removed or “subtracted.” The remaining, pre-cleared library is then exposed to the true target of interest. This process dramatically enriches for aptamers that uniquely recognize the subtle, defining features of your target, minimizing cross-reactivity from the start.

Our Service Workflow: Precision at Every Step

1. Consultation & Strategy Design: Our experts collaborate with you to define your target and, crucially, the optimal counter-targets for subtraction. We tailor the SELEX protocol—including selection format (bead-based, capillary, cell-SELEX) and stringency conditions—to your project’s unique requirements.

2. Library Preparation & Pre-Clearance (Subtraction): We begin with our diverse, high-complexity oligonucleotide libraries. The library undergoes rigorous subtractive rounds against your specified counter-targets, efficiently depleting non-specific binders.

3. Positive Selection & Amplification: The subtracted library is then exposed to your purified target. Bound sequences are recovered, amplified by PCR (for DNA) or RT-PCR (for RNA), and purified to create an enriched pool for the next round.

4. Iterative Enrichment & Monitoring: We perform multiple cycles of subtractive and positive selection, continuously increasing stringency. The enrichment process is monitored using qPCR, flow cytometry, or sequencing to track progress toward high-affinity pools.

5. High-Throughput Sequencing & Bioinformatics: The final enriched pools are analyzed via Next-Generation Sequencing (NGS). Our bioinformatics team employs advanced algorithms to identify convergent sequence families, predict secondary structures, and rank candidate aptamers based on frequency and structural motifs.

6. Candidate Validation & Characterization: We synthesize the top candidate aptamers and perform comprehensive validation. This includes:

   • Binding Affinity (Kd) Measurement: Using techniques like surface plasmon resonance (SPR) or flow cytometry.

   • Specificity Profiling: Testing against a panel of related molecules to confirm minimal cross-reactivity.

   • Functional Analysis: Assessing aptamer activity in your intended application (e.g., inhibition, activation, or delivery).

Why Choose KMD Bioscience for Subtractive SELEX?

• Deep Expertise in Complex Targets: We excel at developing aptamers for difficult targets like transmembrane receptors, complex biomarkers, and specific cell phenotypes.

• Proprietary Counter-Target Strategies: We help you design the most effective subtraction strategy to eliminate background and highlight unique target binding.

• Integrated NGS & Bioinformatics Platform: Our in-house sequencing and analysis pipeline rapidly identifies the most promising leads, accelerating discovery.

• End-to-End Project Management: From initial design to validated, sequence-ready aptamers, we provide full support and detailed reporting.

• Proven Applications: Our generated aptamers are successfully applied in therapeutic development, diagnostic assays, targeted drug delivery, and sophisticated biosensors.

Target Applications

• Diagnostic & Biosensor Development: Create ultra-specific aptamers for point-of-care tests and detection platforms.

• Therapeutic Candidate Discovery: Identify antagonist or agonist aptamers for pathogenic proteins or cell receptors.

• Cell-Specific Targeting: Isolate aptamers that distinguish between healthy and diseased cells, or between different cell lineages.

• Epitope-Specific Probes: Generate aptamers targeting unique protein modifications (phosphorylation, glycosylation) or cryptic epitopes.

Partner with Us

Elevate your research and development with aptamers that combine the affinity of antibodies with the stability and versatility of nucleic acids. The Subtractive SELEX Services at KMD Bioscience provide a direct path to superior molecular recognition tools.

Contact us today to discuss your target and discover how our tailored subtractive SELEX strategy can unlock the next breakthrough in your program.