High-Throughput Sequencing SELEX Aptamer Screening Service

Core Value: From a “Black Box” to a “Data Dashboard”

A traditional SELEX service infers progress indirectly (e.g., via qPCR binding assays). An HTS-SELEX service provides a molecular-level census of the entire evolving library, offering:

• Quantitative Tracking: Exact counts and frequency changes for every sequence across rounds.

• Early Identification: High-affinity aptamer families can be spotted and validated mid-process, often shortening the project.

• Informed Decision-Making: Data guides adjustments in stringency, timing of counter-selection, and when to stop the selection.

Typical Service Workflow & Data Integration

A sophisticated HTS-SELEX service integrates sequencing as follows:

1. Sequencing from the Start: The naive starting library is sequenced to establish baseline diversity.

2. Sequencing at Every Critical Point: Key rounds (e.g., Rounds 3, 5, 7, 9, final) are sequenced, including sometimes the “bound” vs. “unbound” fractions from a single round for comparative analysis.

3. Real-Time Bioinformatics Pipeline:

   • Enrichment Analysis: Calculates the fold-enrichment of every sequence or sequence family across consecutive rounds.

   • Cluster Analysis: Groups sequences into families based on homology, revealing convergent evolution.

   • Motif & Structure Prediction: Identifies conserved primary sequence motifs and consensus secondary structures among enriched families.

4. Informed Selection Steering: Based on the data, the service provider may:

   • Adjust Stringency: Increase selection pressure if enrichment is too slow, or decrease it if diversity is collapsing too fast.

   • Introduce Negative Selection: Add a counter-SELEX round if promiscuous binders are dominating.

   • Terminate Early: Stop the selection once a dominant, enriched family plateaus, saving time and cost.

Key Advantages of the Service

• Shorter Timelines: Ability to identify leads in 4-8 rounds instead of 12-15.

• Higher Success Rate: Mitigates the risk of failure by providing molecular insight; allows correction of a “bad” selection path.

• Discovery of Rare Aptamers: Identifies high-affinity sequences that may be present at low frequency but have excellent properties, which might be lost in traditional cloning.

• Comprehensive Deliverables: Clients receive not just a few cloned sequences, but a complete dataset of the selection landscape.

Final Deliverables

Beyond the standard aptamer list and validation data, an HTS-SELEX service report includes:

• NGS Dataset: Raw and processed sequencing files.

• Enrichment Heatmaps & Graphs: Visualizing the rise and fall of sequence clusters.

• Detailed Cluster Report: Analysis of the top 10-20 enriched families, with consensus sequences, predicted structures, and enrichment kinetics.

In summary, a High-Throughput Sequencing SELEX Aptamer Screening Service represents the state-of-the-art in aptamer discovery. It leverages big-data analytics to transform SELEX from an empirical, iterative art into a precise, efficient, and highly informative engineering process, dramatically increasing the speed, quality, and depth of aptamer generation.