Capture-SELEX Aptamer Screening Service
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Capture-SELEX Aptamer Screening Service

Date：2026-01-17

What is Capture-SELEX?

Unlike traditional SELEX where the target is immobilized, Capture-SELEX immobilizes the initial DNA library itself via a short complementary “capture” sequence. The key target molecule is free in solution. Binding occurs when an aptamer candidate in the library binds to the target, causing a structural change that releases it from the immobilization surface.

This approach offers distinct advantages:

  • Ideal for small molecules and proteins: Especially targets that are difficult to immobilize without affecting their structure.

  • Minimizes non-specific binding: Selection pressure is purely for target-induced structure formation/release.

  • Enriches for structure-switching aptamers: Resulting aptamers often undergo conformational change upon binding, making them excellent for biosensor development.

Typical Capture-SELEX Screening Service Workflow

A professional service provider will manage this complex, iterative process from start to finish. Here’s what you can expect:

Phase 1: Project Design & Library Preparation

  1. Consultation & Target Specification: Defining target properties, desired affinity (Kd), specificity (against which counter-targets), and buffer conditions.

  2. Customized Library Design: Designing a single-stranded DNA library (10^14 – 10^15 unique sequences) with:

    • A central random region (e.g., 30-50 nucleotides).

    • Fixed primer regions for PCR amplification.

    • A capture sequence region complementary to an immobilized oligonucleotide.

  3. Immobilization Matrix Preparation: Coupling the complementary “capture” oligonucleotides to a solid support (e.g., magnetic beads, chromatography resin).

Phase 2: The Iterative Selection (SELEX) Cycles

This is the core, repeated 8-15 times.

  1. Immobilization: The ssDNA library is hybridized to the complementary capture strands on the beads.

  2. Incubation with Target: The free target molecule in solution is introduced. Library strands that can bind the target undergo a conformational change, potentially de-hybridizing and being eluted.

  3. Washing: Weak or non-binders remain immobilized and are washed away.

  4. Elution & Recovery: The eluted (target-binding) fraction is collected. Target is removed, and the DNA is amplified by PCR.

  5. ssDNA Regeneration: The PCR product is converted back to single-stranded DNA for the next selection round.

  6. Monitoring: Service providers use quantitative PCR (qPCR) or next-generation sequencing (NGS) to monitor enrichment and diversity.

Phase 3: Sequencing & Bioinformatics Analysis

  1. High-Throughput Sequencing (NGS): The enriched pools from later rounds are sequenced to obtain millions of reads.

  2. Bioinformatics Analysis:

    • Cluster Analysis: Grouping sequences into families based on homology.

    • Motif Identification: Finding conserved sequence patterns and predicted secondary structures.

    • Candidate Selection: Ranking families/sequences based on frequency, enrichment ratio, and structural properties.

Phase 4: Characterization & Validation

  1. Synthesis: The top 5-20 candidate aptamers are chemically synthesized.

  2. Affinity Measurement: Determining dissociation constant (Kd) using techniques like Surface Plasmon Resonance (SPR), Bio-Layer Interferometry (BLI), or Microscale Thermophoresis (MST).

  3. Specificity Testing: Testing against counter-targets or related molecules to confirm selectivity.

  4. Functional Assay: If applicable, testing in the customer’s intended application (e.g., inhibition, detection in a simple buffer).

Key Deliverables from the Service

  • Final Report: Detailed methodology, analytical data from the SELEX process (enrichment curves, NGS summary).

  • Sequence List: Top ranked aptamer candidates with their Kd values and specificity profiles.

  • Aliquots of Synthesized Aptamers: Ready for your downstream validation and application development.

  • Intellectual Property: Clear assignment of the discovered aptamer sequences to the client.

Considerations When Choosing a Service Provider

Feature Why It Matters
Proven Experience Look for published work or case studies using Capture-SELEX, especially with targets similar to yours (small molecules, ions, proteins).
In-House NGS & Bioinfo Integrated pipeline ensures faster turnaround and deeper sequence analysis.
State-of-the-Art Characterization Access to SPR/BLI/MST for reliable, label-free affinity measurement is crucial.
Project Design Support They should advise on library design, counter-selection strategy, and buffer optimization.
IP Clarity & Flexibility Contract must clearly state you own the developed aptamers. Options for exclusive vs. non-exclusive licensing.
Turnaround Time A full service typically takes 3-6 months from project initiation to validated candidates.

Example Service Providers (Illustrative)

  • Specialized Biotech Companies: Firms like Aptamer Group, Aptagen, LLC, Base Pair Biotechnologies, or Aptamer Sciences often offer custom SELEX services, including Capture-SELEX.

  • Academic Core Facilities: Some university core labs with SELEX/NGS expertise may offer collaborative or fee-for-service projects.

  • CROs (Contract Research Organizations): Larger life science CROs may have an aptamer discovery division.

In summary, a Capture-SELEX Aptamer Screening Service is a turnkey solution for discovering high-affinity, structure-switching DNA aptamers against challenging targets. By outsourcing this technically demanding and resource-intensive process, researchers can rapidly obtain validated aptamer candidates for diagnostic, therapeutic, or sensor applications.