Related Experiment Video
Updated: Mar 25, 2026
12:31
A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay
Published on: February 28, 2015
15.7K
Aptamer selection by direct microfluidic recovery and surface plasmon resonance evaluation
Eric Dausse1, Aurélien Barré2, Ahissan Aimé1
1University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France.
Biosensors & Bioelectronics
|February 14, 2016
Summary
This study developed RNA aptamers targeting XBP1 mRNA using surface plasmon resonance (SPR)-based SELEX. The novel method simultaneously selects and evaluates aptamers, accelerating discovery and identifying high-affinity binders.
Area of Science:
- Molecular Biology
- Biotechnology
- Biophysics
Background:
- X-box binding protein 1 (XBP1) mRNA splicing is crucial in the unfolded protein response.
- Structured RNAs, like XBP1 pre-mRNA hairpins, present challenges for aptamer selection.
- RNA aptamers offer potential as therapeutic or diagnostic tools.
Purpose of the Study:
- To develop RNA aptamers against a structured XBP1 pre-mRNA hairpin using an integrated SPR-SELEX approach.
- To investigate aptamer selection dynamics and binding characteristics.
- To accelerate the aptamer discovery process.
Main Methods:
- Systematic Evolution of Ligands by Exponential Enrichment (SELEX) coupled with Surface Plasmon Resonance (SPR) detection.
- Microfluidic cartridge design for in-situ selection during SPR dissociation phase.
- Real-time evaluation of aptamer pools during SPR association phase.
- High-throughput sequencing for aptamer candidate analysis.
Main Results:
- Identified RNA aptamers forming highly stable loop-loop complexes with the target hairpin (KD = 8nM).
- SPR-SELEX demonstrated simultaneous selection and evaluation, confirming aptamer pool evolution.
- High-throughput sequencing revealed aptamers with non-complementary loops exhibiting significantly faster binding kinetics (79x).
Conclusions:
- The integrated SPR-SELEX approach efficiently selects high-affinity RNA aptamers against structured targets.
- Simultaneous selection and evaluation significantly accelerate aptamer discovery.
- Non-complementary loop interactions can enhance aptamer binding speed and affinity.
