Aptamer selection by direct microfluidic recovery and surface plasmon resonance evaluation

• Published in: Biosensors & bioelectronics Vol. 80; pp. 418 - 425
• Main Authors: Dausse, Eric, Barré, Aurélien, Aimé, Ahissan, Groppi, Alexis, Rico, Alain, Ainali, Chrysanthi, Salgado, Gilmar, Palau, William, Daguerre, Emilie, Nikolski, Macha, Toulmé, Jean-Jacques, Di Primo, Carmelo
• Format: Journal Article
• Language: English
• Published: England Elsevier B.V 15-06-2016; Elsevier
• Subjects: Aptamers; Aptamers, Nucleotide - chemistry; Base Sequence; Bioelectricity; Bioinformatics; Biotechnology; Cartridges; Chemical Sciences; Computer Science; Evolution; Joining; Kinetics; Microfluidic Analytical Techniques - methods; Microfluidic recovery; Microfluidics; Plasmons; Ribonucleic acids; RNA; RNA Precursors - chemistry; RNA Precursors - genetics; SELEX; SELEX Aptamer Technique - methods; Surface plasmon resonance; Surface Plasmon Resonance - methods; X-Box Binding Protein 1 - genetics; Surface plasmon resonance; Kinetics; RNA; Microfluidic recovery; Aptamers; SELEX
• ISSN: 0956-5663; 1873-4235
• DOI: 10.1016/j.bios.2016.02.003

A surface plasmon resonance (SPR)-based SELEX approach has been used to raise RNA aptamers against a structured RNA, derived from XBP1 pre-mRNA, that folds as two contiguous hairpins. Thanks to the design of the internal microfluidic cartridge of the instrument, the selection was performed during the dissociation phase of the SPR analysis by recovering the aptamer candidates directly from the target immobilized onto the sensor chip surface. The evaluation of the pools was performed by SPR, simultaneously, during the association phase, each time the amplified and transcribed candidates were injected over the immobilized target. SPR coupled with SELEX from the first to the last round allowed identifying RNA aptamers that formed highly stable loop–loop complexes (KD equal to 8nM) with the hairpin located on the 5′ side of the target. High throughput sequencing of two key rounds confirmed the evolution observed by SPR and also revealed the selection of hairpins displaying a loop not fully complementary to the loop of its target. These candidates were selected mainly because they bound 79 times faster to the target than those having a complementary loop. SELEX coupled with SPR is expected to speed up the selection process because selection and evaluation are performed simultaneously.
•An SPR-based SELEX approach was used to identify aptamer.•Aptamer candidates were recovered from the target thanks to the microfluidic.•Selection and evaluation by SPR were performed simultaneously.•High affinity aptamers were selected.•The best aptamer does not display a loop fully complementary to the target loop.