title: Aptamer selection by direct microfluidic recovery and surface plasmon resonance evaluation.
abstract: 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.
authors.affiliation: University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Dausse
authors.affiliation: University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Barré
authors.affiliation: University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France.
authors.forename: Ahissan
authors.initials: A
authors.lastname: Aimé
authors.affiliation: University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Groppi
authors.affiliation: Thermo Fisher Scientific, Saint Aubin F-91190, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Rico
authors.affiliation: Thermo Fisher Scientific, Saint Aubin F-91190, France.
authors.forename: Chrysanthi
authors.initials: C
authors.lastname: Ainali
authors.affiliation: University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France.
authors.forename: Gilmar
authors.initials: G
authors.lastname: Salgado
authors.affiliation: University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France.
authors.forename: William
authors.initials: W
authors.lastname: Palau
authors.affiliation: Novaptech, Bordeaux F-33000, France.
authors.forename: Emilie
authors.initials: E
authors.lastname: Daguerre
authors.affiliation: University of Bordeaux, CBiB-LaBRI, Bordeaux F-33000, France.
authors.forename: Macha
authors.initials: M
authors.lastname: Nikolski
authors.affiliation: University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Toulmé
authors.affiliation: University of Bordeaux, Laboratoire ARNA, Bordeaux F-33000, France; INSERM U1212-CNRS UMR 5320, IECB, Pessac F-33600, France. Electronic address: carmelo.diprimo@inserm.fr.
authors.forename: Carmelo
authors.initials: C
authors.lastname: Di Primo
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001483:Base Sequence; D007700:Kinetics; D046210:Microfluidic Analytical Techniques / Q000379:methods; D012322:RNA Precursors / Q000737:chemistry* / Q000235:genetics; D052156:SELEX Aptamer Technique / Q000379:methods*; D020349:Surface Plasmon Resonance / Q000379:methods*; D000071717:X-Box Binding Protein 1 / Q000235:genetics
chemical_list: D052157:Aptamers, Nucleotide; D012322:RNA Precursors; D000071717:X-Box Binding Protein 1
keywords: Aptamers; Kinetics; Microfluidic recovery; RNA; SELEX; Surface plasmon resonance