title: Elongated thrombin binding aptamer: a G-quadruplex cation-sensitive conformational switch.
abstract: Aptamer-based biosensors offer promising perspectives for high performance, specific detection of proteins. The thrombin binding aptamer (TBA) is a G-quadruplex-forming DNA sequence, which is frequently elongated at one end to increase its analytical performances in a biosensor configuration. Herein, we investigate how the elongation of TBA at its 5' end affects its structure and stability. Circular dichroism spectroscopy shows that TBA folds in an antiparallel G-quadruplex conformation with all studied cations (Ba(2+), Ca(2+), K(+), Mg(2+), Na(+), NH(4)(+), Sr(2+) and the [Ru(NH(3))(6)](2+/3+) redox marker) whereas other structures are adopted by the elongated aptamers in the presence of some of these cations. The stability of each structure is evaluated on the basis of UV spectroscopy melting curves. Thermal difference spectra confirm the quadruplex character of all conformations. The elongated sequences can adopt a parallel or an antiparallel structure, depending on the nature of the cation; this can potentially confer an ion-sensitive switch behavior. This switch property is demonstrated with the frequently employed redox complex [Ru(NH(3))(6)](3+), which induces the parallel conformation at very low concentrations (10 equiv per strand). The addition of large amounts of K(+) reverts the conformation to the antiparallel form, and opens interesting perspectives for electrochemical biosensing or redox-active responsive devices.
authors.affiliation: Université Libre de Bruxelles, Faculté des Sciences, Service de Chimie Analytique et Chimie des Interfaces, CP 255, Boulevard du Triomphe 2, 1050 Bruxelles, Belgium.
authors.forename: Aurore
authors.initials: A
authors.lastname: De Rache
authors.forename: Iva
authors.initials: I
authors.lastname: Kejnovská
authors.forename: Michaela
authors.initials: M
authors.lastname: Vorlíčková
authors.forename: Claudine
authors.initials: C
authors.lastname: Buess-Herman
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001483:Base Sequence; D015374:Biosensing Techniques; D002412:Cations / Q000737:chemistry*; D002942:Circular Dichroism; D004055:Differential Thermal Analysis; D004563:Electrochemistry; D054856:G-Quadruplexes; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry* / Q000378:metabolism; D056951:Photoelectron Spectroscopy; D011188:Potassium / Q000737:chemistry* / Q000378:metabolism; D012428:Ruthenium / Q000737:chemistry*; D013917:Thrombin / Q000737:chemistry*
chemical_list: D052157:Aptamers, Nucleotide; D002412:Cations; D009841:Oligonucleotides; D012428:Ruthenium; D013917:Thrombin; D011188:Potassium