title: Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures.
abstract: Guanine-rich sequences show large structural variability, with folds ranging from duplex to triplex and quadruplex helices. Quadruplexes are polymorphic, and can show multiple stoichiometries, parallel and antiparallel strand alignments, and different topological arrangements. We analyze here the equilibrium between intramolecular antiparallel and intermolecular parallel G-quadruplexes in the thrombin-binding aptamer (TBA) sequence. Our theoretical and experimental studies demonstrate that an apparently simple modification at the loops of TBA induces a large change in the monomeric antiparallel structure of TBA to yield a parallel G-quadruplex showing a novel T-tetrad. The present results illustrate the extreme polymorphism of G-quadruplexes and the ease with which their conformation in solution can be manipulated by nucleotide modification.
authors.affiliation: Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Aviñó
authors.forename: Guillem
authors.initials: G
authors.lastname: Portella
authors.forename: Ruben
authors.initials: R
authors.lastname: Ferreira
authors.forename: Raimundo
authors.initials: R
authors.lastname: Gargallo
authors.forename: Stefania
authors.initials: S
authors.lastname: Mazzini
authors.forename: Valérie
authors.initials: V
authors.lastname: Gabelica
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
authors.forename: Ramon
authors.initials: R
authors.lastname: Eritja
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D054856:G-Quadruplexes; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D011110:Polymorphism, Genetic
chemical_list: D052157:Aptamers, Nucleotide; C081676:thrombin aptamer
keywords: DNA polymorphism; G-quadruplex; nucleic acid structure; thermal stability; thrombin-binding aptamer