title: The effect of l-thymidine, acyclic thymine and 8-bromoguanine on the stability of model G-quadruplex structures.
abstract: Guanine-rich oligonucleotides are capable of forming tetrahelical structures known as G-quadruplexes with interesting biological properties. We have investigated the effects of site-specific substitution in the loops and in the tetrads model G-quadruplexes using thymine glycol nucleic acid (GNA) units, l-thymidine and 8-Br-2'-deoxyguanosine.
  
  
  
  Modified oligonucleotides were chemically synthesized and spectroscopic techniques were used to determine the relative stability of the modified G-quadruplex. The double 8-BrdG-modified quadruplexes were further characterized by Nuclear Magnetic Resonance. Binding to thrombin of selected quadruplex was analyzed by gel electrophoresis retention assay.
  
  
  
  The most interesting results were found with a 8-bromoG substitution that had the larger stabilization of the quadruplex. NMR studies indicate a tight relationship between the loops and the tetrads to accommodate 8-bromoG modifications within the TBA.
  
  
  
  The substitutions of loop positions with GNA T affect the TBA stability except for single modification in T7 position. Single l-thymidine substitutions produced destabilization of TBA. Larger changes on quadruplex stability are observed with the use of 8-bromoG finding a single substitution with the highest thermal stabilization found in thrombin binding aptamers modified at the guanine residues and having good affinity for thrombin. Double 8-BrdG modification in anti positions of different tetrads produce a conformational flip from syn to anti conformation of 8-Br-dG to favor loop-tetrad interaction and preserve the overall TBA stability.
  
  
  
  Modified guanine-rich oligonucleotides are valuable tools for the search for G-quadruplex structures with higher thermal stability and may provide compounds with interesting protein-nucleic acid binding properties. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
authors.affiliation: Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain. Electronic address: aaagma@cid.csic.es.
authors.forename: Anna
authors.initials: A
authors.lastname: Aviñó
authors.affiliation: Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Mazzini
authors.affiliation: Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain.
authors.forename: Carme
authors.initials: C
authors.lastname: Fàbrega
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento, s/n, 18016 Armilla, Granada, Spain; Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC - Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Peñalver
authors.affiliation: Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Spain.
authors.forename: Raimundo
authors.initials: R
authors.lastname: Gargallo
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avda. del Conocimiento, s/n, 18016 Armilla, Granada, Spain; Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC - Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain.
authors.forename: Juan Carlos
authors.initials: JC
authors.lastname: Morales
authors.affiliation: Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, 08034 Barcelona, Spain. Electronic address: recgma@cid.csic.es.
authors.forename: Ramon
authors.initials: R
authors.lastname: Eritja
mesh_terms: D003839:Deoxyadenosines / Q000737:chemistry* / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D054856:G-Quadruplexes; D006147:Guanine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009841:Oligonucleotides / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D013329:Structure-Activity Relationship; D013917:Thrombin / Q000737:chemistry / Q000378:metabolism; D013936:Thymidine / Q000737:chemistry* / Q000378:metabolism
chemical_list: C502319:8-bromoguanine; D003839:Deoxyadenosines; D009841:Oligonucleotides; C042464:8-bromo-2'-deoxyadenosine; D006147:Guanine; D013917:Thrombin; D013936:Thymidine
keywords: 8-bromo-2′-deoxyguanine; G-quadruplex; NMR; Thrombin binding aptamer; Thymine glycol nucleic acid; l-thymidine