Journal
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
Volume 1861, Issue 5, Pages 1205-1212Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.bbagen.2016.09.030
Keywords
Thrombin binding aptamer; Thymine glycol nucleic acid; L-thymidine; 8-bromo-2 '-deoxyguanine; G-quadruplex; NMR
Categories
Funding
- Spanish Ministry of Economy (MICINN) [CTQ2014-52588-R, CTQ2014-61758-EXP, CTQ2011-15203-E, CTQ2012-35360, CTQ2015-66254-C2-2-P]
- Generalitat de Catalunya [2014SGR187]
- Institute de Salud Carlos III
- European Regional Development Fund
- VI National RDI Plan
- Iniciativa Ingenio, Consolider Program
- CIBER Actions
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Background: 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. Methods: 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. Results: 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. Conclusions: The substitutions of loop positions with GNAT 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. General significance: 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. (C) 2016 Elsevier B.V. All rights reserved.
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