The evaluation of 5-amino- and 5-hydroxyuracil derivatives as potential quadruplex-forming agents

Gábor Paragi, Zoltán Kupihár, Gábor Endre, Célia Fonseca Guerra, Lajos Kovács

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5-Substituted uracils (NH 2 or OH groups in position 5) have been examined theoretically and experimentally as potential building blocks in quadruplex structures. Our high level Density Functional Theory (DFT) calculations showed that the tetramer formation and stacking energies for 5-substituted uracils are similar to the energies of purine-based xanthine (X) or guanine (G) structures. As tetrads of 5-substituted uracils cover almost exactly the same area as purine tetrads, mixed tetrads or quadruplex structures based on X or G and 5-substituted uracil motifs are possible. According to the calculations, 5-hydroxyuracil-based structures are the best candidates for experimental implementation which was corroborated by the existence of higher complexes in the mass spectra of 1-benzyl-5-hydroxyuracil. These pyrimidine-based molecules can be used as efficient building blocks in different applications including aptamers, bio-sensors or-taking into account the larger cavity in the central region of 5-hydroxyuracil structures-as an artificial ion channel.
Original languageEnglish
Pages (from-to)2174-2184
Number of pages11
JournalOrganic and Biomolecular Chemistry
Issue number10
Early online date20 Dec 2016
Publication statusPublished - 14 Mar 2017


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