Three new double-headed nucleotides with additional nucleobases connected to C-5 of pyrimidines; synthesis,duplex and triplex studies |
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| Institution: | 1. Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark;2. Department of Chemistry, Kurukshetra University, Kurukshetra 136 119, India;1. Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan;2. Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan;1. Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland;2. Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland;1. Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany;2. Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany;1. Department of Oncology, University of Alberta, Canada;2. Department of Chemistry and Chemical Biology, McMaster University, Canada;3. Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Canada;1. Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea;2. Department of Bioactive Material Sciences, Research Center of Bioactive Materials, Chonbuk National University, Jeonju 561-756, South Korea |
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| Abstract: | In the search for double-coding DNA-systems, three new pyrimidine nucleosides, each coded with an additional nucleobase anchored to the major groove face, are synthesized. Two of these building blocks carry a thymine at the 5-position of 2′-deoxyuridine through a methylene linker and a triazolomethylene linker, respectively. The third building block carries an adenine at the 6-position of pyrrolo-2′-deoxycytidine through a methylene linker. These double-headed nucleosides are introduced into oligonucleotides and their effects on the thermal stabilities of duplexes are studied. All studied double-headed nucleotide monomers reduce the thermal stability of the modified duplexes, which is partially compensated by using consecutive incorporations of the modified monomers or by flanking the new double-headed analogs with members of our former series containing propyne linkers. Also their potential in triplex-forming oligonucleotides is studied for two of the new double-headed nucleotides as well as the series of analogs with propyne linkers. The most stable triplexes are obtained with single incorporations of additional pyrimidine nucleobases connected via the propyne linker. |
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| Keywords: | Nucleic acids Duplex Triplex Double-headed nucleosides CuAAC reaction |
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