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175101MCID_676f08609554e7b95a09cff6 39601631 Frank Seela[author] Seela, Frank[Full Author Name] seela, frank[Author] trying2...
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1521-37652024Nov27Chemistry (Weinheim an der Bergstrasse, Germany)Chemistryα-D NUCLEOSIDE BASED SELF-HEALING SUPRAMOLECULAR HYDROGELS DERIVED FROM THE α-D ANOMERS OF 2'-DEOXYGUANOSINE AND FLUORESCENT 8-AZAPURINE 2'-DEOXYRIBOFURANOSIDES.e202403282e20240328210.1002/chem.202403282Self-assembly of α-D nucleosides to supramolecular hydrogels is described in detail. Hydrogel formation was studied on α-D 2'-deoxyguanosine (α-dG), and the fluorescent 8-azapurine α-D nucleosides 2-amino-8-aza-2'-deoxyadenosine (α-2-NH2-z8Ad) and 8-aza-2'-deoxyisoguanosine (α-z8iGd). These compounds were prepared from α-D 8-aza-2'-deoxyguanosine by an activation/amination protocol followed by deamination. Protonation and deprotonation pKa values of monomeric nucleosides were determined. Fluorescence measurements displayed the pH-dependent fluorescence intensity of α-D 8-azapurine nucleosides. α-dG and α-z8iGd self-assemble to gels that are selective for K+-ions. The α-dG gel is transparent and the α-z8iGd gel shows fluorescence. α-2-NH2-z8Ad forms fluorescent gels in the presence of alkali metal ions of different size. SEM images exposed a large condensed and flat structure for the α-dG gel, whereas the α-2-NH2-z8Ad gel consists of flakes that are connected to bundles. A porous structure generated by helical cylindric fibers was found for the α-z8iGd gel. All α-D hydrogels showed long-term lifetime stability. The α-z8iGd hydrogel in KCl solution has the highest Tgel value. The minimum gelation concentration of the hydrogels was 0.3-0.5 mg nucleoside/100 µL alkali ion solution. In periodical step-strain experiments, the hydrogels of α-dG and α-2-NH2-z8Ad and α-z8iGd displayed thixotropy. Based on their self-healing and shear-thinning properties the hydrogels are injectable.© 2024 Wiley‐VCH GmbH.DeshmukhSushmaSCenter for Nanotechnology, Laboratory of Bioorganic Chemistry and Chemical Biology, Heisenbergstrasse, 11, 48149, Münster, GERMANY.Budow-BusseSimoneSCenter for Nanotechnology, Laboratory of Bioorganic Chemistry and Chemical Biology, Heisenbergstrasse, 11, 48149, Münster, GERMANY.KondhareDasharathDCenter for Nanotechnology, Laboratory of Bioorganic Chemistry and Chemical Biology, Heisenbergstrasse, 11, 48149, Münster, GERMANY.SchäferAndreas HAHCenter for Nanotechnology, nanoAnalytics GmbH, Heisenbergstrasse, 11, 48149, Münster, GERMANY.LeonardPeterPCenter for Nanotechnology, Laboratory of Bioorganic Chemistry and Chemical Biology, Heisenbergstrasse 11, 48149, Münster, GERMANY.SeelaFrankFUniversität Osnabrück, Institut für Chemie neuer Materialien, Barbarastrasse 7, 49069, Osnabrück, GERMANY.engJournal Article20241127
GermanyChemistry95137830947-6539IMFluorescent HydrogelsRheologyScanning Electron Microscopyalpha-D 2'-Deoxyguanosinealpha-D 8-Azapurine-2'-deoxyribonucleosides202411272024922024112720241127123420241127123420241127933aheadofprint3960163110.1002/chem.202403282390885642024082120241101
1520-48123582024Aug21Bioconjugate chemistryBioconjug Chem7-Deaza-2'-deoxyisoguanosine, a Noncanonical Nucleoside for Nucleic Acid Code Expansion and New DNA Constructs: Nucleobase Functionalization of Inverse Watson-Crick and Purine-Purine Base Pairs.123312501233-125010.1021/acs.bioconjchem.4c002907-Deaza-2'-deoxyisoguanosine forms stable inverse Watson-Crick base pairs with 5-methyl-2'-deoxyisocytidine and purine-purine base pairs with 2'-deoxyguanosine or 5-aza-7-deaza-2'-deoxyguanosine. Both base pairs expand the genetic coding system. The manuscript reports on the functionalization of these base pairs with halogen atoms and clickable side chains introduced at 7-position of the 7-deazapurine base. Oligonucleotides containing the functionalized base pairs were prepared by solid-phase synthesis. To this end, a series of phosphoramidites were synthesized and clickable side chains with short and long linkers were incorporated in oligonucleotides. Fluorescent pyrene conjugates were obtained by postmodification. Functionalization of DNA with a single inverse Watson-Crick base pair by halogens or clickable residues has only a minor impact on duplex stability. Pyrene click adducts increase (long linker) or decrease (short linker) the double helix stability. Stable hybrid duplexes were constructed containing three consecutive purine-purine pairs of 7-functionalized 7-deaza-2'-deoxyisoguanine with guanine or 5-aza-7-deazaguanine in the center and Watson-Crick pairs at both ends. The incorporation of a hybrid base pair tract of 7-deaza-2'-deoxyisoguanosine/5-aza-7-deaza-2'-deoxyguanosine pairs stabilizes the double helix strongly. Fluorescence intensity of pyrene short linker adducts increased when the 7-deazapurine base was positioned opposite to 5-methylisocytosine (inverse base pair) compared to purine-purine base pairs with guanine or 5-aza-7-deazaguanine in opposite positions. For long liker adducts, the situation is more complex. Circular dichroism (CD) spectra of purine DNA differ to those of Watson-Crick double helices and are indicative for the new DNA constructs. The impact of 7-deaza-2'-deoxyisoguanine base pair functionalization is studied for the first time and all experimental details are reported to prepare DNA functionalized at the 7-deazaisoguanine site. The influence of single and multiple incorporations on DNA structure and stability is shown. Clickable residues introduced at the 7-position of the 7-deazaisoguanine base provide handles for Huisgen-Sharpless-Meldal click cycloadditions without harming the stability of purine-pyrimidine and purine-purine base pairs. Other chemistries might be used for bioconjugation. Our investigation paves the way for the functionalization of a new DNA related recognition system expanding the common Watson-Crick regime.XiaZhenqiangZLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Budow-BusseSimoneSLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20240801
United StatesBioconjug Chem90103191043-18020Purines9007-49-2DNA12133JR80SGuanosine0PyrenesW60KTZ3IZYpurine0OligonucleotidesG9481N71RODeoxyguanosineIMBase PairingPurineschemistryDNAchemistryGuanosinechemistryanalogs & derivativesPyreneschemistryOligonucleotideschemistryDeoxyguanosinechemistryanalogs & derivatives2024821114120248118432024811354ppublish3908856410.1021/acs.bioconjchem.4c00290390528942024081620241010
1520-690489162024Aug16The Journal of organic chemistryJ Org Chem7-Deazapurine and Pyrimidine Nucleoside and Oligonucleotide Cycloadducts Formed by Inverse Diels-Alder Reactions with 3,6-Di(pyrid-2-yl)-1,2,4,5-tetrazine: Ethynylated and Vinylated Nucleobases for Functionalization and Impact of Pyridazine Adducts on DNA Base Pair Stability and Mismatch Discrimination.113041132211304-1132210.1021/acs.joc.4c00982The manuscript reports on 7-deazapurine and pyrimidine nucleoside and oligonucleotide cycloadducts formed by the inverse electron demand Diels-Alder (iEDDA) reaction with 3,6-di(pyrid-2-yl)-1,2,4,5-tetrazine. Cycloadducts were constructed from ethynylated and vinylated nucleobases. Oligonucleotides were synthesized containing iEDDA modifications, and the impact on duplex stability was investigated. iEDDA reactions were performed on nucleoside triple bond side chains. Oxidation was not required in these cases as dihydropyridazine intermediates are not formed. In contrast, oxidation is necessary for reactions performed on alkenyl compounds. This was verified on 5-vinyl-2'-deoxyuridine. A diastereomeric mixture of 1,2-dihydropyridazine cycloadduct intermediates was isolated, characterized, and later oxidized. 12-mer oligonucleotides containing 1,2-pyridazine inverse Diels-Alder cycloadducts and their precursors were hybridized to short DNA duplexes. For that, a series of phosphoramidites was prepared. DNA duplexes with 7-functionalized 7-deazaadenines and 5-functionalized pyrimidines display high duplex stability when spacer units are present between nucleobases and pyridazine cycloadducts. A direct connectivity of the pyridazine moiety to nucleobases as reported for metabolic labeling of vinyl nucleosides reduced duplex stability strongly. Oligonucleotides bearing linkers with and without pyridazine cycloadducts attached to the 7-deazaadenine nucleobase significantly reduced mismatch formation with dC and dG.ChandankarSomnath ShivajiSS0000-0001-6800-0718Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.DeshmukhSushmaSLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.YangHaozheHLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20240725
United StatesJ Org Chem2985193R0022-32630Pyridazines07-deazapurine0Oligonucleotides0Purines0Pyrimidine Nucleosides9007-49-2DNA449GLA0653pyridazineIMPyridazineschemistryOligonucleotideschemistryCycloaddition ReactionBase PairingPurineschemistryMolecular StructurePyrimidine NucleosideschemistryDNAchemistryBase Pair Mismatch2024816642202472612432024725153ppublish3905289410.1021/acs.joc.4c00982382524612024020720240515
2053-229680Pt 22024Feb01Acta crystallographica. Section C, Structural chemistryActa Crystallogr C Struct Chemα-D-2'-Deoxyadenosine, an irradiation product of canonical DNA and a component of anomeric nucleic acids: crystal structure, packing and Hirshfeld surface analysis.212921-2910.1107/S2053229624000457α-D-2'-Deoxyribonucleosides are products of the γ-irradiation of DNA under oxygen-free conditions and are constituents of anomeric DNA. They are not found as natural building blocks of canonical DNA. Reports on their conformational properties are limited. Herein, the single-crystal X-ray structure of α-D-2'-deoxyadenosine (α-dA), C10H13N5O3, and its conformational parameters were determined. In the crystalline state, α-dA forms two conformers in the asymmetric unit which are connected by hydrogen bonds. The sugar moiety of each conformer is arranged in a `clamp'-like fashion with respect to the other conformer, forming hydrogen bonds to its nucleobase and sugar residue. For both conformers, a syn conformation of the nucleobase with respect to the sugar moiety was found. This is contrary to the anti conformation usually preferred by α-nucleosides. The sugar conformation of both conformers is C2'-endo, and the 5'-hydroxyl groups are in a +sc orientation, probably due to the hydrogen bonds formed by the conformers. The formation of the supramolecular assembly of α-dA is controlled by hydrogen bonding and stacking interactions, which was verified by a Hirshfeld and curvedness surface analysis. Chains of hydrogen-bonded nucleobases extend parallel to the b direction and are linked to equivalent chains by hydrogen bonds involving the sugar moieties to form a sheet. A comparison of the solid-state structures of the anomeric 2'-deoxyadenosines revealed significant differences of their conformational parameters.open access.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Budow-BusseSimoneSLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.DaniliucConstantinC0000-0002-6709-3673Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany.SeelaFrankFLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20240122
EnglandActa Crystallogr C Struct Chem1016203132053-22960Nucleic AcidsP582C98ULC2'-deoxyadenosine9007-49-2DNA0Sugars0DeoxyadenosinesIMNucleic AcidschemistryModels, MolecularHydrogen BondingCrystallography, X-RayDNAchemistrySugarsDeoxyadenosinesHirshfeld surface analysisanomercrystal packingcrystal structurenucleosideα-2′-deoxyadenosine2023124202411120242764220241221243202412211442024122ppublish38252461PMC1084495510.1107/S2053229624000457S2053229624000457Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205–8212.5079964Amato, N. J. & Wang, Y. (2014). Chem. Res. Toxicol. 27, 470–479.PMC400212824517165Aramini, J. M., Cleaver, S. H., Pon, R. T., Cunningham, R. P. & Germann, M. W. (2004). J. Mol. Biol. 338, 77–91.15050824Bruker (2019). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.Bruker (2021). APEX4. Bruker AXS Inc., Madison, Wisconsin, USA.Budow-Busse, S., Chai, Y., Müller, S. L., Daniliuc, C. & Seela, F. (2021). Acta Cryst. C77, 202–208.PMC809796433949335Chai, Y., Guo, X., Leonard, P. & Seela, F. (2020). Chem. Eur. J. 26, 13973–13989.PMC770204632667103Ciuffreda, P., Casati, S. & Manzocchi, A. (2007). Magn. Reson. Chem. 45, 781–784.17640032Görbitz, C. H., Nelson, W. H. & Sagstuen, E. (2005). Acta Cryst. E61, o1207–o1209.Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179.PMC482265327048719Hamor, T. A., O’Leary, M. K. & Walker, R. T. (1977). Acta Cryst. B33, 1218–1223.Hoffer, M. (1960). Chem. Ber. 93, 2777–2781.Ide, H., Shimizu, H., Kimura, Y., Sakamoto, S., Makino, K., Glackin, M., Wallace, S. S., Nakamuta, H., Sasaki, M. & Sugimoto, N. (1995). Biochemistry, 34, 6947–6955.7766604IUPAC–IUB Joint Commission on Biochemical Nomenclature (1983). Eur. J. Biochem. 131, 9–15.6832147Johnson, C. N., Spring, A. M., Desai, S., Cunningham, R. P. & Germann, M. W. (2012). J. Mol. Biol. 416, 425–437.PMC347967522227386Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10.PMC445316626089746Latha, Y. S. & Yathindra, N. (1992). Biopolymers, 32, 249–269.1581546Lesiak, K. B. & Wheeler, K. T. (1990). Radiat. Res. 121, 328–337.2315449Morvan, F., Rayner, B., Imbach, J.-L., Chang, D.-K. & Lown, J. W. (1987a). Nucleic Acids Res. 15, 4241–4255.PMC3408453588292Morvan, F., Rayner, B., Imbach, J.-L., Lee, M., Hartley, J. A., Chang, D.-K. & Lown, J. W. (1987b). Nucleic Acids Res. 15, 7027–7044.PMC3061903658672Ness, R. K. (1968). In Synthetic Procedures in Nucleic Acid Chemistry, edited by W. W. Zorbach & R. S. Tipson, pp. 183–187. New York: Interscience Publishers.Ness, R. K. & Fletcher, H. G. Jr (1960). J. Am. Chem. Soc. 82, 3434–3436.Ni, G., Du, Y., Tang, F., Liu, J., Zhao, H. & Chen, Q. (2019). RSC Adv. 9, 14302–14320.PMC906422935519323Paoletti, J., Bazile, D., Morvan, F., Imbach, J.-L. & Paoletti, C. (1989). Nucleic Acids Res. 17, 2693–2704.PMC3176512717407Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259.PMC366130523719469Putz, H. & Brandenburg, K. (2022). DIAMOND. Crystal Impact GbR, Bonn, Germany.Retailleau, P., Ishchenko, A. A., Kuznetsov, N. A., Saparbaev, M. & Moréra, S. (2010). Acta Cryst. F66, 798–800.PMC289846420606276Robins, M. J. & Robins, R. K. (1965). J. Am. Chem. Soc. 87, 4934–4940.5844465Saenger, W. (1984). In Principles of Nucleic Acid Structure, edited by C. R. Cantor. New York: Springer-Verlag.Sato, T. (1984). Acta Cryst. C40, 880–882.Seela, F., Rosemeyer, H., Melenewski, A., Heithoff, E.-M., Eickmeier, H. & Reuter, H. (2002). Acta Cryst. C58, o142–o144.11870307Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.Shinozuka, K., Hirota, Y., Morita, T. & Sawai, H. (1992). Heterocycles, 34, 2117–2121.Spackman, M. A. & Jayatilaka, D. (2009). CrystEngComm, 11, 19–32.Sundaralingam, M. (1971). J. Am. Chem. Soc. 93, 6644–6647.5122780Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia. https://crystalexplorer.net/.Watson, D. G., Sutor, D. J. & Tollin, P. (1965). Acta Cryst. 19, 111–124.5896865Zhang, A., Kondhare, D., Leonard, P. & Seela, F. (2022b). Chem. Eur. J. 28, e202201294.PMC954321235652726Zhang, A., Leonard, P. & Seela, F. (2022a). Chem. Eur. J. 28, e202103872.PMC9304229348782013822728120240202
1520-69048932024Feb02The Journal of organic chemistryJ Org ChemNucleobase-Functionalized 7-Deazaisoguanine and 7-Deazapurin-2,6-diamine Nucleosides: Halogenation, Cross-Coupling, and Cycloaddition.180718221807-182210.1021/acs.joc.3c02514The functionalization in position-7 of 7-deazaisoguanine and 7-deazapurin-2,6-diamine ribo- and 2'-deoxyribonucleosides by halogen atoms (chloro, bromo, iodo), and clickable alkynyl and vinyl side chains for copper-catalyzed and copper-free cycloadditions is described. Problems arising during the synthesis of the 7-iodinated isoguanine ribo- and 2'-deoxyribonucleosides were solved by the action of acetone. The impact of side chains and halogen atoms on the pKa values and hydrophobicity of nucleosides was investigated. Halogenated substituents increase the lipophilic character of nucleosides in the order Cl < Br < I and decrease the pK values of protonation. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of azide-alkyne click adducts bearing pyrene as sensor groups were determined. Pyrene fluorescence was solvent-dependent and changed according to the linker lengths. Excimer emission was observed in dioxane for the long linker adduct. Bioorthogonal inverse-electron-demanding Diels-Alder cycloadditions (iEDDA) were conducted on the electron-rich vinyl groups of 7-deazaisoguanine and 7-deazapurin-2,6-diamine nucleosides as dienophiles and 3,6-dipyridyl-1,2,4,5-tetrazine as diene. The initially formed complex reaction mixture of isomers could be easily oxidized with iodine in tetrahydrofuran (THF)/pyridine leading to single aromatic tetrazine adducts within a short time and in excellent yields.XiaZhenqiangZLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.ChandankarSomnath ShivajiSS0000-0001-6800-0718Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.IngaleSachin ASALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal Article20240116
United StatesJ Org Chem2985193R0022-3263IM202411613432024116134220241161123ppublish3822728110.1021/acs.joc.3c02514376691192023091820231003
1520-690488182023Sep15The Journal of organic chemistryJ Org ChemPurine DNA Constructs Designed to Expand the Genetic Code: Functionalization, Impact of Ionic Forms, and Molecular Recognition of 7-Deazaxanthine-7-Deazapurine-2,6-diamine Base Pairs and Their Purine Counterparts.131491316813149-1316810.1021/acs.joc.3c01370Purine DNA represents an alternative pairing system formed by two purines in the base pair with the recognition elements of Watson-Crick DNA. Base functionalization of 7-deaza-2'-deoxyxanthosine with ethynyl and octadiynyl residues led to clickable side chain derivatives with short and long linker arms. As complementary bases, purine-2,6-diamine or 7-deazapurine-2,6-diamine 2'-deoxyribonucleosides were used. 7-Deaza-7-iodo-2'-deoxyxanthosine served as a starting material for Sonogashira cross-coupling and the p-nitrophenylethyl group for base protection. Phosphoramidite building blocks for DNA synthesis were prepared. Oligonucleotides containing single modifications or runs of three purine base pairs embedded in 12-mer Watson-Crick DNA were synthesized and hybridized with complementary strands with purine- or 7-deazapurine-2,6-diamine located opposite to the xanthine derivatives. The stability of base pairs was evaluated in a comparative study on the basis of DNA melting experiments and Tm values. As 7-deazaxanthine and xanthine nucleosides form anionic forms at neutral pH, duplex stability became pK-dependent, and the system with 7-deazapurine displayed a significant higher stability as that containing xanthine. Alkynyl side chains are well accommodated in the purine-purine helix. Click adducts with pyrene showed that short linker arms destabilize duplexes, whereas long linkers increase duplex stability. CD and fluorescence measurements provide further insights into purine-purine base pairing.ChandankarSomnath ShivajiSS0000-0001-6800-0718Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal Article20230905
United StatesJ Org Chem2985193R0022-3263W60KTZ3IZYpurine07-deazapurine07-deazaxanthine0Purines1AVZ07U9S7Xanthine0Diamines0IonsIMBase PairingGenetic CodePurinesXanthineDiaminesIons2023918124220239518412023951212ppublish3766911910.1021/acs.joc.3c01370374277992023072120230721
1520-48123472023Jul19Bioconjugate chemistryBioconjug ChemWatson-Crick Base Pairs with Protecting Groups: The 2-Amino Groups of Purine- and 7-Deazapurine-2,6-Diamine as Target Sites for DNA Functionalization by Selective Nucleobase Acylation.129013031290-130310.1021/acs.bioconjchem.3c00169The recognition of Watson-Crick base pairs carrying nucleobase protecting groups is reported as a new approach for DNA functionalization. The 2-amino groups of purine- and 7-deazapurine-2,6-diamine 2'-deoxyribonucleosides served as molecular targets for this functionalization. The 2-amino group withstands oligonucleotide deprotection with ammonia, whereas all other protecting groups are released after chemical DNA synthesis. On this basis, a method was developed for the selective functionalization of oligonucleotides at the 2-position of purines and 7-deazapurines. Melting experiments and Tm values obtained from hybridization studies revealed that duplexes with protected (2-amino-dA) and (2-amino-7-deaza-dA)-dT base pairs are as stable as their nonprotected counterparts. Mismatch discrimination of protected purine- and 7-deazapurine-2,6-diamine DNA was superior to that of nonprotected DNA. Click functionalization in the minor groove of the DNA double helix became accessible via introduction of heptynoyl protecting groups bearing a terminal triple bond. Click reactions with pyrene azide validated the usability. DNA conjugates with bulky pyrene residues at the 2-position (minor groove) developed the same high stability as those functionalized at the 7-position (major groove). This demonstrates the potential of our new method using protected base pairs for DNA functionalization and paves the way for new DNA labeling strategies.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.HeddingaXeniaXLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20230710
United StatesBioconjug Chem90103191043-1802W60KTZ3IZYpurine07-deazapurine0Purines9007-49-2DNA0Oligonucleotides0PyrenesIMBase PairingPurineschemistryDNAchemistryOligonucleotideschemistryPyrenesNucleic Acid Conformation202372164420237101352023710733ppublish3742779910.1021/acs.bioconjchem.3c00169367358592023021620230309
1520-48123422023Feb15Bioconjugate chemistryBioconjug ChemThe Base Pairs of Isoguanine and 8-Aza-7-deazaisoguanine with 5-Methylisocytosine as Targets for DNA Functionalization.422432422-43210.1021/acs.bioconjchem.2c00584The isoguanine-isocytosine base pair (isoG-isoC) represents an important expansion of the DNA coding system. The base pair is more stable than the canonical adenine-thymine or guanine-cytosine pairs. However, nothing is known on the functionalization of the noncanonical isoG-isoC pair at the isoguanine site. In this work, functionalization of the isoG-isoC and the isosteric base pair that contains 8-aza-7-deazaisoguanine in place of isoguanine is studied. Short ethynyl, more space demanding octadiynyl, and dendritic tripropargylamine residues attached to the isoG-isoC base pairs were introduced to oligonucleotides. 12-mer duplexes were formed by hybridization with single base pair modification. The use of the two modified nucleobases gave us the freedom to shift nucleobase substituents within the major groove of double helical DNA. Clickable side chains at position-7 stabilize the base pair, whereas 8-substituents reduce its stability strongly. The weak isoguanine-thymine or 8-aza-7-deazaisoguanine-thymine base pairs show a similar sensitivity to the position of nucleobase functionalization as base pair matches formed with 5-methylisocytosine. CD spectra of all modified duplexes display the typical shape of a B-DNA with only marginal changes. Fluorescent pyrene labeled DNA with long, short, and branched linkers was generated using click chemistry. Pyrene click adducts with long linkers are essential to maintain or to increase base pair stability. Labeled duplexes are more fluorescent than corresponding single strands. For the dendritic linker excimer emission was observed for single strands but only monomer emission in duplexes.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal Article20230203
United StatesBioconjug Chem90103191043-180207-deazaisoguanineE335PK4428isoguanineQR26YLT7LTThymine9007-49-2DNA5Z93L87A1RGuanine0PyrenesIMBase PairingThymineDNAchemistryGuaninechemistryPyrenesNucleic Acid Conformation20232460202321760202323152ppublish3673585910.1021/acs.bioconjchem.2c00584361783162022122920240916
1521-376528722022Dec27Chemistry (Weinheim an der Bergstrasse, Germany)ChemistryDNA Strand Displacement with Base Pair Stabilizers: Purine-2,6-Diamine and 8-Aza-7-Bromo-7-Deazapurine-2,6-Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction.e202202412e202202412e20220241210.1002/chem.202202412Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA-dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single-stranded invaders with single and multiple incorporations of stabilizers. Displacement is driven by negative enthalpy changes between target and displaced duplex. Toeholds are not required. Two new environmental sensitive fluorescent pyrene sensors were developed to monitor the progress of displacement reactions. Pyrene was connected to the nucleobase in the invader or to a dendritic linker in the output strand. Both new sensors were constructed by click chemistry; phosphoramidites and oligonucleotides were prepared. Sensors show monomer or excimer emission. Fluorescence intensity changes when the displacement reaction progresses. Our work demonstrates that strand displacement with base pair stabilizers is applicable to DNA, RNA and to related biopolymers with applications in chemical biology, nanotechnology and medicinal diagnostics.© 2022 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany.engJournal Article20221115
GermanyChemistry95137830947-65390Oligonucleotides07-deazapurine0Nucleosides9007-49-2DNA0Purines0Coloring Agents0PyrenesIMOligonucleotidesBase PairingNucleosidesDNAPurinesColoring AgentsPyrenesbase pair stabilizerhybridizationoligonucleotidespyrene fluorescencestrand displacementThe authors declare no conflict of interest.202283202210160202212306020229309322023413ppublish36178316PMC1010033710.1002/chem.202202412 Simmel F. C., Yurke B., Singh H. R., Chem. Rev. 2019, 119, 6326–6369;30714375Connolly A. R., Seow N., Fenati R. A., Ellis A. V., Comprehensive nanoscience and nanotechnology (Eds.: Andrews D. L., Lipson R. H., Nann T.) Elsevier B. V. 2019, 2, 1–29;Wang F., Liu X., Willner I., Angew. Chem. Int. Ed. 2015, 54, 1098–1129,25521588Angew. Chem. 2015, 127, 1112–1144;Bi S., Yue S., Zhang S., Chem. Soc. Rev. 2017, 46, 4281–4298;28573275Zhou L., Kim S. C., Ho K. H., O'Flaherty D. K., Giurgiu C., Wright T. H., Szostak J. W., eLife 2019, 8, e51888;PMC687220931702557Zhang D. 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1520-481233102022Oct19Bioconjugate chemistryBioconjug ChemPurine-Purine Base Pairs in Parallel DNA: β-D Anomeric 8-Aza-7-deazaisoguanine and 7-Functionalized Conjugates Form Stable Base Pairs with α-D 5-Aza-7-deaza-2'-deoxyguanosine.179618021796-180210.1021/acs.bioconjchem.2c00387Anomeric purine-purine DNA represents a new recognition system with strands in parallel orientation. This work investigates the new heterochiral system and the positional impact of nucleobase functionalization. Tracts of anomeric isoguanine/8-aza-7-deazaisoguanine base pairs with 5-aza-7-deazaguanine were embedded in anomeric Watson-Crick DNA. It was discovered that stable purine-purine base pairs are formed in anomeric DNA. Nucleobase functionalization of the novel base pair system with short ethynyl and bulky octadiynyl chains showed that the position of functionalization is critical. From Tm values and thermodynamic data, it is disclosed that side chains at 7-position of the β-D 8-aza-7-deaza-2'-deoxyisoguanosine-α-D 5-aza-7-deaza-2'-deoxyguanosine purine-purine pair are well accommodated in this new heterochiral DNA, whereas functionalization at 8-position of isoguanine hinders base pair formation. The new DNA base pair system has the potential to be applied in chemical biology, bioconjugation, and nanobiotechnology.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal Article20220920
United StatesBioconjug Chem90103191043-180207-deazaisoguanine05-aza-7-deaza-2'-deoxyguanosine9007-49-2DNA0PurinesIMBase PairingDNAchemistryPurineschemistryNucleic Acid Conformation2022921602022102160202292073ppublish3612503110.1021/acs.bioconjchem.2c00387359484212022082220220919
1520-690487162022Aug19The Journal of organic chemistryJ Org ChemDNA with Purine-Purine Base Pairs: Size and Position of Isoguanine and 8-Aza-7-deazaisoguanine Clickable Residues Control the Molecular Recognition of Guanine and 5-Aza-7-deazaguanine.106301065010630-1065010.1021/acs.joc.2c00812Purine-purine base pairs represent an alternative recognition system to the purine-pyrimidine pairing reported by Watson and Crick. Modified purines are the source for non-canonical interactions. To mimic dG-dC interactions, 2'-deoxyisoguanosine (1a) and 8-aza-7-deaza-2'-deoxyisoguanosine (2a) are used to construct base pairs with 2'-deoxyguanosine or 5-aza-7-deaza-2'-deoxyguanosine (dZ). This work reports the chemical functionalization of 1a and its shape mimic 2a in purine-purine base pairs. Clickable rigid ethynyl and more flexible octadiynyl side chain derivatives of 1a and 2a were synthesized. They were protected and converted into phosphoramidites. Building blocks were employed in the synthesis of base-modified 12-mer oligonucleotides with clickable side chains. Pyrene azide was clicked to the linkers. After hybridization, oligonucleotides with purine-purine base pairs were constructed with linkers and pyrene adducts at position-8 of isoguanine and at position-7 of 8-aza-7-deazaisoguanine. Recognition and stability of purine-purine base pairs were explored using Tm values, thermodynamic data, and CD-spectroscopic changes. Side chains at position-7 of 8-aza-7-deazaisoguanine-guanine base pairs or with 5-aza-7-deazaguanine are well accommodated in DNA, whereas functionalization at 8-position of isoguanine makes the DNA unstable. Pyrene click adducts verified the observation. In conclusion, position-7 is the place of choice for purine-purine base pair functionalization.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal Article20220810
United StatesJ Org Chem2985193R0022-326307-deazaisoguanine0Oligonucleotides0Purines0Pyrenes0Pyrimidines0Pyrroles5Z93L87A1RGuanine9007-49-2DNAE335PK4428isoguanineGPL8T5ZO3M7-deazaguanineW60KTZ3IZYpurineIMBase PairingDNAchemistryGuanineanalogs & derivativeschemistryNucleic Acid ConformationOligonucleotideschemistryPurinesPyrenesPyrimidinesPyrroles20228116020228236020228102140ppublish3594842110.1021/acs.joc.2c00812357885022022070620240831
2053-229678Pt 72022Jul01Acta crystallographica. Section C, Structural chemistryActa Crystallogr C Struct ChemThe 2'-deoxyribofuranoside of 3-phenyltetrahydropyrimido[4,5-c]pyridazin-7-one: a bicyclic nucleoside with sugar residues in N and S conformations, and its molecular recognition.382389382-38910.1107/S2053229622005964The title compound 3-phenyltetrahydropyrimido[4,5-c]pyridazine 2'-deoxyribonucleoside [systematic name: 6-(2-deoxy-β-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-3-phenylpyrimido[4,5-c]pyridazin-7-one monohydrate, C17H18N4O4·H2O, 1] shows two conformations in the crystalline state and the two conformers (1a and 1b) adopt different sugar puckers. The sugar residue of 1a shows a C2'-endo S-type conformation, while 1b displays a C3'-endo N-type sugar pucker. Both conformers adopt similar anti conformations around the N-glycosylic bonds, with χ = -97.5 (3)° for conformer 1a and χ = -103.8 (3)° for conformer 1b. The extended crystalline network is stabilized by several intermolecular hydrogen bonds involving nucleoside and water molecules. The nucleobases and phenyl substituents of the two conformers (1a and 1b) are stacked and display a reverse alignment. A Hirshfeld surface analysis supports the hydrogen-bonding pattern, while curvedness surfaces visualize the stacking interactions of neighbouring molecules. The recognition face of nucleoside 1 for base-pair formation mimics that of 2'-deoxythymidine. Nucleoside 1 shows two pKa values: 1.8 for protonation and 11.2 for deprotonation. DNA oligonucleotides containing nucleoside 1 were synthesized and hybridized with complementary DNA strands. Nucleoside 1 forms a stable base pair with dA which is as stable as the canonical dA-dT pair. The bidentate 1-dA base pair is strengthened by a third hydrogen bond provided by the dA analogue 3-bromopyrazolo[3,4-d]pyrimidine-4,6-diamine 2'-deoxyribofuranoside (4). By this, duplex stability is increased and the suggested base-pairing patterns are supported.open access.MeiHuiHLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Budow-BusseSimoneSLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.EickmeierHenningHAnorganische Chemie II, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.ReuterHansH0000-0002-1251-0783Anorganische Chemie II, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.SeelaFrankFLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20220613
EnglandActa Crystallogr C Struct Chem1016203132053-22960Nucleosides0SugarsIMCrystallography, X-RayHydrogen BondingMolecular ConformationNucleosideschemistrySugars2′-deoxyribonucleosidebase paircrystal structurehydrogen bondingpKa valuepyrimido[4,5-c]pyridazine2022413202262202275183020227660202277602022613ppublish35788502PMC925591410.1107/S2053229622005964S2053229622005964Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205–8212.5079964Brandenburg, K. (2005). DIAMOND. Crystal Impact GbR, Bonn, Germany.Bruker (2008). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.Chazin, W. J., Rance, M., Chollet, A. & Luepin, W. (1991). Nucleic Acids Res. 19, 5507–5513.PMC3289491945828Flack, H. D. (1983). Acta Cryst. A39, 876–881.He, J., Becher, G., Budow, S. & Seela, F. (2003). Nucleosides Nucleotides Nucleic Acids, 22, 573–576.14565231Hirao, I., Kimoto, M. & Yamashige, R. (2012). Acc. Chem. Res. 45, 2055–2065.22263525Hollenstein, M. (2012). Molecules, 17, 13569–13591.PMC626887623154273Hudson, R. H. E. & Ghorbani-Choghamarani, A. (2007). Synlett, 2007, 0870–0873.IUPAC–IUB Joint Commission on Biochemical Nomenclature (1983). Eur. J. Biochem. 131, 9–15.6832147Krishnamurthy, R. (2012). Acc. Chem. Res. 45, 2035–2044.PMC352505022533519Loakes, D., Brown, D. M., Salisbury, S. A., McDougall, M. G., Neagu, C., Nampalli, S. & Kumar, S. (2003a). Helv. Chim. Acta, 86, 1193–1204.Loakes, D., Brown, D. M., Salisbury, S. A., McDougall, M. G., Neagu, C., Nampalli, S. & Kumar, S. (2003b). Tetrahedron Lett. 44, 3387–3389.McDowell, J. A. & Turner, D. H. (1996). Biochemistry, 35, 14077–14089.8916893Mei, H., Ingale, S. A. & Seela, F. (2014). Chem. Eur. J. 20, 16248–16257.25336305Mei, H., Ingale, S. A. & Seela, F. (2015). Tetrahedron, 71, 6170–6175.Meiser, L. C., Antkowiak, P. L., Koch, J., Chen, W. D., Kohll, A. X., Stark, W. J., Heckel, R. & Grass, R. N. (2020). Nat. Protoc. 15, 86–101.31784718Mieczkowski, A., Tomczyk, E., Makowska, M. A., Nasulewicz-Goldeman, A., Gajda, R., Woźniak, K. & Wietrzyk, J. (2016). Synthesis, 48, 566–572.Saenger, W. (1984). In Principles of Nucleic Acid Structure, edited by C. R. Cantor. New York: Springer-Verlag.Seela, F. & Becher, G. (2001). Nucleic Acids Res. 29, 2069–2078.PMC5545311353076Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.18156677Spackman, M. A. & Jayatilaka, D. (2009). CrystEngComm, 11, 19–32.Spek, A. L. (2020). Acta Cryst. E76, 1–11.PMC694408831921444Topal, M. D. & Fresco, J. R. (1976). Nature (London), 263, 289–293.958483Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia. https://crystalexplorer.scb.uwa.edu.au/.0356527262022082420240905
1521-376528472022Aug22Chemistry (Weinheim an der Bergstrasse, Germany)ChemistryAnomeric DNA Strand Displacement with α-D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β-, β/β- and α/α-D Configuration.e202201294e202201294e20220129410.1002/chem.202201294DNA strand displacement is a technique to exchange one strand of a double stranded DNA by another strand (invader). It is an isothermal, enzyme free method driven by single stranded overhangs (toeholds) and is employed in DNA amplification, mismatch detection and nanotechnology. We discovered that anomeric (α/β) DNA can be used for heterochiral strand displacement. Homochiral DNA in β-D configuration was transformed to heterochiral DNA in α-D/β-D configuration and further to homochiral DNA with both strands in α-D configuration. Single stranded α-D DNA acts as invader. Herein, new anomeric displacement systems with and without toeholds were designed. Due to their resistance against enzymatic degradation, the systems are applicable to living cells. The light-up intercalator ethidium bromide is used as fluorescence sensor to follow the progress of displacement. Anomeric DNA displacement shows benefits over canonical DNA in view of toehold free displacement and simple detection by ethidium bromide.© 2022 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany.engJournal Article20220704
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2053-229678Pt 32022Mar01Acta crystallographica. Section C, Structural chemistryActa Crystallogr C Struct Chem8-Furylimidazolo-2'-deoxycytidine: crystal structure, packing, atropisomerism and fluorescence.141147141-14710.1107/S20532296220010008-Furylimidazolo-2'-deoxycytidine (furImidC), C14H14N4O5, is a fluorescent analogue of 2'-deoxycytidine, also displaying the same recognition face. As a constituent of DNA, furImidC forms extraordinarily strong silver-mediated self-pairs. Crystal structure determination revealed that furImidC adopts two types of disordered residues: the sugar unit and the furyl moiety. The disorder of the sugar residue amounts to an 87:13 split. The disorder of the furyl ring results from axial chirality at the C8-C2'' bond connecting the nucleobase to the heterocycle. The two atropisomers are present in unequal proportions [occupancies of 0.69 (2) and 0.31 (2)], and the nucleobase and the furyl moiety are coplanar. Considering the atomic sites with predominant occupancy, an anti conformation with χ = - 147.2 (7)° was found at the glycosylic bond and the 2'-deoxyribosyl moiety shows a C2'-endo (S, 2T1) conformation, with P = 160.0°. A 1H NMR-based conformational analysis of the furanose puckering revealed that the S conformation predominates also in solution. In the solid state, two neighbouring furImidC molecules are arranged in a head-to-tail fashion, but with a notable tilt of the molecules with respect to each other. Consequently, one N-H...N hydrogen bond is found for neighbouring molecules within one layer, while a second N-H...N hydrogen bond is formed to a molecule of an adjacent layer. In addition, hydrogen bonding is observed between the nucleobase and the sugar residue. A Hirshfeld surface analysis was performed to visualize the intermolecular interactions observed in the X-ray study. In addition, the fluorescence spectra of furImidC were measured in solvents of different polarity and viscosity. furImidC responds to microenvironmental changes (polarity and viscosity), which is explained by a hindered rotation of the furyl residue in solvents of high viscosity.open access.Budow-BusseSimoneSLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.JanaSunit KSKLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.DaniliucConstantinC0000-0002-6709-3673Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany.SeelaFrankFLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20220209
EnglandActa Crystallogr C Struct Chem1016203132053-22960W860991D6Deoxycytidine9007-49-2DNAIMCrystallography, X-RayDNAchemistryDeoxycytidinechemistryHydrogen BondingMolecular Conformation8-furylimidazolo-2′-deoxycytidineHirshfeld surface analysisatropisomerismcrystal packingcrystal structurefluorescence20218182022128202234171120223560202231760202229ppublish35245210PMC889652510.1107/S2053229622001000S2053229622001000Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205–8212.5079964Bruker (2014). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.Bruker (2015). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.Bruker (2016). APEX3. Bruker AXS Inc., Madison, Wisconsin, USA.Budow-Busse, S., Chai, Y., Müller, S. L., Daniliuc, C. & Seela, F. (2021). Acta Cryst. C77, 202–208.PMC809796433949335Clayden, J., Moran, W. J., Edwards, P. J. & LaPlante, S. R. (2009). Angew. Chem. Int. Ed. 48, 6398–6401.19637174Clever, G. H., Kaul, C. & Carell, T. (2007). Angew. Chem. Int. Ed. 46, 6226–6236.17640011Greco, N. J. & Tor, Y. (2007). Tetrahedron, 63, 3515–3527.PMC186855418431439Hübschle, C. B., Sheldrick, G. M. & Dittrich, B. (2011). J. Appl. Cryst. 44, 1281–1284.PMC324683322477785Hudson, R. H. E. & Ghorbani-Choghamarani, A. (2007). Synlett, 6, 870–873.Inoue, H., Imura, A. & Ohtsuka, E. (1987). Nippon Kagaku Kaishi, pp. 1214–1220.IUPAC–IUB Joint Commission on Biochemical Nomenclature (1983). Eur. J. Biochem. 131, 9–15.6832147Jana, S. K., Guo, X., Mei, H. & Seela, F. (2015). Chem. Commun. 51, 17301–17304.26463426Kovaliov, M., Segal, M. & Fischer, B. (2013). Tetrahedron, 69, 3698–3705.Kovaliov, M., Weitman, M., Major, D. T. & Fischer, B. (2014). J. Org. Chem. 79, 7051–7062.24992467Lee, S.-C., Heo, J., Woo, H. C., Lee, J.-A., Seo, Y. H., Lee, C.-L., Kim, S. & Kwon, O.-P. (2018). Chem. Eur. J. 24, 13706–13718.29700889Mei, H., Ingale, S. A. & Seela, F. (2014). Chem. Eur. J. 20, 16248–16257.25336305Ming, X. & Seela, F. (2012). Chem. Eur. J. 18, 9590–9600.22767494Noé, M. S., Ríos, A. C. & Tor, Y. (2012). Org. Lett. 14, 3150–3153.PMC342665722646728Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259.PMC366130523719469Reichardt, C. (1994). Chem. Rev. 94, 2319–2358.Saenger, W. (1984). In Principles of Nucleic Acid Structure, edited by C. R. Cantor. New York: Springer-Verlag.Seela, F., Becher, G. & Chen, Y. (2000). Nucleosides Nucleotides Nucleic Acids, 19, 1581–1598.11200261Seela, F. & Chen, Y. (1995). Nucleosides Nucleotides Nucleic Acids, 14, 863–866.0Seela, F., Chen, Y., Bindig, U. & Kazimierczuk, Z. (1994). Helv. Chim. Acta, 77, 194–202.Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.0Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.0Sinkeldam, R. W., Wheat, A. J., Boyaci, H. & Tor, Y. (2011). ChemPhysChem, 12, 567–570.PMC310279521344595Smith, D. E., Marquez, I., Lokensgard, M. E., Rheingold, A. L., Hecht, D. A. & Gustafson, J. L. (2015). Angew. Chem. Int. Ed. 54, 11754–11759.26276764Spackman, M. A. & Jayatilaka, D. (2009). CrystEngComm, 11, 19–32.Tinsley, R. A. & Walter, N. G. (2006). RNA, 12, 522–529.PMC138358916431979Toenjes, S. T. & Gustafson, J. L. (2018). Future Med. Chem. 10, 409–422.PMC596735829380622Tokugawa, M., Masaki, Y., Canggadibrata, J. C., Kaneko, K., Shiozawa, T., Kanamori, T., Grøtli, M., Wilhelmsson, L. M., Sekine, M. & Seio, K. (2016). Chem. Commun. 52, 3809–3812.26865112Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia. http://hirshfeldsurface.net.0Van Wijk, L., Haasnoot, C. A. G., de Leeuw, F. A. A. M., Huckriede, B. D., Westra Hoekzema, A. J. A. & Altona, C. (1999). PSEUROT 6.3. Leiden Institute of Chemistry, Leiden University, The Netherlands.Wahba, A. S., Esmaeili, A., Damha, M. J. & Hudson, R. H. E. (2010). Nucleic Acids Res. 38, 1048–1056.PMC281745519933258Wilhelmsson, L. M. (2010). Q. Rev. Biophys. 43, 159–183.20478079Young, D. W. & Wilson, H. R. (1975). Acta Cryst. B31, 961–965.348782012022021820240901
1521-37652892022Feb16Chemistry (Weinheim an der Bergstrasse, Germany)ChemistryAnomeric DNA: Functionalization of α-d Anomers of 7-Deaza-2'-deoxyadenosine and 2'-Deoxyuridine with Clickable Side Chains and Click Adducts in Homochiral and Heterochiral Double Helices.e202103872e202103872e20210387210.1002/chem.202103872Anomeric base pairs in heterochiral DNA with strands in the α-d and β-d configurations and homochiral DNA with both strands in α-d configuration were functionalized. The α-d anomers of 2'-deoxyuridine and 7-deaza-2'-deoxyadenosine were synthesized and functionalized with clickable octadiynyl side chains. Nucleosides were protected and converted to phosphoramidites. Solid-phase synthesis furnished 12-mer oligonucleotides, which were hybridized. Pyrene click adducts display fluorescence, a few of them with excimer emission. Tm values and thermodynamic data revealed the following order of duplex stability α/α-d≫β/β-d≥α/β-d. CD spectra disclosed that conformational changes occur during hybridization. Functionalized DNAs were modeled and energy minimized. Clickable side chains and bulky click adducts are well accommodated in the grooves of anomeric DNA. The investigation shows for the first time that anomeric DNAs can be functionalized in the same way as canonical DNA for potential applications in nucleic acid chemistry, chemical biology, and DNA material science.© 2021 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany.engJournal Article20220114
GermanyChemistry95137830947-653960129-59-12'-deoxytubercidin9007-49-2DNAM351LCX45YTubercidinW78I7AY22CDeoxyuridineIMBase PairingDNAchemistryDeoxyuridineTubercidinanalogs & derivativesanomeric DNAchiralityclick chemistryhybridizationoligonucleotidesThe authors declare no conflict of interest.2021102720211296020222196020211289252022722ppublish34878201PMC930422910.1002/chem.202103872 Morvan F., Rayner B., Imbach J.-L., Lee M., Hartley J. A., Chang D. K., Lown J. W., Nucleic Acids Res. 1987, 15, 7027–7044;PMC3061903658672Paoletti J., Bazile D., Morvan F., Imbach J.-L., Paoletti C., Nucleic Acids Res. 1989, 17, 2693–2704;PMC3176512717407Aramini J. M., Kalisch B. W., Pon R. T., van de Sande J. H., Germann M. W., Biochemistry 1996, 35, 9355–9365;8755713Keller B. M., Leumann C. J., Synthesis 2002, 6, 789–796.Chai Y., Kondhare D., Zhang A., Leonard P., Seela F., Chem. Eur. J. 2021, 27, 2093–2103.PMC789864633090562Chai Y., Guo X., Leonard P., Seela F., Chem. Eur. J. 2020, 26, 13973–13989.PMC770204632667103Aoyama H., Bull. Chem. Soc. Jpn. 1987, 60, 2073–2077.Hoffer M., Chem. Ber. 1960, 93, 2777–2781.H. Thomas, PhD thesis, University of Osnabrück (Germany), 1995.Seela F., Sirivolu V. R., Chittepu P., Bioconjugate Chem. 2008, 19, 211–224.18020404Seela F., Zulauf M., Reuter H., Kastner G., Acta Crystallogr. Sect. C 1999, 55, 1560–1562.10815222Seela F., Sirivolu V. R., Chem. Biodiversity 2006, 3, 509–514.17193286Meldal M., Tornøe C. W., Chem. Rev. 2008, 108, 2952–3015.18698735Kolb H. C., Finn M. G., Sharpless K. B., Angew. Chem. Int. Ed. 2001, 40, 2004–2021;11433435Angew. Chem. 2001, 113, 2056–2075.McDowell J. A., Turner D. H., Biochemistry 1996, 35, 14077–14089.8916893Ide H., Shimizu H., Kimura Y., Sakamoto S., Makino K., Glackin M., Wallace S. S., Nakamuta H., Sasaki M., Sugimoto N., Biochemistry 1995, 34, 6947–6955.7766604Miyahara T., Nakatsuji H., Sugiyama H., J. Phys. Chem. A 2013, 117, 42–55.23234566Kypr J., Kejnovská I., Renčiuk D., Vorličková M., Nucleic Acids Res. 2009, 37, 1713–1725.PMC266521819190094Tanaka H., Vickart P., Bertrand J.-R., Rayner B., Morvan F., Imbach J.-L., Paulin D., Malvy C., Nucleic Acids Res. 1994, 22, 3069–3074.PMC3102778065920Kowal E. A., Ganguly M., Pallan P. S., Marky L. A., Gold B., Egli M., Stone M. P., J. Phys. Chem. B 2011, 115, 13925–13934.PMC322501422059929Wing R., Drew H., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R. E., Nature 1980, 287, 755–758.7432492Østergaard M. E., Hrdlicka P. J., Chem. Soc. Rev. 2011, 40, 5771–5788.PMC364499521487621Paris L. P., Langenhan J. M., Kool E. T., Nucleic Acids Res. 1998, 26, 3789–3793.PMC1477559685497Mei H., Ingale S. A., Tetrahedron 2013, 69, 4731–4742.Seela F., Wei C., Helv. Chim. Acta 1999, 82, 726–745.Nucleic Acids in Chemistry and Biology (Eds.: Blackburn G. M., Gait M. J., Loakes D., Williams D. M.), The Royal Society of Chemistry, Cambridge, 2006.Saenger W., Principles of Nucleic Acid Structure, Springer, New York, 1984.Modified Nucleosides in Biochemistry, Biotechnology and Medicine (Ed.: Herdewijn P.), Wiley-VCH, Weinheim, 2008.Fantoni N. Z., El-Sagheer A. H., Brown T., Chem. Rev. 2021, 121, 7122–7154.33443411346614072022012520220125
1520-690486212021Nov05The Journal of organic chemistryJ Org ChemIsoguanine (2-Hydroxyadenine) and 2-Aminoadenine Nucleosides with an 8-Aza-7-deazapurine Skeleton: Synthesis, Functionalization with Fluorescent and Clickable Side Chains, and Impact of 7-Substituents on Physical Properties.144611447514461-1447510.1021/acs.joc.1c012837-Functionalized 8-aza-7-deaza-2'-deoxyisoguanine and 8-aza-7-deaza-2-aminoadenine 2'-deoxyribonucleosides decorated with fluorescent pyrene or benzofuran sensor tags or clickable side chains with terminal triple bonds were synthesized. 8-Aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine was used as the central intermediate and was accessible by an improved two-step glycosylation/amination protocol. Functionalization of position-7 was performed either on 8-aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine followed by selective deamination of the 2-amino group or on 7-iodinated 8-aza-7-deaza-2'-deoxyisoguanosine. Sonogashira and Suzuki-Miyaura cross-coupling reactions were employed for this purpose. Octadiynyl side chains were selected as linkers for click reactions with azido pyrenes. KTaut values calculated from H2O/dioxane mixtures revealed that side chains have a significant influence on the tautomeric equilibrium. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of the new 8-aza-7-deazapurine nucleosides with fluorescent side chains were determined. Remarkably, a strong excimer fluorescence in H2O was observed for pyrene dye conjugates of 8-aza-7-deazaisoguanine and 2-aminoadenine nucleosides with a long linker. In other solvents including methanol, excimer fluorescence was negligible. The 2-aminoadenine and isoguanine nucleosides with the 8-aza-7-deazapurine skeleton expand the class of nucleosides applicable to fluorescence detection with respect to diagnostic and therapeutic purposes.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie Neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20211018
United StatesJ Org Chem2985193R0022-326307-deazapurine0Nucleosides0Oligonucleotides0Purines452-06-22-Aminopurine49P95BAU4Z2,6-diaminopurine5Z93L87A1RGuanine9007-49-2DNAE335PK4428isoguanineIM2-Aminopurineanalogs & derivativesDNAGuanineNucleosidesOligonucleotidesPurinesSkeleton2021101960202212760202110181217ppublish3466140710.1021/acs.joc.1c01283340140062021072320240403
1521-376527412021Jul21Chemistry (Weinheim an der Bergstrasse, Germany)ChemistryAnomeric and Enantiomeric 2'-Deoxycytidines: Base Pair Stability in the Absence and Presence of Silver Ions.105741057710574-1057710.1002/chem.202101253Dodecamer duplex DNA containing anomeric (α/β-d) and enantiomeric (β-l/β-d) 2'-deoxycytidine mismatches was studied with respect to base pair stability in the absence and presence of silver ions. Stable duplexes with silver-mediated cytosine-cytosine pairs were formed by all anomeric and enantiomeric combinations. Stability changes were observed depending on the composition of the mismatches. Most strikingly, the new silver-mediated base pair of anomeric α-d-dC with enantiomeric β-l-dC is superior to the well-noted β-d/β-d-dC pair in terms of stability. CD spectra were used to follow global helical changes of DNA structure.© 2021 The Authors. Published by Wiley-VCH GmbH.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Budow-BusseSimoneSLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany.engJournal Article20210610
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2053-229677Pt 52021May01Acta crystallographica. Section C, Structural chemistryActa Crystallogr C Struct ChemThe α-D-anomer of 2'-deoxycytidine: crystal structure, nucleoside conformation and Hirshfeld surface analysis.202208202-20810.1107/S2053229621003430β-2'-Deoxyribonucleosides are the constituents of nucleic acids, whereas their anomeric α-analogues are rarely found in nature. Moreover, not much information is available on the structural and conformational parameters of α-2'-deoxyribonucleosides. This study reports on the single-crystal X-ray structure of α-2'-deoxycytidine, C9H13N3O4 (1), and the conformational parameters characterizing 1 were determined. The conformation at the glycosylic bond is anti, with χ = 173.4 (2)°, and the sugar residue adopts an almost symmetrical C2'-endo-C3'-exo twist (23T; S-type), with P = 179.7°. Both values lie outside the conformational range usually preferred by α-nucleosides. In addition, the amino group at the nucleobase shows partial double-bond character. This is supported by two separated signals for the amino protons in the 1H NMR spectrum, indicating a hindered rotation around the C4-N4 bond and a relatively short C-N bond in the solid state. Crystal packing is controlled by N-H...O and O-H...O contacts between the nucleobase and sugar moieties. Moreover, two weak C-H...N contacts (C1'-H1' and C3'-H3'A) are observed. A Hirshfeld surface analysis was carried out and the results support the intermolecular interactions observed by the X-ray analysis.open access.Budow-BusseSimoneSLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.ChaiYingyingYLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.MüllerSebastian LarsSLLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.DaniliucConstantinC0000-0002-6709-3673Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany.SeelaFrankFLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20210409
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1521-376527262021May06Chemistry (Weinheim an der Bergstrasse, Germany)Chemistry5-Aza-7-deazaguanine-Isoguanine and Guanine-Isoguanine Base Pairs in Watson-Crick DNA: The Impact of Purine Tracts, Clickable Dendritic Side Chains, and Pyrene Adducts.745374667453-746610.1002/chem.202005199The Watson-Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson-Crick and purine-purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5-aza-7-deaza-2'-deoxyguanosine, its tripropargylamine derivative, and 2'-deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine-purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5-aza-7-deazaguanine-isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine-isoguanine base pair. Spacious residues are well accommodated in the large groove of purine-purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double-helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs.© 2021 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany.engJournal Article20210318
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1521-37652762021Jan26Chemistry (Weinheim an der Bergstrasse, Germany)ChemistryThe 2-Amino Group of 8-Aza-7-deaza-7-bromopurine-2,6-diamine and Purine-2,6-diamine as Stabilizer for the Adenine-Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration.209321032093-210310.1002/chem.202004221Stabilization of DNA is beneficial for many applications in the fields of DNA therapeutics, diagnostics, and materials science. Now, this phenomenon is studied on heterochiral DNA, an autonomous DNA recognition system with complementary strands in α-D and β-D configuration showing parallel strand orientation. The 12-mer heterochiral duplexes were constructed from anomeric (α/β-D) oligonucleotide single-strands. Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides having the capability to form tridentate base pairs with dT were used to strengthen the stability of the dA-dT base pair. Tm data and thermodynamic values obtained from UV melting profiles indicated that the 8-aza-7-deaza 2'-deoxyribonucleoside decorated with a bromo substituent is so far the most efficient stabilizer for heterochiral DNA. Compared with that, the stabilizing effect of the purine-2,6-diamine 2'-deoxyribonucleoside is low. Global changes of helix structures were identified by circular dichroism (CD) spectra during melting.© 2020 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.ChaiYingyingYLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Department of Respiratory, Critical Care Medicine Targeted Tracer, Research and Development Laboratory, West China Hospital, Sichuan, 610041, P. R. China.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany.engJournal Article20201221
GermanyChemistry95137830947-65390Diamines0Purines9007-49-2DNAJAC85A2161AdenineQR26YLT7LTThymineIMAdenineBase PairingCircular DichroismDNAchemistryDiaminesNucleic Acid ConformationPurinesThymineconfigurationheterochiralparallel DNApurine-2,6-diaminepyrazolo[3,4-d]pyrimidineThe authors declare no conflict of interest.202091620201023602021223602020102212202021222ppublish33090562PMC789864610.1002/chem.202004221 Modified nucleosides, Biochemistry, Biotechnology and Medicine, (Ed.: Herdewijn P.), Wiley-VCH, Weinheim, 2008;Saenger W., Modified nucleosides and nucleotides, nucleoside di- and triphosphates, coenzymes and antibiotics, in Principles of Nucleic Acid Structure, Springer Advanced Texts in Chemistry. Springer, New York, NY, 1984;Limbach P. A., Crain P. F., McCloskey J. A., Nucleic Acids Res. 1994, 22, 2183–2196;PMC5236727518580Modified Nucleosides and Cancer, in Recent Results in Cancer Research, (Ed.: Nass G.) Springer, New York, 1983. Iwamoto R. H., Acton E. M., Goodman L., J. 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1520-690485162020Aug21The Journal of organic chemistryJ Org ChemAlkynylated and Dendronized 5-Aza-7-deazaguanine Nucleosides: Cross-Coupling with Tripropargylamine and Linear Alkynes, Click Functionalization, and Fluorescence of Pyrene Adducts†.105251053810525-1053810.1021/acs.joc.0c00926The change of the recognition face of 5-aza-7-deazaguanine bridgehead nucleosides with respect to purine nucleosides permits the construction of new purine-purine or purine-pyrimidine base pairs in DNA and RNA. Clickable derivatives of 5-aza-7-deazaguanine were synthesized by introducing ethynyl, 1,7-octadiynyl, and tripropargylamino side chains in the 7-position of the 5-aza-7-deazapurine moiety by Sonogashira cross-coupling. Click reactions were performed with 1-azidomethylpyrene by the copper-catalyzed azide-alkyne cycloaddition. The copper(I)-catalyzed click reaction on the tripropargylamino nucleoside was significantly faster and higher yielding than that for nucleosides carrying linear alkynyl chains. Also, this reaction could be performed with copper(II) as the catalyst. An autocatalyzed cycle was suggested in which the click product acts as a catalyst. Pyrene click adducts of linear alkynylated nucleosides showed pyrene monomer emission, while tripropargylamino adducts showed monomer and excimer fluorescence. The fluorescence intensities of the 5-aza-7-deazaguanine nucleosides were higher than those of their 7-deazaguanine counterparts. The reported clickable nucleosides can be utilized to functionalize or to cross-link monomeric nucleosides or DNA for diagnostic or imaging purposes and other applications in nucleic acid chemistry and biotechnology.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.ZhangAiguiALaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20200810
United StatesJ Org Chem2985193R0022-32630Alkynes0Azides0Nucleosides0Oligonucleotides0Pyrenes5Z93L87A1RGuanine789U1901C5CopperGPL8T5ZO3M7-deazaguanineIMAlkynesAzidesClick ChemistryCopperGuanineanalogs & derivativesNucleosidesOligonucleotidesPyrenes202072460202162460202072460ppublish3270090910.1021/acs.joc.0c00926326671032021022520240330
1521-376526612020Nov02Chemistry (Weinheim an der Bergstrasse, Germany)ChemistryHeterochiral DNA with Complementary Strands with α-d and β-d Configurations: Hydrogen-Bonded and Silver-Mediated Base Pairs with Impact of 7-Deazapurines Replacing Purines.139731398913973-1398910.1002/chem.202002765Heterochiral DNA with hydrogen-bonded and silver-mediated base pairs have been constructed using complementary strands with nucleosides with α-d or β-d configuration. Anomeric phosphoramidites were employed to assemble the oligonucleotides. According to the Tm values and thermodynamic data, the duplex stability of the heterochiral duplexes was similar to that of homochiral DNA, but mismatch discrimination was better in heterochiral DNA. Replacement of purines by 7-deazapurines resulted in stable parallel duplexes, thereby confirming Watson-Crick-type base pairing. When cytosine was facing cytosine, thymine or adenine residues, duplex DNA formed silver-mediated base pairs in the presence of silver ions. Although the CD spectra of single strands with α-d configuration display mirror-like shapes to those with the β-d configuration, the CD spectra of the hydrogen-bonded duplexes and those with a limited number of silver pairs show a B-type double helix almost indistinguishable from natural DNA. Nonmelting silver ion-DNA complexes with entirely different CD spectra were generated when the number of silver ions was equal to the number of base pairs.© 2020 The Authors. Published by Wiley-VCH GmbH.ChaiYingyingYLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, 610041, Sichuan, P. R. China.GuoXiurongXLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany.engJournal Article20200930
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Eur. J. 2016, 22, 13336–13346.27492501Funai T., Nakamura J., Miyazaki Y., Kiriu R., Nakagawa O., Wada S.-i., Ono A., Urata H., Angew. Chem. Int. Ed. 2014, 53, 6624–6627;24719384Angew. Chem. 2014, 126, 6742–6745. Takezawa Y., Müller J., Shionoya M., Chem. Lett. 2017, 46, 622–633;Sinha I., Fonseca Guerra C., Müller J., Angew. Chem. Int. Ed. 2015, 54, 3603–3606;25631645Angew. Chem. 2015, 127, 3674–3677.Swasey S. M., Espinosa Leal L., Lopez-Acevedo O., Pavlovich J., Gwinn E. G., Sci Rep. 2015, 5, 10163–10171.PMC443141825973536Liu H., Shen F., Haruehanroengra P., Yao Q., Cheng Y., Chen Y., Yang C., Zhang J., Wu B., Luo Q., Cui R., Li J., Ma J., Sheng J., Gan J., Angew. Chem. Int. Ed. 2017, 56, 9430–9434;28635152Angew. Chem. 2017, 129, 9558–9562.Bloomfield V. A., Crothers D. M., I. Tinoco, Jr. , Physical Chemistry of Nucleic Acids (Ed.: Wernick L.), Harper & Row, New York, 1974.Schmidbaur H., Schier A., Angew. Chem. Int. Ed. 2015, 54, 746–784;25393553Angew. Chem. 2015, 127, 756–797.Szabat M., Kierzek R., FEBS J. 2017, 284, 3986–3998.28771935Seela F., Driller H., Nucleic Acids Res. 1989, 17, 901–910.PMC3317112922275323678342020080420240729
2053-229676Pt 52020May01Acta crystallographica. Section C, Structural chemistryActa Crystallogr C Struct Chem7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization.513523513-52310.1107/S2053229620004684The positional change of nitrogen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson-Crick proton donor site N3-H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-deazaguanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4'-endo) for the ribose moiety, with an antiperiplanar orientation of the 5'-hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2' of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O-H...O and N-H...O). The concept of pK-value differences to evaluate base-pair stability was applied to purine-purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.open access.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.Budow-BusseSimoneSLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.DaniliucConstantinCOrganisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany.SeelaFrankFLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20200429
EnglandActa Crystallogr C Struct Chem1016203132053-229607-iodo-7-deazaguanosine0Nucleic Acids0Purines0Ribonucleosides12133JR80SGuanosine3M4G523W1GSilver9007-49-2DNAW60KTZ3IZYpurineIMBase PairingCrystallography, X-RayDNAchemistryGuanosineanalogs & derivativeschemistryMolecular ConformationNucleic AcidschemistryPurineschemistryRibonucleosideschemistrySilverchemistry7-iodo-5-aza-7-deazaguanosineHirshfeld surface analysisall-purine RNAbase-pair predictioncrystal packingcrystal structurepKa valuesribonucleoside20202192020432020566020205660202085602020429ppublish32367834PMC719919710.1107/S2053229620004684S2053229620004684Agrofoglio, L. A., Gillaizeau, I. & Saito, Y. (2003). Chem. Rev. 103, 1875–1916.12744695Altona, C. & Sundaralingam, M. (1972). J. Am. Chem. Soc. 94, 8205–8212.5079964Blackburn, G. M., Gait, M. J., Loakes, D. & Williams, D. M. (2006). Editors. Nucleic Acids in Chemistry and Biology, 3rd ed. Cambridge: RSC Publishing.Bruker (1998). XP. Version 5.1. Bruker AXS Inc., Madison, Wisconsin, USA.Bruker (2014). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.Bruker (2015). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.Bruker (2016). APEX3. Bruker AXS Inc., Madison, Wisconsin, USA.Greco, N. J. & Tor, Y. (2007). Tetrahedron, 63, 3515–3527.PMC186855418431439Guo, X., Leonard, P., Ingale, S. A., Liu, J., Mei, H., Sieg, M. & Seela, F. (2018). Chem. Eur. J. 24, 8883–8892.29573347Hoshika, S., Singh, I., Switzer, C., Molt, R. W. Jr, Leal, N. A., Kim, M.-J., Kim, M.-S., Kim, H.-J., Georgiadis, M. M. & Benner, S. A. (2018). J. Am. Chem. Soc. 140, 11655–11660.30148365IUPAC–IUB Joint Commission on Biochemical Nomenclature (1983). Eur. J. Biochem. 131, 9–15.6832147Kojić-Prodić, B., Ružić-Toroš, Ž., Golič, L., Brdar, B. & Kobe, J. (1982). Biochim. Biophys. Acta, 698, 105–110.7126582Krishnamurthy, R. (2012). Acc. Chem. Res. 45, 2035–2044.PMC352505022533519Laos, R., Lampropoulos, C. & Benner, S. A. (2019). Acta Cryst. C75, 22–28.30601127Leonard, P. (2020). Personal communication.Leonard, P., Kondhare, D., Jentgens, X., Daniliuc, C. & Seela, F. (2019). J. Org. Chem. 84, 13313–13328.31584277Lin, W., Zhang, X. & Seela, F. (2004). Helv. Chim. Acta, 87, 2235–2244.Manna, S., Sarkar, D. & Srivatsan, S. G. (2018). J. Am. Chem. Soc. 140, 12622–12633.PMC634810330192541Müller, S. L., Zhou, X., Leonard, P., Korzhenko, O., Daniliuc, C. & Seela, F. (2019). Chem. Eur. J. 25, 3077–3090.30520165Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259.PMC366130523719469Ramzaeva, N. & Seela, F. (1996). Helv. Chim. Acta, 79, 1549–1558.Rosemeyer, H. & Seela, F. (1987). J. Org. Chem. 52, 5136–5143.Saenger, W. (1984). In Principles of Nucleic Acid Structure, edited by C. R. Cantor. New York: Springer-Verlag.Seela, F., Amberg, S., Melenewski, A. & Rosemeyer, H. (2001). Helv. Chim. Acta, 84, 1996–2014.Seela, F. & Melenewski, A. (1999). Eur. J. Org. Chem. 1999, 485–496.Seela, F., Melenewski, A. & Wei, C. (1997). Bioorg. Med. Chem. Lett. 7, 2173–2176.Seela, F., Ramzaeva, N. & Rosemeyer, H. (2003). Science of Synthesis, Vol. 16, edited by Y. Yamamoto, pp. 945–1108. Stuttgart: Georg Thieme Verlag.Seela, F. & Rosemeyer, H. (2002). Recent Advances in Nucleosides: Chemistry and Chemotherapy, edited by C. K. Chu, pp. 505–533. Amsterdam: Elsevier.Seela, F., Rosemeyer, H., Melenewski, A., Heithoff, E.-M., Eickmeier, H. & Reuter, H. (2002). Acta Cryst. C58, o142–o144.11870307Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.0Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.0Spackman, M. A. & Jayatilaka, D. (2009). CrystEngComm, 11, 19–32.Tanpure, A. A. & Srivatsan, S. G. (2018). ChemBioChem, 13, 2392–2399.23070860Tokugawa, M., Masaki, Y., Canggadibrata, J. C., Kaneko, K., Shiozawa, T., Kanamori, T., Grøtli, M., Wilhelmsson, L. M., Sekine, M. & Seio, K. (2016). Chem. Commun. 52, 3809–3812.26865112Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D. & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia. http://hirshfeldsurface.net.Van Wijk, L., Haasnoot, C. A. G., de Leeuw, F. A. A. M., Huckriede, B. D., Westra Hoekzema, A. J. A. & Altona, C. (1999). PSEUROT6.3. Leiden Institute of Chemistry, Leiden University, The Netherlands.Wächtershäuser, G. (1988). Proc. Natl Acad. Sci. USA, 85, 1134–1135.PMC2797203422484Watson, J. D. & Crick, F. H. (1953). Nature, 171, 737–738.13054692Winnacker, M. & Kool, E. T. (2013). Angew. Chem. Int. Ed. 52, 12498–12508.PMC549705924249550315842772020051920200519
1520-690484212019Nov01The Journal of organic chemistryJ Org ChemNucleobase-Functionalized 5-Aza-7-deazaguanine Ribo- and 2'-Deoxyribonucleosides: Glycosylation, Pd-Assisted Cross-Coupling, and Photophysical Properties.133131332813313-1332810.1021/acs.joc.9b01347The special nucleobase recognition pattern of 5-aza-7-deazaguanine nucleosides makes them valuable for construction of homo purine DNA, silver-mediated base pairs, and expansion of the four letter genetic coding system. To widen the utility of 5-aza-7-deazaguanine nucleosides, side chains were introduced at position-7 of the nucleobase. As key compounds, 7-iodo nucleosides were synthesized. Nucleobase anion glycosylation of the iodo derivative of isobutyrylated 5-aza-7-deazaguanine with the bromo sugar of 2,3,5-tri-O-benzoyl-1-O-acetyl-d-ribofuranose gave the pure β-D anomeric N-9 glycosylation product (67%), whereas one-pot Vorbrüggen conditions gave only 42% of the iodinated nucleoside. The noniodinated nucleoside was formed in 84%. For the synthesis of 2'-deoxyribonucleosides, anion glycosylation performed with Hoffer's 2'-deoxyhalogenose yielded an anomeric mixture (α-D = 33% and β-D = 39%) of 2'-deoxyribonucleosides. Various side chain derivatives were prepared from nonprotected nucleosides by Pd-assisted Sonogashira or Suzuki-Miyaura cross-coupling. Among the functionalized ribonucleosides and anomeric 2'-deoxyribonucleosides, some of them showed strong fluorescence. Benzofuran and pyrene derivatives display high quantum yields in non-aqueous solvents and solvatochromism. Single-crystal X-ray analysis of 7-iodo-5-aza-7-deaza-2'-deoxyguanosine displayed intermolecular iodo-oxygen interactions in the crystal and channels filled with solvent molecules.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology , Center for Nanotechnology , Heisenbergstrasse 11 , 48149 Münster , Germany.KondhareDasharathDLaboratory of Bioorganic Chemistry and Chemical Biology , Center for Nanotechnology , Heisenbergstrasse 11 , 48149 Münster , Germany.JentgensXeniaXLaboratory of Bioorganic Chemistry and Chemical Biology , Center for Nanotechnology , Heisenbergstrasse 11 , 48149 Münster , Germany.DaniliucConstantinCInstitut für Organische Chemie , Universität Münster , Corrensstrasse 40 , 48149 Münster , Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology , Center for Nanotechnology , Heisenbergstrasse 11 , 48149 Münster , Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien , Universität Osnabrück , Barbarastrasse 7 , 49069 Osnabrück , Germany.engJournal ArticleResearch Support, Non-U.S. Gov't20191023
United StatesJ Org Chem2985193R0022-3263IM201910560201910561201910560ppublish3158427710.1021/acs.joc.9b013473158375520240328
1521-376525722019Dec20Chemistry (Weinheim an der Bergstrasse, Germany)ChemistrySilver-Mediated Homochiral and Heterochiral α-dC/β-dC Base Pairs: Synthesis of α-dC through Glycosylation and Impact of Consecutive, Isolated, and Multiple Metal Ion Pairs on DNA Stability.166391665116639-1665110.1002/chem.201903915Isolated and consecutive heterochiral α-dC- base pairs have been incorporated into 12-mer oligonucleotide duplexes at various positions, thereby replacing Watson-Crick pairs. To this end, a new synthesis of the α-d anomer of dC has been developed, and oligonucleotides containing α-dC residues have been synthesized. Silver-mediated base pairs were formed upon the addition of silver ions. Furthermore, we have established that heterochiral α-dC-dC base pairs can approach the stability of a Watson-Crick pair, whereas homochiral dC-dC pairs are significantly less stable. A positional change of the silver-mediated base pairs affects the duplex stability and reveals the nearest-neighbor influence. When the number of silver ions was equivalent to the number of duplex base pairs (12), non-melting silver-rich complexes were formed. Structural changes have been supported by circular dichroism (CD) spectra, which showed that the B-DNA structure was maintained whilst the silver ion concentration was low. At high silver ion concentration, silver-rich complexes displaying different CD spectra were formed.© 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.ChaiYingyingYLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, West China Hospital, Sichuan University, Sichuan, 610041, P. R. China.LeonardPeterPLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.GuoXiurongXLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.SeelaFrankF0000-0002-4810-4840Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany.engJournal Article20191128
GermanyChemistry95137830947-6539IMDNAbase pairingcircular dichroismnucleobasessilverThe authors declare no conflict of interest.201910220198272019105602019105612019105602020121ppublish31583755PMC697270110.1002/chem.201903915 Ono A., Torigoe H., Tanaka Y., Okamoto I., Chem. Soc. Rev. 2011, 40, 5855–5866;21826352Shamsi M. H., Kraatz H.-B., J. Inorg. Organomet. Polym. 2013, 23, 4–23;Scharf P., Müller J., ChemPlusChem 2013, 78, 20–34;Takezawa Y., Müller J., Shionoya M., Chem. Lett. 2017, 46, 622–633;Takezawa Y., Shionoya M., Acc. Chem. Res. 2012, 45, 2066–2076;22452649Clever G. H., Kaul C., Carell T., Angew. Chem. Int. Ed. 2007, 46, 6226–6236;17640011Angew. Chem. 2007, 119, 6340–6350;Ma D.-L., He H.-Z., Chan D. S.-H., Leung C.-H., Chem. Sci. 2013, 4, 3366–3380;Tanaka Y., Kondo J., Sychrovský V., Šebera J., Dairaku T., Saneyoshi H., Urata H., Torigoe H., Ono A., Chem. Commun. 2015, 51, 17343–17360.26466090 Yamane T., Davidson N., Biochim. Biophys. 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A., Seela F., Chem. Eur. J. 2014, 20, 16248–16257;25336305Yang H., Mei H., Seela F., Chem. Eur. J. 2015, 21, 10207–10219;26096946Mei H., Röhl I., Seela F., J. Org. Chem. 2013, 78, 9457–9463.23965151 Kondo J., Tada Y., Dairaku T., Hattori Y., Saneyoshi H., Ono A., Tanaka Y., Nat. Chem. 2017, 9, 956–960;28937663Liu H., Shen F., Haruehanroengra P., Yao Q., Cheng Y., Chen Y., Yang C., Zhang J., Wu B., Luo Q., Cui R., Li J., Ma J., Sheng J., Gan J., Angew. Chem. Int. Ed. 2017, 56, 9430–9434;28635152Angew. Chem. 2017, 129, 9558–9562. Santamaría-Díaz N., Méndez-Arriaga J. M., Salas J. M., Galindo M. A., Angew. Chem. Int. Ed. 2016, 55, 6170–6174;27005864Angew. Chem. 2016, 128, 6278–6282;Méndez-Arriaga J. M., Maldonado C. R., Dobado J. A., Galindo M. A., Chem. Eur. J. 2018, 24, 4583–4589.29226453 Zimmermann N., Meggers E., Schultz P. G., J. Am. Chem. Soc. 2002, 124, 13684–13685;12431092Lippert B., Sanz Miguel P. J., Acc. Chem. 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α-D NUCLEOSIDE BASED SELF-HEALING SUPRAMOLECULAR HYDROGELS DERIVED FROM THE α-D ANOMERS OF 2'-DEOXYGUANOSINE AND FLUORESCENT 8-AZAPURINE 2'-DEOXYRIBOFURANOSIDES.
Sushma Deshmukh Simone Budow-Busse Dasharath Kondhare Andreas H Schäfer Peter Leonard Frank Seela

Chemistry

November 2024

Self-assembly of α-D nucleosides to supramolecular hydrogels is described in detail. Hydrogel formation was studied on α-D 2'-deoxyguanosine (α-dG), and the fluorescent 8-azapurine α-D nucleosides 2-amino-8-aza-2'-deoxyadenosine (α-2-NH2-z8Ad) and 8-aza-2'-deoxyisoguanosine (α-z8iGd). These compounds were prepared from α-D 8-aza-2'-deoxyguanosine by an activation/amination protocol followed by deamination.

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7-Deaza-2'-deoxyisoguanosine, a Noncanonical Nucleoside for Nucleic Acid Code Expansion and New DNA Constructs: Nucleobase Functionalization of Inverse Watson-Crick and Purine-Purine Base Pairs.
Zhenqiang Xia Dasharath Kondhare Simone Budow-Busse Peter Leonard Frank Seela

Bioconjug Chem

August 2024

7-Deaza-2'-deoxyisoguanosine forms stable inverse Watson-Crick base pairs with 5-methyl-2'-deoxyisocytidine and purine-purine base pairs with 2'-deoxyguanosine or 5-aza-7-deaza-2'-deoxyguanosine. Both base pairs expand the genetic coding system. The manuscript reports on the functionalization of these base pairs with halogen atoms and clickable side chains introduced at 7-position of the 7-deazapurine base.

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7-Deazapurine and Pyrimidine Nucleoside and Oligonucleotide Cycloadducts Formed by Inverse Diels-Alder Reactions with 3,6-Di(pyrid-2-yl)-1,2,4,5-tetrazine: Ethynylated and Vinylated Nucleobases for Functionalization and Impact of Pyridazine Adducts on DNA Base Pair Stability and Mismatch Discrimination.
Somnath Shivaji Chandankar Dasharath Kondhare Sushma Deshmukh Haozhe Yang Peter Leonard Frank Seela

J Org Chem

August 2024

Article Synopsis
  • The manuscript discusses the synthesis of 7-deazapurine and pyrimidine nucleoside cycloadducts created through the inverse electron demand Diels-Alder (iEDDA) reaction with a specific 3,6-di(pyrid-2-yl)-1,2,4,5-tetrazine compound.
  • Experimental findings show that the addition of spacer units between nucleobases and pyridazine cycloadducts enhances the stability of DNA duplexes, while direct connections diminish stability.
  • The study also highlights the significance of oxidation in reactions involving alkenyl compounds and the impact of synthesized oligonucleotides on mismatch formation, indicating that linkers can help reduce errors in certain interactions with
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α-D-2'-Deoxyadenosine, an irradiation product of canonical DNA and a component of anomeric nucleic acids: crystal structure, packing and Hirshfeld surface analysis.
Peter Leonard Aigui Zhang Simone Budow-Busse Constantin Daniliuc Frank Seela

Acta Crystallogr C Struct Chem

February 2024

α-D-2'-Deoxyribonucleosides are products of the γ-irradiation of DNA under oxygen-free conditions and are constituents of anomeric DNA. They are not found as natural building blocks of canonical DNA. Reports on their conformational properties are limited.

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Nucleobase-Functionalized 7-Deazaisoguanine and 7-Deazapurin-2,6-diamine Nucleosides: Halogenation, Cross-Coupling, and Cycloaddition.
Zhenqiang Xia Dasharath Kondhare Somnath Shivaji Chandankar Sachin A Ingale Peter Leonard Frank Seela

J Org Chem

February 2024

The functionalization in position-7 of 7-deazaisoguanine and 7-deazapurin-2,6-diamine ribo- and 2'-deoxyribonucleosides by halogen atoms (chloro, bromo, iodo), and clickable alkynyl and vinyl side chains for copper-catalyzed and copper-free cycloadditions is described. Problems arising during the synthesis of the 7-iodinated isoguanine ribo- and 2'-deoxyribonucleosides were solved by the action of acetone. The impact of side chains and halogen atoms on the p values and hydrophobicity of nucleosides was investigated.

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Purine DNA Constructs Designed to Expand the Genetic Code: Functionalization, Impact of Ionic Forms, and Molecular Recognition of 7-Deazaxanthine-7-Deazapurine-2,6-diamine Base Pairs and Their Purine Counterparts.
Somnath Shivaji Chandankar Dasharath Kondhare Peter Leonard Frank Seela

J Org Chem

September 2023

Purine DNA represents an alternative pairing system formed by two purines in the base pair with the recognition elements of Watson-Crick DNA. Base functionalization of 7-deaza-2'-deoxyxanthosine with ethynyl and octadiynyl residues led to clickable side chain derivatives with short and long linker arms. As complementary bases, purine-2,6-diamine or 7-deazapurine-2,6-diamine 2'-deoxyribonucleosides were used.

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Watson-Crick Base Pairs with Protecting Groups: The 2-Amino Groups of Purine- and 7-Deazapurine-2,6-Diamine as Target Sites for DNA Functionalization by Selective Nucleobase Acylation.
Dasharath Kondhare Xenia Heddinga Peter Leonard Frank Seela

Bioconjug Chem

July 2023

The recognition of Watson-Crick base pairs carrying nucleobase protecting groups is reported as a new approach for DNA functionalization. The 2-amino groups of purine- and 7-deazapurine-2,6-diamine 2'-deoxyribonucleosides served as molecular targets for this functionalization. The 2-amino group withstands oligonucleotide deprotection with ammonia, whereas all other protecting groups are released after chemical DNA synthesis.

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The Base Pairs of Isoguanine and 8-Aza-7-deazaisoguanine with 5-Methylisocytosine as Targets for DNA Functionalization.
Dasharath Kondhare Peter Leonard Frank Seela

Bioconjug Chem

February 2023

The isoguanine-isocytosine base pair (isoG-isoC) represents an important expansion of the DNA coding system. The base pair is more stable than the canonical adenine-thymine or guanine-cytosine pairs. However, nothing is known on the functionalization of the noncanonical isoG-isoC pair at the isoguanine site.

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DNA Strand Displacement with Base Pair Stabilizers: Purine-2,6-Diamine and 8-Aza-7-Bromo-7-Deazapurine-2,6-Diamine Oligonucleotides Invade Canonical DNA and New Fluorescent Pyrene Click Sensors Monitor the Reaction.
Aigui Zhang Dasharath Kondhare Peter Leonard Frank Seela

Chemistry

December 2022

Purine-2,6-diamine and 8-aza-7-deaza-7-bromopurine-2,6-diamine 2'-deoxyribonucleosides (1 and 2) were implemented in isothermal DNA strand displacement reactions. Nucleoside 1 is a weak stabilizer of dA-dT base pairs, nucleoside 2 evokes strong stabilization. Strand displacement reactions used single-stranded invaders with single and multiple incorporations of stabilizers.

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Purine-Purine Base Pairs in Parallel DNA: β-D Anomeric 8-Aza-7-deazaisoguanine and 7-Functionalized Conjugates Form Stable Base Pairs with α-D 5-Aza-7-deaza-2'-deoxyguanosine.
Aigui Zhang Dasharath Kondhare Peter Leonard Frank Seela

Bioconjug Chem

October 2022

Anomeric purine-purine DNA represents a new recognition system with strands in parallel orientation. This work investigates the new heterochiral system and the positional impact of nucleobase functionalization. Tracts of anomeric isoguanine/8-aza-7-deazaisoguanine base pairs with 5-aza-7-deazaguanine were embedded in anomeric Watson-Crick DNA.

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DNA with Purine-Purine Base Pairs: Size and Position of Isoguanine and 8-Aza-7-deazaisoguanine Clickable Residues Control the Molecular Recognition of Guanine and 5-Aza-7-deazaguanine.
Dasharath Kondhare Aigui Zhang Peter Leonard Frank Seela

J Org Chem

August 2022

Purine-purine base pairs represent an alternative recognition system to the purine-pyrimidine pairing reported by Watson and Crick. Modified purines are the source for non-canonical interactions. To mimic dG-dC interactions, 2'-deoxyisoguanosine () and 8-aza-7-deaza-2'-deoxyisoguanosine () are used to construct base pairs with 2'-deoxyguanosine or 5-aza-7-deaza-2'-deoxyguanosine (dZ).

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The 2'-deoxyribofuranoside of 3-phenyltetrahydropyrimido[4,5-c]pyridazin-7-one: a bicyclic nucleoside with sugar residues in N and S conformations, and its molecular recognition.
Hui Mei Simone Budow-Busse Dasharath Kondhare Henning Eickmeier Hans Reuter Frank Seela

Acta Crystallogr C Struct Chem

July 2022

Article Synopsis
  • The compound 3-phenyltetrahydropyrimido[4,5-c]pyridazine 2'-deoxyribonucleoside exists in two distinct conformations in its crystalline state, each with different sugar pucker configurations.
  • Conformers 1a and 1b both maintain similar anti conformations around their N-glycosylic bonds and are stabilized by intermolecular hydrogen bonds, with Hirshfeld surface analysis confirming their bonding patterns.
  • The nucleoside effectively pairs with dA, showing stability comparable to the canonical dA-dT pair, and its duplex stability is further enhanced by interactions with a dA analogue.
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Anomeric DNA Strand Displacement with α-D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β-, β/β- and α/α-D Configuration.
Aigui Zhang Dasharath Kondhare Peter Leonard Frank Seela

Chemistry

August 2022

DNA strand displacement is a technique to exchange one strand of a double stranded DNA by another strand (invader). It is an isothermal, enzyme free method driven by single stranded overhangs (toeholds) and is employed in DNA amplification, mismatch detection and nanotechnology. We discovered that anomeric (α/β) DNA can be used for heterochiral strand displacement.

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8-Furylimidazolo-2'-deoxycytidine: crystal structure, packing, atropisomerism and fluorescence.
Simone Budow-Busse Sunit K Jana Dasharath Kondhare Constantin Daniliuc Frank Seela

Acta Crystallogr C Struct Chem

March 2022

8-Furylimidazolo-2'-deoxycytidine (ImidC), CHNO, is a fluorescent analogue of 2'-deoxycytidine, also displaying the same recognition face. As a constituent of DNA, ImidC forms extraordinarily strong silver-mediated self-pairs. Crystal structure determination revealed that ImidC adopts two types of disordered residues: the sugar unit and the furyl moiety.

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Anomeric DNA: Functionalization of α-d Anomers of 7-Deaza-2'-deoxyadenosine and 2'-Deoxyuridine with Clickable Side Chains and Click Adducts in Homochiral and Heterochiral Double Helices.
Aigui Zhang Peter Leonard Frank Seela

Chemistry

February 2022

Anomeric base pairs in heterochiral DNA with strands in the α-d and β-d configurations and homochiral DNA with both strands in α-d configuration were functionalized. The α-d anomers of 2'-deoxyuridine and 7-deaza-2'-deoxyadenosine were synthesized and functionalized with clickable octadiynyl side chains. Nucleosides were protected and converted to phosphoramidites.

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Isoguanine (2-Hydroxyadenine) and 2-Aminoadenine Nucleosides with an 8-Aza-7-deazapurine Skeleton: Synthesis, Functionalization with Fluorescent and Clickable Side Chains, and Impact of 7-Substituents on Physical Properties.
Dasharath Kondhare Peter Leonard Frank Seela

J Org Chem

November 2021

7-Functionalized 8-aza-7-deaza-2'-deoxyisoguanine and 8-aza-7-deaza-2-aminoadenine 2'-deoxyribonucleosides decorated with fluorescent pyrene or benzofuran sensor tags or clickable side chains with terminal triple bonds were synthesized. 8-Aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine was used as the central intermediate and was accessible by an improved two-step glycosylation/amination protocol. Functionalization of position-7 was performed either on 8-aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine followed by selective deamination of the 2-amino group or on 7-iodinated 8-aza-7-deaza-2'-deoxyisoguanosine.

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Anomeric and Enantiomeric 2'-Deoxycytidines: Base Pair Stability in the Absence and Presence of Silver Ions.
Aigui Zhang Simone Budow-Busse Peter Leonard Frank Seela

Chemistry

July 2021

Dodecamer duplex DNA containing anomeric (α/β-d) and enantiomeric (β-l/β-d) 2'-deoxycytidine mismatches was studied with respect to base pair stability in the absence and presence of silver ions. Stable duplexes with silver-mediated cytosine-cytosine pairs were formed by all anomeric and enantiomeric combinations. Stability changes were observed depending on the composition of the mismatches.

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The α-D-anomer of 2'-deoxycytidine: crystal structure, nucleoside conformation and Hirshfeld surface analysis.
Simone Budow-Busse Yingying Chai Sebastian Lars Müller Constantin Daniliuc Frank Seela

Acta Crystallogr C Struct Chem

May 2021

β-2'-Deoxyribonucleosides are the constituents of nucleic acids, whereas their anomeric α-analogues are rarely found in nature. Moreover, not much information is available on the structural and conformational parameters of α-2'-deoxyribonucleosides. This study reports on the single-crystal X-ray structure of α-2'-deoxycytidine, CHNO (1), and the conformational parameters characterizing 1 were determined.

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5-Aza-7-deazaguanine-Isoguanine and Guanine-Isoguanine Base Pairs in Watson-Crick DNA: The Impact of Purine Tracts, Clickable Dendritic Side Chains, and Pyrene Adducts.
Aigui Zhang Dasharath Kondhare Peter Leonard Frank Seela

Chemistry

May 2021

The Watson-Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson-Crick and purine-purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5-aza-7-deaza-2'-deoxyguanosine, its tripropargylamine derivative, and 2'-deoxyisoguanosine were synthesized.

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The 2-Amino Group of 8-Aza-7-deaza-7-bromopurine-2,6-diamine and Purine-2,6-diamine as Stabilizer for the Adenine-Thymine Base Pair in Heterochiral DNA with Strands in Anomeric Configuration.
Yingying Chai Dasharath Kondhare Aigui Zhang Peter Leonard Frank Seela

Chemistry

January 2021

Article Synopsis
  • Stabilization of DNA is important for various applications, including gene therapy, diagnostics, and materials science, and this study focuses on heterochiral DNA with distinct strand configurations.
  • Researchers created 12-mer heterochiral duplexes using specially designed oligonucleotides and tested two types of nucleosides that can enhance the stability of base pairs, finding that one compound is particularly effective.
  • The study utilized UV melting profiles to measure the stability, along with circular dichroism (CD) spectra to observe structural changes in the DNA during melting, revealing insights into DNA stabilization techniques.
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Alkynylated and Dendronized 5-Aza-7-deazaguanine Nucleosides: Cross-Coupling with Tripropargylamine and Linear Alkynes, Click Functionalization, and Fluorescence of Pyrene Adducts†.
Dasharath Kondhare Aigui Zhang Peter Leonard Frank Seela

J Org Chem

August 2020

The change of the recognition face of 5-aza-7-deazaguanine bridgehead nucleosides with respect to purine nucleosides permits the construction of new purine-purine or purine-pyrimidine base pairs in DNA and RNA. Clickable derivatives of 5-aza-7-deazaguanine were synthesized by introducing ethynyl, 1,7-octadiynyl, and tripropargylamino side chains in the 7-position of the 5-aza-7-deazapurine moiety by cross-coupling. Click reactions were performed with 1-azidomethylpyrene by the copper-catalyzed azide-alkyne cycloaddition.

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Heterochiral DNA with Complementary Strands with α-d and β-d Configurations: Hydrogen-Bonded and Silver-Mediated Base Pairs with Impact of 7-Deazapurines Replacing Purines.
Yingying Chai Xiurong Guo Peter Leonard Frank Seela

Chemistry

November 2020

Heterochiral DNA with hydrogen-bonded and silver-mediated base pairs have been constructed using complementary strands with nucleosides with α-d or β-d configuration. Anomeric phosphoramidites were employed to assemble the oligonucleotides. According to the T values and thermodynamic data, the duplex stability of the heterochiral duplexes was similar to that of homochiral DNA, but mismatch discrimination was better in heterochiral DNA.

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7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization.
Dasharath Kondhare Simone Budow-Busse Constantin Daniliuc Frank Seela

Acta Crystallogr C Struct Chem

May 2020

The positional change of nitrogen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson-Crick proton donor site N3-H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs.

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Nucleobase-Functionalized 5-Aza-7-deazaguanine Ribo- and 2'-Deoxyribonucleosides: Glycosylation, Pd-Assisted Cross-Coupling, and Photophysical Properties.
Peter Leonard Dasharath Kondhare Xenia Jentgens Constantin Daniliuc Frank Seela

J Org Chem

November 2019

The special nucleobase recognition pattern of 5-aza-7-deazaguanine nucleosides makes them valuable for construction of homo purine DNA, silver-mediated base pairs, and expansion of the four letter genetic coding system. To widen the utility of 5-aza-7-deazaguanine nucleosides, side chains were introduced at position-7 of the nucleobase. As key compounds, 7-iodo nucleosides were synthesized.

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Silver-Mediated Homochiral and Heterochiral α-dC/β-dC Base Pairs: Synthesis of α-dC through Glycosylation and Impact of Consecutive, Isolated, and Multiple Metal Ion Pairs on DNA Stability.
Yingying Chai Peter Leonard Xiurong Guo Frank Seela

Chemistry

December 2019

Isolated and consecutive heterochiral α-dC- base pairs have been incorporated into 12-mer oligonucleotide duplexes at various positions, thereby replacing Watson-Crick pairs. To this end, a new synthesis of the α-d anomer of dC has been developed, and oligonucleotides containing α-dC residues have been synthesized. Silver-mediated base pairs were formed upon the addition of silver ions.

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