Synthesis of 1,8‐Naphthyridine C‐Nucleosides and Their Base‐Pairing Properties in Oligodeoxynucleotides: Thermally Stable Naphthyridine:Imidazopyridopyrimidine Base‐Pairing Motifs*
This work was supported in part by a Grant‐in‐Aid for Scientific Research on Priority Areas and Encouragement of Young Scientists from the Ministry of Education, Science, Sports, and Culture of Japan. This paper constitutes Part 229 of Nucleosides and Nucleotides. Part 228 is reference [15].
Abstract
Out with the old, in with the new: Novel 1,8‐naphthyridine C‐nucleosides, Na‐NO and Na‐ON (see formulae), were synthesized through Heck coupling reactions. Oligodeoxynucleotides containing the Na‐NO and Na‐ON nucleosides formed extremely stable duplexes by the base‐pairing motifs Na‐NO:Im‐ON and Na‐ON:Im‐NO.
Number of times cited: 47
- Amit M. Jabgunde, Faten Jaziri, Omprakash Bande, Matheus Froeyen, Mikhail Abramov, Hoai Nguyen, Guy Schepers, Eveline Lescrinier, Vitor B. Pinheiro, Valérie Pezo, Philippe Marlière and Piet Herdewijn, Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo, Chemistry – A European Journal, 24, 48, (12695-12707), (2018).
- Irina Novosjolova, Scott D. Kennedy and Eriks Rozners, 2‐Methoxypyridine as a Thymidine Mimic in Watson–Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies, ChemBioChem, 18, 21, (2165-2170), (2017).
- P. Aparna, Mary Varughese, Mathew K. Varghese, P. Haris, C. Sudarsanakumar and David Case, Conformational features of benzo‐homologated yDNA duplexes by molecular dynamics simulation, Biopolymers, 105, 2, (55-64), (2015).
- Helio G. Bonacorso, Tainara P. Calheiro, Bernardo A. Iglesias, Iuri R.C. Berni, Eufrânio N. da Silva Júnior, João B.T. Rocha, Nilo Zanatta and Marcos A.P. Martins, Synthesis, 11B- and 19F NMR spectroscopy, and optical and electrochemical properties of novel 9-aryl-3-(aryl/heteroaryl)-1,1-difluoro-7-(trifluoromethyl)-1H-[1,3,5,2]oxadiazaborinino[3,4-a][1,8]naphthyridin-11-ium-1-uide complexes, Tetrahedron Letters, 57, 46, (5017), (2016).
- Noriko Tarashima, Yasuo Komatsu, Kazuhiro Furukawa and Noriaki Minakawa, Faithful PCR Amplification of an Unnatural Base‐Pair Analogue with Four Hydrogen Bonds, Chemistry – A European Journal, 21, 30, (10688-10695), (2015).
- Yusaku Nomura, Satoshi Kashiwagi, Kousuke Sato and Akira Matsuda, Selective Transcription of an Unnatural Naphthyridine:Imidazopyridopyrimidine Base Pair Containing Four Hydrogen Bonds with T7 RNA Polymerase, Angewandte Chemie International Edition, 53, 47, (12844-12848), (2014).
- Yusaku Nomura, Satoshi Kashiwagi, Kousuke Sato and Akira Matsuda, Selective Transcription of an Unnatural Naphthyridine:Imidazopyridopyrimidine Base Pair Containing Four Hydrogen Bonds with T7 RNA Polymerase, Angewandte Chemie, 126, 47, (13058-13062), (2014).
- Antarip Halder, Ayan Datta, Dhananjay Bhattacharyya and Abhijit Mitra, Why Does Substitution of Thymine by 6-Ethynylpyridone Increase the Thermostability of DNA Double Helices?, The Journal of Physical Chemistry B, 10.1021/jp412416p, 118, 24, (6586-6596), (2014).
- Yosuke Higuchi, Kazuhiro Furukawa, Tadashi Miyazawa and Noriaki Minakawa, Development of a New Dumbbell-Shaped Decoy DNA Using a Combination of the Unnatural Base Pair ImON:NaNO and a CuAAC Reaction, Bioconjugate Chemistry, 25, 7, (1360), (2014).
- Laibin Zhang, Liuzhu Zhou, Jianxiang Tian and Xiaoming Li, Structural, electronic, and photophysical properties of thieno-expanded tricyclic purine analogs: a theoretical study, Physical Chemistry Chemical Physics, 10.1039/c3cp54505a, 16, 9, (4338), (2014).
- Laibin Zhang, Liuzhu Zhou, Jianxiang Tian and Xiaoming Li, Hetero-ring-expansion design for purine analogs: A theoretical study on the structural, electronic, and excited-state properties, Chemical Physics Letters, 10.1016/j.cplett.2014.02.033, 597, (69-74), (2014).
- Malte Winnacker and Eric T. Kool, Artificial Genetic Sets Composed of Size‐Expanded Base Pairs, Angewandte Chemie International Edition, 52, 48, (12498-12508), (2013).
- Malte Winnacker and Eric T. Kool, Künstliche genetische Systeme bestehend aus vergrößerten Basenpaaren, Angewandte Chemie, 125, 48, (12728-12739), (2013).
- Marco Minuth and Clemens Richert, A Nucleobase Analogue that Pairs Strongly with Adenine, Angewandte Chemie, 125, 41, (11074-11077), (2013).
- Marco Minuth and Clemens Richert, A Nucleobase Analogue that Pairs Strongly with Adenine, Angewandte Chemie International Edition, 52, 41, (10874-10877), (2013).
- Chun-Ho Wong and Steven C. Zimmerman, Orthogonality in organic, polymer, and supramolecular chemistry: from Merrifield to click chemistry, Chemical Communications, 10.1039/c2cc37316e, 49, 17, (1679), (2013).
- Laibin Zhang, Tingqi Ren, Jianxiang Tian, Xiuqin Yang, Liuzhu Zhou and Xiaoming Li, Excited State Properties of Naphtho-Homologated xxDNA Bases and Effect of Methanol Solution, Deoxyribose, and Base Pairing, The Journal of Physical Chemistry B, 10.1021/jp3123242, 117, 15, (3983-3992), (2013).
- Scott D. Burley, Vicky V. Lam, Frederick J. Lakner, B. Mikael Bergdahl and Matthew A. Parker, New Route to the Ergoline Skeleton via Cyclization of 4-Unsubstituted Indoles, Organic Letters, 10.1021/ol400620a, 15, 11, (2598-2600), (2013).
- Omar Boutureira, M. Isabel Matheu, Yolanda Díaz and Sergio Castillón, Synthesis of C‐Nucleosides, Chemical Synthesis of Nucleoside Analogues, (263-316), (2013).
- Chun‐Ho Wong, Stacie L. Richardson, Yen‐Jun Ho, Alex M. H. Lucas, Tiziano Tuccinardi, Anne M. Baranger and Steven C. Zimmerman, Investigating the Binding Mode of an Inhibitor of the MBNL1⋅RNA Complex in Myotonic Dystrophy Type 1 (DM1) Leads to the Unexpected Discovery of a DNA‐Selective Binder, ChemBioChem, 13, 17, (2505-2509), (2012).
- Noriko Tarashima, Yosuke Higuchi, Yasuo Komatsu and Noriaki Minakawa, A practical post-modification synthesis of oligodeoxynucleotides containing 4,7-diaminoimidazo[5′,4′:4,5]pyrido[2,3-d]pyrimidine nucleoside, Bioorganic & Medicinal Chemistry, 20, 24, (7095), (2012).
- Yu Lian Duan, Yong Gang Shi, Jian Hua Chen, Xiang Hua Wu, Guang Ke Wang, Ying Zhou and Jun Feng Zhang, 1,8-Naphthyridine modified rhodamine B derivative and Cu2+ complex: colorimetric sensing of thiols in aqueous media, Tetrahedron Letters, 10.1016/j.tetlet.2012.09.089, 53, 48, (6544-6547), (2012).
- William Fraser, Nucleobases with Designed Patterns of Hydrogen Bonding, Advances in Heterocyclic Chemistry Volume 107, 10.1016/B978-0-12-396532-5.00001-9, (1-39), (2012).
- José Ramón Blas, Oscar Huertas, Carolina Tabares, Bobby G. Sumpter, Miguel Fuentes-Cabrera, Modesto Orozco, Pablo Ordejón and F. Javier Luque, Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases, The Journal of Physical Chemistry A, 10.1021/jp205122c, 115, 41, (11344-11354), (2011).
- Andrew T. Krueger, Larryn W. Peterson, Jijumon Chelliserry, Daniel J. Kleinbaum and Eric T. Kool, Encoding Phenotype in Bacteria with an Alternative Genetic Set, Journal of the American Chemical Society, 10.1021/ja208025e, 133, 45, (18447-18451), (2011).
- Yasuyuki Hirama, Noriaki Minakawa and Akira Matsuda, Synthesis and characterization of oligodeoxynucleotides containing a novel tetraazabenzo[cd]azulene:naphthyridine base pair, Bioorganic & Medicinal Chemistry, 19, 1, (352), (2011).
- Kazuyuki Kuramoto, Noriko Tarashima, Yasuyuki Hirama, Yusaku Kikuchi, Noriaki Minakawa and Akira Matsuda, New imidazopyridopyrimidine:naphthyridine base-pairing motif, ImNN:NaOO, consisting of a DAAD:ADDA hydrogen bonding pattern, markedly stabilize DNA duplexes, Chemical Communications, 47, 38, (10818), (2011).
- Filip Wojciechowski and Christian J. Leumann, Alternative DNA base-pairs: from efforts to expand the genetic code to potential material applications, Chemical Society Reviews, 10.1039/c1cs15027h, 40, 12, (5669), (2011).
- Ichiro Hirao and Michiko Kimoto, Expansion of the Genetic Alphabet in Nucleic Acids by Creating New Base Pairs, The Chemical Biology of Nucleic Acids, (39-62), (2010).
- Haige Lu, Andrew T. Krueger, Jianmin Gao, Haibo Liu and Eric T. Kool, Toward a designed genetic system with biochemical function: polymerase synthesis of single and multiple size-expanded DNA base pairs, Organic & Biomolecular Chemistry, 10.1039/c002766a, 8, 12, (2704), (2010).
- Yasuyuki Hirama, Hiroshi Abe, Noriaki Minakawa and Akira Matsuda, Synthesis and properties of a novel nucleoside derivative possessing a 2,3,5,6-tetraazabenzo[cd]azulene skeleton, Tetrahedron, 66, 43, (8402), (2010).
- Haige Lu, Stephen R. Lynch, Alex H. F. Lee and Eric T. Kool, Structure and Replication of yDNA: A Novel Genetic Set Widened by Benzo‐Homologation, ChemBioChem, 10, 15, (2530-2538), (2009).
- James C. Delaney, Jianmin Gao, Haibo Liu, Nidhi Shrivastav, John M. Essigmann and Eric T. Kool, Efficient Replication Bypass of Size‐Expanded DNA Base Pairs in Bacterial Cells, Angewandte Chemie, 121, 25, (4594-4597), (2009).
- James C. Delaney, Jianmin Gao, Haibo Liu, Nidhi Shrivastav, John M. Essigmann and Eric T. Kool, Efficient Replication Bypass of Size‐Expanded DNA Base Pairs in Bacterial Cells, Angewandte Chemie International Edition, 48, 25, (4524-4527), (2009).
- Donald E. Bergstrom, Unnatural Nucleosides with Unusual Base Pairing Properties, Current Protocols in Nucleic Acid Chemistry, 37, 1, (1.4.1-1.4.32), (2009).
- Noriaki Minakawa, Shintaro Ogata, Mayumi Takahashi and Akira Matsuda, Selective Recognition of Unnatural Imidazopyridopyrimidine:Naphthyridine Base Pairs Consisting of Four Hydrogen Bonds by the Klenow Fragment, Journal of the American Chemical Society, 131, 5, (1644), (2009).
- Shintaro Ogata, Mayumi Takahashi, Noriaki Minakawa and Akira Matsuda, Unnatural imidazopyridopyrimidine:naphthyridine base pairs: selective incorporation and extension reaction by Deep Vent (exo− ) DNA polymerase, Nucleic Acids Research, 37, 17, (5602), (2009).
- Andrew T. Krueger and Eric T. Kool, Redesigning the Architecture of the Base Pair: Toward Biochemical and Biological Function of New Genetic Sets, Chemistry & Biology, 10.1016/j.chembiol.2008.12.004, 16, 3, (242-248), (2009).
- Jijumon Chelliserrykattil, Haige Lu, Alex H. F. Lee and Eric T. Kool, Polymerase Amplification, Cloning, and Gene Expression of Benzo‐Homologous “yDNA” Base Pairs, ChemBioChem, 9, 18, (2976-2980), (2008).
- , References, Chemistry of Heterocyclic Compounds, (295-336), (2008).
- Björn C.G. Söderberg, Transition metals in organic synthesis: Highlights for the year 2005, Coordination Chemistry Reviews, 10.1016/j.ccr.2007.03.011, 252, 1-2, (57-133), (2008).
- Andrew T Krueger and Eric T Kool, Model systems for understanding DNA base pairing, Current Opinion in Chemical Biology, 10.1016/j.cbpa.2007.09.019, 11, 6, (588-594), (2007).
- Milan Balaz, Benjamin C. Li, Steffen Jockusch, George A. Ellestad and Nina Berova, Tetraarylporphyrin as a Selective Molecular Cap for Non‐Watson–Crick Guanine–Adenine Base‐Pair Sequences, Angewandte Chemie International Edition, 45, 21, (3530-3533), (2006).
- Sadao Hikishima, Noriaki Minakawa, Kazuyuki Kuramoto, Shintaro Ogata and Akira Matsuda, Synthesis and Characterization of Oligodeoxynucleotides Containing Naphthyridine:Imidazopyridopyrimidine Base Pairs at their Sticky Ends. Application as Thermally Stabilized Decoy Molecules, ChemBioChem, 7, 12, (1970-1975), (2006).
- Milan Balaz, Benjamin C. Li, Steffen Jockusch, George A. Ellestad and Nina Berova, Tetraarylporphyrin as a Selective Molecular Cap for Non‐Watson–Crick Guanine–Adenine Base‐Pair Sequences, Angewandte Chemie, 118, 21, (3610-3613), (2006).
- Shinpei Hirano, Satoshi Ichikawa and Akira Matsuda, Total Synthesis of Caprazol, a Core Structure of the Caprazamycin Antituberculosis Antibiotics, Angewandte Chemie International Edition, 44, 12, (1854-1856), (2005).
- Shinpei Hirano, Satoshi Ichikawa and Akira Matsuda, Total Synthesis of Caprazol, a Core Structure of the Caprazamycin Antituberculosis Antibiotics, Angewandte Chemie, 117, 12, (1888-1890), (2005).




