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Okamura H, Trinh GH, Dong Z, Masaki Y, Seio K, Nagatsugi F. Selective and stable base pairing by alkynylated nucleosides featuring a spatially-separated recognition interface. Nucleic Acids Res 2022; 50:3042-3055. [PMID: 35234916 PMCID: PMC8989583 DOI: 10.1093/nar/gkac140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/27/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Unnatural base pairs (UBPs) which exhibit a selectivity against pairing with canonical nucleobases provide a powerful tool for the development of nucleic acid-based technologies. As an alternative strategy to the conventional UBP designs, which involve utility of different recognition modes at the Watson–Crick interface, we now report that the exclusive base pairing can be achieved through the spatial separation of recognition units. The design concept was demonstrated with the alkynylated purine (NPu, OPu) and pyridazine (NPz, OPz) nucleosides endowed with nucleobase-like 2-aminopyrimidine or 2-pyridone (‘pseudo-nucleobases’) on their major groove side. These alkynylated purines and pyridazines exhibited exclusive and stable pairing properties by the formation of complementary hydrogen bonds between the pseudo-nucleobases in the DNA major groove as revealed by comprehensive Tm measurements, 2D-NMR analyses, and MD simulations. Moreover, the alkynylated purine-pyridazine pairs enabled dramatic stabilization of the DNA duplex upon consecutive incorporation while maintaining a high sequence-specificity. The present study showcases the separation of the recognition interface as a promising strategy for developing new types of UBPs.
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Affiliation(s)
- Hidenori Okamura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Giang Hoang Trinh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Zhuoxin Dong
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.,JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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2
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Beck KM, Ruder L, Nicolai TS, Pham RL, Risgaard NA, Hornum M, Nielsen P. Double‐Headed Nucleotides with Non‐Native Nucleobases: Synthesis and Duplex Studies. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Kasper M. Beck
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Linette Ruder
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Tine S. Nicolai
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Robert L. Pham
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Nikolaj A. Risgaard
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Mick Hornum
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
| | - Poul Nielsen
- Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 5230 Odense M Denmark
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Kurosaki F, Chiba J, Oda Y, Hino A, Inouye M. 2-Aminopyridine as a Nucleobase Substitute for Adenine in DNA-like Architectures: Synthesis of Alkynyl C-Nucleotides and Their Hybridization Characteristics. J Org Chem 2020; 85:2666-2671. [PMID: 31875396 DOI: 10.1021/acs.joc.9b02750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Halogenated 2-aminopyridine was attached to the acetylene terminal of ethynyl C-2-deoxy-β-d-ribofuranoside as a nucleobase substitute, and then, the C-nucleoside was incorporated into natural DNAs. The resulting chimeric DNA constructed double helical structures with the complementary chimeric DNA. In the duplex, 2-aminopyridine functioned as an adenine analogue that formed a base pair with a non-natural thymine isostere. Artificial homooligomers were also prepared only from the adenine-type C-nucleoside and proven to form completely artificial double helices with the corresponding artificial thymine-type homooligomers.
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Affiliation(s)
- Fumihiro Kurosaki
- Graduate School of Pharmaceutical Sciences , University of Toyama , Toyama 930-0194 , Japan
| | - Junya Chiba
- Graduate School of Pharmaceutical Sciences , University of Toyama , Toyama 930-0194 , Japan
| | - Yutaro Oda
- Graduate School of Pharmaceutical Sciences , University of Toyama , Toyama 930-0194 , Japan
| | - Airi Hino
- Graduate School of Pharmaceutical Sciences , University of Toyama , Toyama 930-0194 , Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences , University of Toyama , Toyama 930-0194 , Japan
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Jena NR. Electron and hole interactions with P, Z, and P:Z and the formation of mutagenic products by proton transfer reactions. Phys Chem Chem Phys 2020; 22:919-931. [DOI: 10.1039/c9cp05367k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Z would act as an electron acceptor and P would capture a hole in the unnatural DNA. The latter process would produce mutagenic products via a proton transfer reaction.
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Affiliation(s)
- N. R. Jena
- Discipline of Natural Sciences
- Indian Institute of Information Technology, Design, and Manufacturing
- Jabalpur-482005
- India
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5
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Behera B, Das P, Jena NR. Accurate Base Pair Energies of Artificially Expanded Genetic Information Systems (AEGIS): Clues for Their Mutagenic Characteristics. J Phys Chem B 2019; 123:6728-6739. [PMID: 31290661 DOI: 10.1021/acs.jpcb.9b04653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, several artificial nucleobases, such as B, S, J, V, X, K, P, and Z, have been proposed to help in the expansion of the genetic information system and diagnosis of diseases. Among these bases, P and Z were identified to form stable DNA and to participate in the replication. However, the stabilities of P:Z and other artificial base pairs are not fully understood. The abilities of these unnatural nucleobases in mispairing with themselves and with natural bases are also not known. Here, the ωB97X-D dispersion-corrected density functional theoretical and complete basis set (CBS-QB3) methods are used to obtain accurate structural and energetic data related to base pair interactions involving these unnatural nucleobases. The roles of protonation and deprotonation of certain artificial bases in inducing mutations are also studied. It is found that each artificial purine has a complementary artificial pyrimidine, the base pair interactions between which are similar to those of the natural Watson-Crick base pairs. Hence, these base pairs will function naturally and would not impart mutagenicity. Among these base pairs, the J:V complex is found to be the most stable and promising artificial base pair. Remarkably, the noncomplementary artificial nucleobases are found to form stable mispairs, which may generate mutagenic products in DNA. Similarly, the misinsertions of natural bases opposite artificial bases are also found to be mutagenic. The mechanisms of these mutations are explained in detail. These results are in agreement with earlier biochemical studies. It is thus expected that this study would aid in the advancement of the synthetic biology to design more robust artificial nucleotides.
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Affiliation(s)
- B Behera
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Jabalpur 482005 , India
| | - P Das
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Jabalpur 482005 , India
| | - N R Jena
- Discipline of Natural Sciences , Indian Institute of Information Technology, Design and Manufacturing , Jabalpur 482005 , India
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Oda Y, Chiba J, Kurosaki F, Yamade Y, Inouye M. Additive‐Free Enzymatic Phosphorylation and Ligation of Artificial Oligonucleotides with C‐Nucleosides at the Reaction Points. Chembiochem 2019; 20:1945-1952. [DOI: 10.1002/cbic.201900217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Yutaro Oda
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
| | - Junya Chiba
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
| | - Fumihiro Kurosaki
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
| | - Yusuke Yamade
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical SciencesUniversity of Toyama 2630 Sugitani Toyama 930-0194 Japan
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Chiba J, Inouye M. Synthesis of Nonnatural Oligonucleotides Made Exclusively of Alkynyl C-Nucleosides with Nonnatural Bases. ACTA ACUST UNITED AC 2015; 61:4.62.1-4.62.22. [PMID: 26344228 DOI: 10.1002/0471142700.nc0462s61] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This unit describes detailed procedures for the preparation of nonnatural C-nucleosides comprising seven types of nonnatural nucleobases attached to 1'-position of 2'-deoxyribose through an acetylene bond with the β-configuration. In addition, derivatization of these alkynyl C-nucleosides into the corresponding phosphoramidites and the subsequent oligonucleotide synthesis are also presented. The processes are depicted in three parts. The first basic protocol deals with the synthesis of a key intermediate, 5-O-DMTr-protected 1-ethynyl-2-deoxy-β-D-ribofuranoside. The second basic protocol mentions the procedures of the preparation of nonnatural C-nucleosides by a palladium-catalyzed coupling reaction of the ethynyl intermediate and halogen-attached nonnatural nucleobases. The synthetic procedures of the corresponding nonnatural phosporamidites are also described. The third basic protocol presents the solid-phase, automated synthesis of nonnatural oligonucleotides composed exclusively of the nonnatural C-nucleotides.
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Affiliation(s)
- Junya Chiba
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences, University of Toyama, Toyama, Japan
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