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Four-Hydrogen-Bonding Base Pairs in Oligonucleotides: Design, Synthesis, and Properties

  • Noriko Saito-Tarashima
  • Akira Matsuda
  • Noriaki Minakawa
Chapter

Abstract

Oligodeoxynucleotides (ODNs) having four-hydrogen-bonding (H-bonding) unnatural base pairs have been developed. These examples of nucleobase modification have been designed and prepared to address the fundamental question: why did Watson–Crick base pairs come to contain two or three H-bonds during the evolution of life? As the first generation of four-H-bonding base pairs, imidazo[5′,4′:4,5]pyrido[2,3-d]pyrimidine (Im) was selected as an aglycon to append a fourth H-bonding site to nucleobases. The stability of Im:Im pairs in duplexes depends on the mode of incorporation. Conversely, the second generation of four-H-bonding base pairs comprising Im and 1,8-naphthyridine (Na) C-nucleosides, formed duplexes with drastically enhanced thermal stability (especially ImNN:NaOO pair), independent of the modification pattern. In addition, the ImNN:NaOO pair was replicated with the highest efficiency and selectivity among the series of Im:Na pairs using in vitro replication systems owing to the synergistic effect of favorable thermal and thermodynamic contributions from base pairing and specific H-bonding geometries. ImON:NaNO and ImNN:NaOO pairs are transcribed under the optimized concentrations of UTP and rNaTP in in vitro transcription catalyzed by T7 RNA polymerase.

Keywords

Hydrogen-bonding Unnatural base pair Imidazo[5′4′:4,5]pyrido[2,3-d]pyrimidine 1,8-naphthyridine Base pairing Thermodynamics Enzymatic recognition 

Notes

Acknowledgements

We thank all of our colleagues, especially Dr. N. Kojima, Dr. S. Hikishima, Mr. K. Kuramoto, Mr. S. Ogata, Dr. Y. Nomura, and Dr. K. Sato who contributed to the studies described here. This work was supported by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (JSPS). N.T. thanks the research program for the development of intelligent Tokushima artificial exosome (iTEX) from Tokushima University.

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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Noriko Saito-Tarashima
    • 1
  • Akira Matsuda
    • 2
  • Noriaki Minakawa
    • 1
  1. 1.Faculty of Pharmaceutical ScienceTokushima UniversityTokushimaJapan
  2. 2.Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical SciencesHokkaido UniversitySapporoJapan

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