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Minimal nucleotide duplex formation in water through enclathration in self-assembled hosts

Nature Chemistry volume 1, pages 53–56 (2009)Cite this article

Abstract

Short nucleotide fragments such as mono- and dinucleotides are generally unable to form stable hydrogen-bonded base pairs or duplexes in water. Within the hydrophobic pockets of enzymes, however, even short fragments form stable duplexes to transmit genetic information. Here, we demonstrate the efficient formation of hydrogen-bonded base pairs from mononucleotides in water through enclathration in the hydrophobic cavities of self-assembled cages. Crystallographic studies and 1H- and 15N-NMR spectroscopy clearly reveals pair-selective recognition of mononucleotides and the selective formation of an anti-Hoogsteen-type base pair in the cage's cavity. Within an analogous expanded cage, dinucleotides are also found to form a stable duplex in water. These results emphasize how hydrogen-bonded base pairing is amplified in a local hydrophobic area isolated from aqueous solution.

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Figure 1: Structures of the organic pillared coordination cages 1–4.
Figure 2: 1H-NMR spectroscopic observations for the formation of the 5·6 nucleotide base pair.
Figure 3: Crystal structure of the 2⊃(5·6) inclusion complex.
Figure 4: 1H-NMR spectroscopic observations for the formation of the duplex 3⊃(9)2.
Figure 5: Crystal structure of [4⊃(9)2]n.

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Acknowledgements

We thank Masaki Kawano of The University of Tokyo for help with X-ray crystallographic analysis.

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Author notes

  1. Michito Yoshizawa

    Present address: Present address: Chemical Research Laboratory, Tokyo Institute of Technology, 4259, Nagatsuta, Midori-ku, Yokohama 226-8503, Japan,

Authors and Affiliations

  1. Department of Applied Chemistry, School of Engineering, The University of Tokyo, Japan

    Tomohisa Sawada, Michito Yoshizawa, Sota Sato & Makoto Fujita

  2. Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan

    Makoto Fujita

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  1. Tomohisa Sawada
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Corresponding author

Correspondence to Makoto Fujita.

Supplementary information

Supplementary Information

Supplementary information (PDF 2166 kb)

Supplementary Information

Crystallographic data for heteroduplex of compounds 5 and 6 inside cage 2 (CIF 78 kb)

Supplementary Information

Crystallographic data for homoduplex of compound 9 inside cage 4 (CIF 60 kb)

Supplementary Information

Crystallographic data for homoduplex of compound 13 inside cage 3 (CIF 24 kb)

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Sawada, T., Yoshizawa, M., Sato, S. et al. Minimal nucleotide duplex formation in water through enclathration in self-assembled hosts. Nature Chem 1, 53–56 (2009). https://doi.org/10.1038/nchem.100

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