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

Nature Chemistry

Volumn 1, Issue 1, 2009, Pages 53-56

  Sawada, Tomohisa ^a   Yoshizawa, Michito ^a,c   Sato, Sota ^a   Fujita, Makoto ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEOTIDE; WATER;

ARTICLE; BASE PAIRING; CHEMICAL PHENOMENA; CHEMISTRY; CONFORMATION; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; X RAY CRYSTALLOGRAPHY;

BASE PAIRING; CRYSTALLOGRAPHY, X-RAY; DNA; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR CONFORMATION; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; WATER;

EID: 65349103780     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.100     Document Type: Article

References (21)

1. Watson, J. D. & Crick, F. H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171, 737-738 (1953).
2. Saenger, W. Principles of Nucleic Acid Structure (Springer, 1984).
3. Philp, D. & Stoddart, J. F. Self-assembly in natural and unnatural systems. Angew. Chem. Int. Ed. Engl. 35, 1154-1196 (1996).
4. Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H. F. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126, 1065-1077 (2006).
5. Westover, K. D., Bushnell, D. A. & Kornberg, R. D. Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell 119, 481-489 (2004).
6. Kumazawa, K., Biradha, K., Kusukawa, T., Okano, T. & Fujita, M. Multicomponent assembly of a pyrazine-pillared coordination cage that selectively binds planar guests by intercalation. Angew. Chem. Int. Ed. 42, 3909-3913 (2003).
7. Hoogsteen, K. The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallogr. 16, 907-916 (1963).
8. Hosseini, M. W., Blacker, A. J. & Lehn, J.-M. Multiple molecular recognition and catalysis. A multifunctional anion receptor bearing an anion binding site, an intercalating group, and a catalytic site for nucleotide binding and hydrolysis. J. Am. Chem. Soc. 112, 3896-3904 (1990).
9. Kobayashi, K., Asakawa, Y., Kato, Y. & Aoyama, Y. Complexation of hydrophobic sugars and nucleosides in water with tetrasulfonate derivatives of resorcinol cyclic tetramer having a polyhydroxy aromatic cavity: importance of guest-host CH-π interaction. J. Am. Chem. Soc. 114, 10307-10313 (1992).
10. Jasper, C., Schrader, T., Panitzky, J. & Klärner, F.-G. Selective complexation of N-alkylpyridinium salts: recognition of NAD in water. Angew. Chem. Int. Ed. 41, 1355-1358 (2002).
11. Butterfield, S. M. & Waters, M. L. A designed β-hairpin peptide for molecular recognition of ATP in water. J. Am. Chem. Soc. 125, 9580-9581 (2003).
12. McCleskey, S. C., Griffin, M. J., Schneider, S. E., McDevitt, J. T. & Anslyn, E. V. Differential receptors create patterns diagnostic for ATP and GTP. J. Am. Chem. Soc. 125, 1114-1115 (2003).
13. Prins, L. J., Reinhoudt, D. N. & Timmerman, P. Noncovalent synthesis using hydrogen bonding. Angew. Chem. Int. Ed. 40, 2382-2426 (2001).
14. Nowick, J. S., Chen, J. S. & Noronha, G. Molecular recognition in micelles: the roles of hydrogen bonding and hydrophobicity in adenine-thymine base-pairing in SDS micelles. J. Am. Chem. Soc. 115, 7636-7644 (1993).
15. Kato, Y., Conn, M. M. & Rebek, J. Jr Hydrogen bonding in water using synthetic receptors. Proc. Natl Acad. Sci. USA 92, 1208-1212 (1995).
16. Asanuma, H., Ban, T., Gotoh, S., Hishiya, T. & Komiyama, M. Hydrogen bonding in water by poly(vinyldiaminotriazine) for the molecular recognition of nucleic acid bases and their derivatives. Macromolecules 31, 371-377 (1998).
17. Hirschberg, J. H. K. K. et al. Helical self-assembled polymers from cooperative stacking of hydrogen-bonded pairs. Nature 407, 167-170 (2000).
18. Raszka, M. & Kaplan, N. O. Association by hydrogen bonding of mononucleotides in aqueous solution. Proc. Natl Acad. Sci. USA 69, 2025-2029 (1972).
19. Yoshizawa, M. et al. Discrete stacking of large aromatic molecules within organic-pillared coordination cages. Angew. Chem. Int. Ed. 44, 1810-1813 (2005).
20. Cheng, D. M. & Sarma, R. H. Intimate details of the conformational characteristics of deoxyribonucleoside monophosphates in aqueous solution. J. Am. Chem. Soc. 99, 7333-7348 (1977).
21. Hosur, R. V. & Govil, G. Sequence effects in structures of the dinucleotides d-pApT and d-pTpA. J. Mol. Struct. 72, 261-267 (1981).