Synthesis 2014; 46(20): 2815-2825
DOI: 10.1055/s-0034-1378451
paper
© Georg Thieme Verlag Stuttgart · New York

Synthesis of C4-Linked C0- and C2-Imidazole 2′-Deoxyribonucleoside Phos­phoramidites and Imidazole Base-Pairing Effects on DNA

Shinya Harusawa*
a   Laboratory of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan   Fax: +81(72)6901086   eMail: harusawa@gly.oups.ac.jp
,
Hiroki Yoneyama
a   Laboratory of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan   Fax: +81(72)6901086   eMail: harusawa@gly.oups.ac.jp
,
Yoshihide Usami
a   Laboratory of Pharmaceutical Organic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan   Fax: +81(72)6901086   eMail: harusawa@gly.oups.ac.jp
,
Daisuke Yamamoto
b   Biomedical Computation Center, Osaka Medical College, 2-7 Daigakucho, Takatsuki, Osaka 569-8686, Japan
,
Zheng-yun Zhao
c   Centre for Plant Science & Bio-polymer Research, Faculty of Engineering, Computing and Creative Industries, Edinburgh Napier University, 10 Colinton Road, Edinburgh, EH10 5DT, UK
› Institutsangaben
Weitere Informationen

Publikationsverlauf

Received: 20. Mai 2014

Accepted after revision: 17. Juni 2014

Publikationsdatum:
31. Juli 2014 (online)


Abstract

The synthesis of C4-linked imidazole C0- and C2-2′-deoxyribonucleoside phosphoramidites (dPAs), in which the final phosphitylations are greatly improved by 4,5-dicyanoimidazole-promoted conversion, is described. The respective dPAs are successfully incorporated into the sequence of a 15-nt DNA, and the abilities of one or two imidazoles to pair with different bases are investigated through thermal melting (T m) experiments on the resulting DNA duplexes. Furthermore, computational models of the imidazole-modified DNAs are found to be in good agreement with the results of the thermal melting experiments.

Supporting Information

 
  • References

  • 1 Grimmett MR. Imidazoles . In Comprehensive Heterocyclic Chemistry II . Vol. 3. Katritzky AR, Rees CW, Scriven EF. V. Pergamon; Oxford: 1996: 77
    • 2a Kopple JD, Swendseid ME. J. Clin. Invest. 1975; 55: 881
    • 2b Fahey RC. Annu. Rev. Microbiol. 2001; 55: 333
    • 3a Marieb EN In Human Anatomy & Physiology . Benjamin-Cummings; San Francisco: 2001. 414, 796, 824 and 90
    • 3b Repka-Ramirez MS. Curr. Allergy Rep. 2003; 30: 227
    • 3c Hough LB. Mol. Pharmacol. 2001; 59: 415
    • 4a Madasu SB, Vekariya NA, Koteswaramma C, Islam A, Sanasi PD, Korupolu RB. Org. Process Res. Dev. 2012; 16: 2025
    • 4b Walsh AJ, Davis ML, Fraser W. Molecules 2006; 11: 486
    • 4c Mangas-Sánchez J, Busto E, Gotor-Fernández V, Malpartida F, Gotor V. J. Org. Chem. 2011; 76: 2115
    • 4d Liang J, Lv W, Li X, An K, Cushman M, Wang H, Xu Y. Bioorg. Med. Chem. Lett. 2013; 23: 1387

      For oligodeoxyribonucleotides containing an imidazole N-nucleoside, see:
    • 5a Johannsen S, Megger N, Böhme D, Siegel RK. O, Müller J. Nat. Chem. 2010; 2: 229
    • 5b Durland RH, Rao TS, Bodepudi V, Seth DM, Jayaraman K, Revankar GR. Nucleic Acids Res. 1995; 23: 647
    • 5c Johnson WT, Zhang P, Bergstrom DE. Nucleic Acid Res. 1997; 25: 559
    • 6a Araki L, Harusawa S, Yamaguchi M, Yonezawa S, Taniguchi N, Lilley DM. J, Zhao Z, Kurihara T. Tetrahedron Lett. 2004; 45: 2657
    • 6b Araki L, Harusawa S, Yamaguchi M, Yonezawa S, Taniguchi N, Lilley DM. J, Zhao Z, Kurihara T. Tetrahedron 2005; 61: 11976
    • 6c Araki L, Morita K, Yamaguchi M, Zhao Z, Wilson TJ, Lilley DM. J, Harusawa S. J. Org. Chem. 2009; 74: 2350
    • 6d Araki L, Zhao Z, Lilley DM. J, Harusawa S. Heterocycles 2010; 81: 1861
    • 6e Harusawa S, Fujii K, Nishiura M, Araki L, Usami Y, Zhao Z, Lilley DM. J. Heterocycles 2011; 83: 2041
    • 6f Araki L, Harusawa S. Yakugaku Zasshi 2010; 130: 1707
  • 7 Lilley DM. J. The Hairpin and Varkud Satellite Ribozymes . In Ribozymes and RNA Catalysis . Lilley DM. J, Eckstein F. Royal Society of Chemistry; Cambridge: 2008: 66
    • 8a Zhao Z, McLeod A, Harusawa S, Araki L, Yamaguchi M, Kurihara T, Lilley DM. J. J. Am. Chem. Soc. 2005; 127: 5026
    • 8b Wilson TJ, Ouellet J, Zhao Z, Harusawa S, Araki L, Kurihara T, Lilley DM. J. RNA 2006; 12: 980
    • 8c Lilley DM. J. Biol. Chem. 2007; 388: 699
    • 9a Harusawa S, Yoneyama H, Fujisue D, Nishimura M, Fujitake M, Usami Y, Zhao Z, McPhee SA, Wilson TJ, Lilley DM. J. Tetrahedron Lett. 2012; 45: 5891
    • 9b Yoneyama H, Usami Y, Komeda S, Harusawa S. Synthesis 2013; 45: 1051
    • 9c The typical debenzylation of 3,5-di-O-benzyl-2-deoxy-β-d-riboses with Pd(OH)2/C–cyclohexene in ethanol at reflux temperature proceeds slowly, giving moderate yields of the products.
  • 10 Li Z, Zhou H, Wu X, Yao H. Curr. Med. Chem. 2013; 20: 3641
    • 11a Sakthivel K, Barbas III CF. Angew. Chem. Int. Ed. 1998; 37: 2872
    • 11b Lee SE, Sidorov A, Gourlain T, Mignet N, Thorpe SJ, Brazier JA, Dickman MJ, Hornby DP, Grasby JA, Williams DM. Nucleic Acids Res. 2001; 29: 1565
    • 11c Sawai H, Ozaki AN, Satoh F, Ohbayashi T, Masud MM, Ozaki H. Chem. Commun. 2001; 2604
    • 11d Perrin DM, Garestier T, Hélène C. J. Am. Chem. Soc. 2001; 123: 1556

      For recent reviews on C-nucelosides, see:
    • 12a Boutureira O, Matheu MI, Díaz Y, Castillón S. Synthesis of C-Nucleosides . In Chemical Synthesis of Nucleoside Analogues . Merino P. Wiley; Hoboken: 2013: 263
    • 12b Wu Q, Simons C. Synthesis 2004; 1533
    • 12c Štambaský J, Hocek M, Kočovský P. Chem. Rev. 2009; 109: 6729

      For the synthesis of C4-linked imidazole 2′-deoxyribo­-nucleosides, see:
    • 13a Bergstrom DE, Zhang P, Zhou J. J. Chem. Soc., Perkin Trans. 1 1994; 3029
    • 13b Harusawa S, Murai Y, Moriyama H, Imazu T, Ohishi H, Yoneda R, Kurihara T. J. Org. Chem. 1996; 61: 4405
    • 14a Beaucage SL. Oligodeoxyribonucleoside Synthesis. In Protocols for Oligonucleotides and Analogs. Agrawal S. Humana Press; Totowa (NJ): 1993: 33
    • 14b Vargeese C, Carter J, Yegge J, Krivjansky S, Settle A, Kropp E, Peterson K, Pieken W. Nucleic Acids Res. 1998; 26: 1046
  • 15 Seitz G, Lachmann J. Z. Naturforsch. 1999; 54b: 549
    • 16a The synthesis of a C2-α/β mixture (9αβ) of a furancarbaldehyde was reported (see ref. 16b), but the selective synthesis of was first carried out in this paper.
    • 16b Krishna PR, Reddy VV. R, Srinivas R. Tetrahedron 2007; 63: 9871
    • 17a Fujitake M, Harusawa S, Araki L, Yamaguchi M, Lilley DM. J, Zhao Z, Kurihara T. Tetrahedron 2005; 61: 4689
    • 17b Harusawa S, Fujitake M, Kurihara T, Zhao Z, Lilley DM. J. Mass Determination of Phosphoramidites . In Current Protocols in Nucleic Acid Chemistry . Beaucage SL, Bergstrom DE, Herdewijn P, Matsuda A. John Wiley & Sons; New York: 2006. 10.11.1
    • 17c Fujitake M, Harusawa S. Yakugaku Zasshi 2013; 133: 823
  • 18 Manchester J, Bassani DM, Duprey J.-LH. A, Giordano L, Vyle JS, Zhao Z.-y, Tucker JH. R. J. Am. Chem. Soc. 2012; 134: 10791
  • 19 Beaucage SL, Caruthers MH. Tetrahedron Lett. 1981; 22: 1859
  • 20 Xia J, Noronha A, Toudjarska I, Li F, Akinc A, Braich R, Frank-Kamenetsky M, Rajeev KG, Egli M, Manoharan M. ACS Chem. Biol. 2006; 1: 176
  • 21 Salomon-Ferrer R, Case DA, Walker RC. WIREs Comput. Mol. Sci. 2013; 3: 198
  • 22 Sturgeon JB, Laird BB. J. Chem. Phys. 2000; 112: 3474