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

Shinya Harusawa; Hiroki Yoneyama; Yoshihide Usami; Daisuke Yamamoto; Zheng-yun Zhao

doi:10.1055/s-0034-1378451

Synthesis, Table of Contents

Synthesis 2014; 46(20): 2815-2825
DOI: 10.1055/s-0034-1378451

paper

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

Shinya Harusawa*

^aLaboratory 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

^aLaboratory 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

^aLaboratory 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

^bBiomedical Computation Center, Osaka Medical College, 2-7 Daigakucho, Takatsuki, Osaka 569-8686, Japan

,

Zheng-yun Zhao

^cCentre for Plant Science & Bio-polymer Research, Faculty of Engineering, Computing and Creative Industries, Edinburgh Napier University, 10 Colinton Road, Edinburgh, EH10 5DT, UK

› Author Affiliations

Abstract

All articles of this category

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.

Key words

imidazole - phosphoramidite - C-deoxyribonucleoside - base pairing - DNA

Full Text

References

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 9β 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

Supplementary Material

Supporting Information

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

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