Synlett 2014; 25(11): 1499-1510
DOI: 10.1055/s-0033-1341060
account
© Georg Thieme Verlag Stuttgart · New York

Development of External Stimuli-Responsive Nucleic Acids by Sugar, Backbone, and Nucleobase Modification

Kunihiko Morihiro
a   Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan   Fax: +81(6)68798204   Email: obika@phs.osaka-u.ac.jp
b   National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
,
Tetsuya Kodama
c   Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
,
Satoshi Obika*
a   Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan   Fax: +81(6)68798204   Email: obika@phs.osaka-u.ac.jp
b   National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
› Author Affiliations
Further Information

Publication History

Received: 26 January 2014

Accepted: 18 February 2014

Publication Date:
03 April 2014 (online)


Abstract

Nucleic acids are the principal materials for the preservation and flow of genetic information. The control of the properties of nucleic acids by using external stimuli is important for regulating biological processes and for the possibility of developing unique molecular machines. This account summarizes the development of external stimuli-responsive nucleic acids by our group. Our external stimuli-responsive nucleic acids are designed and synthesized through sugar, backbone, and nucleobase modifications. Various external stimuli, such as light, acids, or oxidants/reductants can trigger changes in nucleic acid structure. By means of such structural alterations, various properties of nucleic acid, including their hybridization ability, nuclease resistance, backbone degradability, and base-recognition ability, can be changed.

1 Introduction

2 External Stimuli-Responsive Nucleic Acids

2.1 2′,4′-Bridged Nucleic Acid Analogues Bearing External Stimuli-Responsive Bridged Moieties

2.2 Oligonucleotides Containing a P–N Phosphoramidite Linkage for Double-Stranded DNA-Templated Digestion

2.3 Light-Triggered Change in the Hydrogen-Bonding Pattern of a Nucleobase Analogue Enables a Strand-Exchange ­Reaction

3 Conclusions

 
  • References

    • 1a Crooke ST. Annu. Rev. Med. 2004; 55: 61
    • 1b Chan JH.-P, Lim S, Wong W.-S. Clin. Exp. Pharmacol. Physiol. 2006; 33: 533
    • 1c Yamamoto T, Nakatani M, Narukawa K, Obika S. Future Med. Chem. 2011; 3: 339
    • 2a Mayer G. Angew. Chem. Int. Ed. 2009; 48: 2672
    • 2b Keefe AD, Pai S, Ellington A. Nat. Rev. Drug Discovery 2010; 9: 537
    • 3a Novina CD, Sharp PA. Nature 2004; 430: 161
    • 3b Shukla S, Sumaria CS, Pradeepkumar PI. ChemMedChem 2010; 5: 328
  • 4 Seeman NC. Nature 2003; 421: 427
    • 5a Kuzuya A, Komiyama M. Nanoscale 2010; 2: 309
    • 5b Tørring T, Voigt NV, Nangreave J, Yan H, Gothelf KV. Chem. Soc. Rev. 2011; 40: 5636
    • 5c Pinheiro AV, Han D, Shin WM, Yan H. Nat. Nanotechnol. 2011; 6: 763
    • 6a He L, Hannon GJ. Nat. Rev. Genet. 2004; 5: 522
    • 6b Carthew RW. Curr. Opin. Genet. Dev. 2006; 16: 203
    • 6c Schickel R, Boyerinas B, Park S.-M, Peter ME. Oncogene 2008; 27: 5959
    • 7a Siddiqui-Jain CL, Grand DJ, Bearss LH, Hurley LH. Proc. Natl. Acad. Sci. U. S. A. 2002; 99: 11593
    • 7b Phan AT, Modi YS, Patel DJ. J. Am. Chem. Soc. 2004; 126: 8710
    • 8a Lipps HJ, Rhodes D. Trends Cell Biol. 2009; 19: 414
    • 8b Bugaut A, Balasubramanian S. Nucleic Acids Res. 2012; 40: 4727
    • 8c Belotserkovskii BP, Mirkin SM, Hanawalt PC. Chem. Rev. 2013; 113: 8620
    • 9a Jones PA, Takai D. Science 2001; 293: 1068
    • 9b Egger G, Liang G, Aparicio A, Jones PA. Nature 2004; 429: 457
    • 9c Hirst M, Marra MA. Int. J. Biochem. Cell Biol. 2009; 41: 136
  • 10 Winkler W, Nahvi A, Breaker RR. Nature 2002; 419: 952
    • 11a Link KH, Breaker RR. Gene Ther. 2009; 16: 1189
    • 11b Cheng AL, Wolf JJ, Smolke CD. Curr. Opin. Biotechnol. 2012; 23: 679
  • 12 Prakash TP. Chem. Biodiversity 2011; 8: 1616
  • 13 Lavergne T, Baraguey C, Dupouy C, Parey N, Wuensche W, Sczakiel G, Vasseur J.-J, Debart F. J. Org. Chem. 2011; 76: 5719
  • 14 Ochi Y, Nakagawa O, Sakaguchi K, Wada S, Urata H. Chem. Commun. 2013; 49: 7620
    • 15a Rahman SM. A, Imanishi T, Obika S. Chem. Lett. 2009; 38: 512
    • 15b Obika S, Rahman SM. A, Fujisaka A, Kawada Y, Baba T, Imanishi T. Heterocycles 2010; 81: 1347
    • 16a Obika S, Nanbu D, Hari Y, Morio K.-i, In Y, Ishida T, Imanishi T. Tetrahedron Lett. 1997; 38: 8735
    • 16b Obika S, Nanbu D, Hari Y, Ando J, Morio K.-i, Doi T, Imanishi T. Tetrahedron Lett. 1998; 39: 5401
  • 17 Singh SK, Nielsen P, Koshkin AA, Wengel J. Chem. Commun. 1998; 455
  • 18 Sebej P, Solomek T, Hroudna L, Brancova P, Klan P. J. Org. Chem. 2009; 74: 8647
    • 19a Morihiro K, Kodama T, Nishida M, Imanishi T, Obika S. ChemBioChem 2009; 10: 1784
    • 19b Morihiro K, Kodama T, Obika S. Chem. Eur. J. 2011; 17: 7918
  • 20 Kodama T., Morihiro K., Obika S.; Curr. Protocol Nucleic Acid Chem.; in press.
  • 21 Buff R, Stoeckli-Evans H, Hunziker J. Acta Crystallogr., Sect. C 1998; 54: 1860
  • 22 Nielsen KD, Kirpekar F, Roepstorff P, Wengel J. Bioorg. Med. Chem. 1995; 3: 1493
  • 23 Baba T, Kodama T, Mori K, Imanishi T, Obika S. Chem. Commun. 2010; 46: 8058
  • 24 Altone C, Sundaralingam M. J. Am. Chem. Soc. 1973; 95: 2333
  • 25 Shrestha AR, Hari Y, Yahara A, Osawa T, Obika S. J. Org. Chem. 2011; 76: 9891
  • 26 Xu J, Liu Y, Dupouy C, Chattopadhyaya J. J. Org. Chem. 2009; 74: 6534
  • 27 Seth PP, Allerson CR, Berdeja A, Siwkowsli A, Pallan PS, Gaus H, Prakesh TP, Watt AT, Egli M, Swayze EE. J. Am. Chem. Soc. 2010; 132: 14942
  • 28 Morihiro K, Kodama T, ; Kentefu; Moai Y, Veedu RN, Obika S. Angew. Chem. Int. Ed. 2013; 52: 5074
  • 29 Liu H, Pinto BM. J. Org. Chem. 2005; 70: 753
  • 30 Banerjee D, Madhusoodanan UK, Nayak S, Jacob J. Clin. Chim. Acta 2003; 334: 205
  • 31 Rice ME. Neuroscientist 2011; 17: 389
  • 32 Ordoukhanian P, Taylor J.-S. J. Am. Chem. Soc. 1995; 117: 9570
    • 33a Zhang K, Taylor J.-S. J. Am. Chem. Soc. 1999; 121: 11579
    • 33b Zhang K, Taylor J.-S. Biochemistry 2001; 40: 153
  • 34 Bannwarth W. Helv. Chim. Acta 1988; 71: 1517
    • 35a Shchepinov MS, Denissenko MF, Smylie KJ, Wörl RJ, Leppin AL, Cantor CR, Rodi CP. Nucleic Acids Res. 2001; 29: 3864
    • 35b Wolfe JL, Wang BH, Kawate T, Stanton VP. Jr. J. Am. Chem. Soc. 2003; 125: 10500
  • 36 Gryaznov SM, Letsinger RL. Nucleic Acids Res. 1992; 20: 3403
  • 37 Obika S, Nakagawa O, Hiroto A, Hari Y, Imanishi T. Chem. Commun. 2003; 2202
  • 38 Obika S, Tomizu M, Negoro Y, Osaki T, Orita A, Ueyama Y, Nakagawa O, Imanishi T. Nucleosides, Nucleotides, Nucleic Acids 2007; 26: 893
  • 39 Obika S, Tomizu M, Negoro Y, Orita A, Nakagawa O, Imanishi T. ChemBioChem 2007; 8: 1924
  • 40 Ito KR, Kodama T, Tomizu M, Negoro Y, Orita A, Osaki T, Hosoki N, Tanaka T, Imanishi T, Obika S. Nucleic Acids Res. 2010; 38: 7332
  • 41 Ito KR, Kodama T, Makimura F, Hosoki N, Osaki T, Orita A, Imanishi T, Obika S. Molecules 2011; 16: 10695
  • 42 Yoshimura Y, Fujimoto K. Org. Lett. 2008; 10: 3227
    • 43a Young DD, Lusic H, Lively MO, Yoder JA, Deiters A. ChemBioChem 2008; 9: 2937
    • 43b Young DD, Lively MO, Deiters A. J. Am. Chem. Soc. 2010; 132: 6183
    • 44a Mikat V, Heckel A. RNA 2007; 13: 2341
    • 44b Govan JM, Young DD, Lusic H, Liu Q, Lively MO, Deiters A. Nucleic Acids Res. 2013; 41: 10518
  • 45 Heckel A, Mayer G. J. Am. Chem. Soc. 2005; 127: 822
    • 46a Höbartner C, Silverman SK. Angew. Chem. Int. Ed. 2005; 44: 7305
    • 46b Nierth A, Singer M, Jäschke A. Chem. Commun. 2010; 46: 7975
    • 47a Lusic H, Young DD, Lively MO, Deiters A. Org. Lett. 2007; 9: 1903
    • 47b Lusic H, Lively MO, Deiters A. Mol. BioSyst. 2008; 4: 508
  • 48 Joshi KB, Vlachos A, Mikat V, Deller T, Heckel A. Chem. Commun. 2012; 48: 2746
  • 49 Schmidt TL, Koeppel MB, Thevarpadam J, Gonçalves DP. N, Heckel A. Small 2011; 7: 2163
    • 50a Prokup A, Hemphill J, Deiters A. J. Am. Chem. Soc. 2012; 134: 3810
    • 50b Hemphill J, Deiters A. J. Am. Chem. Soc. 2013; 135: 10512
  • 51 Rodrigues-Correia A, Weyel XM. M, Heckel A. Org. Lett. 2013; 15: 5500
  • 52 Morihiro K, Kodama T, Waki R, Obika S. Chem. Sci. 2014; 5: 744
  • 53 Patchornik A, Amit B, Woodward RB. J. Am. Chem. Soc. 1970; 92: 6333
  • 54 Hoffer M. Chem. Ber. 1960; 93: 2777
  • 55 Adams JM, Cory S. Science 1998; 281: 1322