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Photo-Cross-Linkable Artificial Nucleic Acid: Synthesis and Properties of 3-Cyanovinylcarbazole-Modified Nucleic Acids and Its Photo-Induced Gene-Silencing Activity in Cells

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Synthesis of Therapeutic Oligonucleotides
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Abstract

The inter-strand photo-cross-linking reaction between nucleic acid strands has wide potential for regulating gene expression specifically and spatiotemporally due to its sequence specificity and high photo irradiation operability. Therefore, photo-cross-linkable artificial nucleic acids are required to be specific and effective drugs without adverse effects and also be good tools for investigating gene functions in cells.

As one of the most reactive photo-cross-linkable artificial nucleic acids, in this review, 3-cyanovinylcarbazole modified oligodeoxyribonucleotides that can photo-crosslink with their complementary nucleic acid within a few seconds of photoirradiation are examined. The details of the synthetic method, properties and the applications for regulating gene expression in cells are discussed.

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References

  1. Bhan P, Miller PS (1990) Photo-cross-linking of psoralen-derivatized oligonucleoside methylphosphonates to single-stranded DNA. Bioconjug Chem 1(1):82–88

    Article  CAS  PubMed  Google Scholar 

  2. Cassidy RA, Kondo NS, Miller PS (2000) Triplex formation by psoralen-conjugated chimeric oligonucleoside methylphosphonates. Biochemistry 39(29):8683–8691

    Article  CAS  PubMed  Google Scholar 

  3. Chang EH, Miller PS, Cushman C, Devadas K, Pirollo KF, Ts’o PO, Yu ZP (1991) Antisense inhibition of ras p21 expression that is sensitive to a point mutation. Biochemistry 30(34):8283–8286

    Article  CAS  PubMed  Google Scholar 

  4. Fujimoto K, Konishi-Hiratsuka K, Sakamoto T, Yoshimura Y (2010) Site-specific cytosine to uracil transition by using reversible DNA photo-crosslinking. Chembiochem 11(12):1661–1664

    Article  CAS  PubMed  Google Scholar 

  5. Fujimoto K, Konishi-Hiratsuka K, Sakamoto T, Yoshimura Y (2010) Site-specific photochemical RNA editing. Chem Commun 46(40):7545–7547

    Article  CAS  Google Scholar 

  6. Fujimoto K, Yamada A, Yoshimura Y, Tsukaguchi T, Sakamoto T (2013) Details of the ultrafast DNA photo-cross-linking reaction of 3-cyanovinylcarbazole nucleoside: cis-trans isomeric effect and the application for SNP-based genotyping. J Am Chem Soc 135(43):16161–16167

    Article  CAS  PubMed  Google Scholar 

  7. Giovannangéli C, Thuong NT, Hélène C (1992) Oligodeoxynucleotide-directed photo-induced cross-linking of HIV proviral DNA via triple-helix formation. Nucleic Acids Res 20(16):4275–4281

    Article  PubMed  PubMed Central  Google Scholar 

  8. Grigoriev M, Praseuth D, Guieysse AL, Robin P, Thuong NT, Hélène C, Harel-Bellan A (1993) Inhibition of gene expression by triple helix-directed DNA cross-linking at specific sites. Proc Natl Acad Sci U S A 90(8):3501–3505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Hall LM, Gerowska M, Brown T (2012) A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5 and Cy3B monomers. Nucleic Acids Res 40(14):e108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Heck RF, Nolley JP (1972) Palladium-catalyzed vinylic hydrogen substitution reactions with aryl, benzyl, and styryl halides. J Org Chem 37(14):2320–2322

    Article  CAS  Google Scholar 

  11. Higuchi M, Kobori A, Yamayoshi A, Murakami A (2009) Synthesis of antisense oligonucleotides containing 2′-O-psoralenylmethoxyalkyl adenosine for photodynamic regulation of point mutations in RNA. Bioorg Med Chem 17(2):475–483

    Article  CAS  PubMed  Google Scholar 

  12. Higuchi M, Yamayoshi A, Kato K, Kobori A, Wake N, Murakami A (2010) Specific regulation of point-mutated K-ras-immortalized cell proliferation by a photodynamic antisense strategy. Oligonucleotides 20(1):37–44

    Article  CAS  PubMed  Google Scholar 

  13. Higuchi M, Yamayoshi A, Yamaguchi T, Iwase R, Yamaoka T, Kobori A, Murakami A (2007) Selective photo-cross-linking of 2′-O-psoralen-conjugated oligonucleotide with RNAs having point mutations. Nucleosides Nucleotides Nucleic Acids 26(3):277–290

    Article  CAS  PubMed  Google Scholar 

  14. Lee BL, Blake KR, Miller PS (1988) Interaction of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates with synthetic DNA containing a promoter for T7 RNA polymerase. Nucleic Acids Res 16(22):10681–11097

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Lee BL, Murakami A, Blake KR, Lin SB, Miller PS (1988) Interaction of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates with single-stranded DNA. Biochemistry 27(9):3197–3203

    Article  CAS  PubMed  Google Scholar 

  16. Lin M, Hultquist KL, Oh DH, Bauer EA, Hoeffler WK (1995) Inhibition of collagenase type I expression by psoralen antisense oligonucleotides in dermal fibroblasts. FASEB J 9(13):1371–1377

    Article  CAS  PubMed  Google Scholar 

  17. Matsuyama Y, Yamayoshi A, Kobori A, Murakami A (2014) Functional regulation of RNA-induced silencing complex by photoreactive oligonucleotides. Bioorg Med Chem 22(3):1003–1007

    Google Scholar 

  18. Miller PS, Bi G, Kipp SA, Fok V, DeLong RK (1996) Triplex formation by a psoralen-conjugated oligodeoxyribonucleotide containing the base analog 8-oxo-adenine. Nucleic Acids Res 24(4):730–736

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Miller PS, Kipp SA, McGill C (1999) A psoralen-conjugated triplex-forming oligodeoxyribonucleotide containing alternating methylphosphonate-phosphodiester linkages: synthesis and interactions with DNA. Bioconjug Chem 10(4):572–577

    Article  CAS  PubMed  Google Scholar 

  20. Mizoroki T, Mori K, Ozaki A (1971) Arylation of olefin with aryl iodide catalyzed by palladium. Bull Chem Soc J 44(2):581

    Article  CAS  Google Scholar 

  21. Mochizuki Y, Suzuki T, Fujimoto K, Nemoto N (2015) A versatile puromycin-linker using CNVK for high-throughput in vitro selection by cDNA display. J Biotechnol 212(20):174–180

    Article  CAS  PubMed  Google Scholar 

  22. Murakami A, Yamayoshi A, Iwase R, Nishida J, Yamaoka T, Wake N (2001) Photodynamic antisense regulation of human cervical carcinoma cell growth using psoralen-conjugated oligo(nucleoside phosphorothioate). Eur J Pharm Sci 13(1):25–34

    Article  CAS  PubMed  Google Scholar 

  23. Nakamura S, Fujimoto K (2014) Creation of DNA array structure equipped with heat resistance by ultrafast photocrosslinking. J Chem Tech Biotech 89(7):1086–1090

    Article  CAS  Google Scholar 

  24. Pieles U, Englisch U (1989) Psoralen covalently linked to oligodeoxyribonucleotides: synthesis, sequence specific recognition of DNA and photo-cross-linking to pyrimidine residues of DNA. Nucleic Acids Res 17(1):285–299

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Sakamoto T, Shigeno A, Ohtaki Y, Fujimoto K (2014) Photo-regulation of constitutive gene expression in living cells by using ultrafast photo-cross-linking oligonucleotides. Biomater Sci 2:1154–1157

    Article  CAS  Google Scholar 

  26. Sakamoto T, Tanaka Y, Fujimoto K (2015) DNA photo-cross-linking using 3-cyanovinylcarbazole modified oligonucleotide with threoninol linker. Org Lett 17(4):936–939

    Article  CAS  PubMed  Google Scholar 

  27. Shigeno A, Sakamoto T, Yoshimura Y, Fujimoto K (2012) Quick regulation of mRNA functions by a few seconds of photoirradiation. Org Biomol Chem 10(38):7820–7825

    Article  CAS  PubMed  Google Scholar 

  28. Tagawa M, Shohda K, Fujimoto K, Suyama A (2011) Stabilization of DNA nanostructures by photo-cross-linking. Soft Matter 7:10931–10934

    Article  CAS  Google Scholar 

  29. Takasugi M, Guendouz A, Chassignol M, Decout JL, Lhomme J, Thuong NT, Hélène C (1991) Sequence-specific photo-induced cross-linking of the two strands of double-helical DNA by a psoralen covalently linked to a triple helix-forming oligonucleotide. Proc Natl Acad Sci U S A 88(13):5602–5606

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Yoshimura Y, Fujimoto K (2008) Ultrafast reversible photo-cross-linking reaction: toward in situ DNA manipulation. Org Lett 10(15):3227–3230

    Article  CAS  PubMed  Google Scholar 

  31. Wang G, Glazer PM (1995) Altered repair of targeted psoralen photoadducts in the context of an oligonucleotide-mediated triple helix. J Biol Chem 270(38):22595–22601

    Article  CAS  PubMed  Google Scholar 

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Correspondence to Kenzo Fujimoto .

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Sakamoto, T., Fujimoto, K. (2018). Photo-Cross-Linkable Artificial Nucleic Acid: Synthesis and Properties of 3-Cyanovinylcarbazole-Modified Nucleic Acids and Its Photo-Induced Gene-Silencing Activity in Cells. In: Obika, S., Sekine, M. (eds) Synthesis of Therapeutic Oligonucleotides. Springer, Singapore. https://doi.org/10.1007/978-981-13-1912-9_10

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