Advertisement

Development of a New Method for Synthesis of Tandem Hairpin Pyrrole–Imidazole Polyamide Probes Targeting Human Telomeres

  • Yusuke KawamotoEmail author
Chapter
Part of the Springer Theses book series (Springer Theses)

Abstract

Pyrrole–imidazole (PI) polyamides bind to the minor groove of DNA in a sequence-specific manner without causing denaturation of DNA. To visualize telomeres specifically, tandem hairpin PI polyamides conjugated with a fluorescent dye have been synthesized, but the study of telomeres using these PI polyamides has not been reported because of difficulties synthesizing these tandem hairpin PI polyamides. To synthesize tandem hairpin PI polyamides more easily, we have developed new PI polyamide fragments and have used them as units in Fmoc solid-phase peptide synthesis. Using this new method, we synthesized four fluorescent polyamide probes for the human telomeric repeat TTAGGG, and we examined the binding affinities and specificities of the tandem hairpin PI polyamides, the UV-visible absorption and fluorescence spectra of the fluorescent polyamide probes, and telomere staining in mouse MC12 and human HeLa cells. The polyamides synthesized using the new method successfully targeted to human and mouse telomeres under a mild condition and allow easier labeling of telomeres in the cells while maintaining the telomere structure. Using the fluorescent polyamides, we demonstrated that the telomere length at a single telomere level is related to the abundance of TRF1 protein, a shelterin complex component in the telomere.

Keywords

Pyrrole–imidazole polyamides Tandem hairpin polyamides Solid-phase peptide synthesis Telomere Cellular imaging TRF1 

References

  1. 1.
    Blackburn EH (2010) Angew Chem Int Ed 49:7405–7421CrossRefGoogle Scholar
  2. 2.
    Nandakumar J, Cech TR (2013) Nat Rev Mol Cell Biol 14:69–82CrossRefGoogle Scholar
  3. 3.
    Zakian VA (2012) Exp Cell Res 318:1456–1460CrossRefGoogle Scholar
  4. 4.
    Smogorzewska A, de Lange T (2004) Annu Rev Biochem 73:177–208CrossRefGoogle Scholar
  5. 5.
    Smogorzewska A, van Steensel B, Bianchi A, Oelmann S, Schaefer MR, Schnapp G, de Lange T (2000) Mol Cell Biol 20:1659–1668CrossRefGoogle Scholar
  6. 6.
    (a) Dervan PB (2001) Bioorg Med Chem 9:2215–2235; (b) Dervan PB, Edelson BS (2003) Curr Opin Struc Biol 13:284–299; (c) Dervan PB, Doss RM, Marques MA (2005) Curr Med Chem –Anti-Cancer Agents 5:373–387; (d) Blackledge MS, Melander C (2013) Bioorg Med Chem 21:6101–6114Google Scholar
  7. 7.
    White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB (1998) Nature 391:468–471CrossRefGoogle Scholar
  8. 8.
    (a) Turner JM, Swalley SE, Baird EE, Dervan PB (1998) J Am Chem Soc 120:6219–6226; (b) Wang CC, Ellervik U, Dervan PB (2001) Bioorg Med Chem 9:653–657Google Scholar
  9. 9.
    (a) de Clairac RPL, Geierstanger BH, Mrksich M, Dervan PB, Wemmer DE (1997) J Am Chem Soc 119:7909–7916; (b) Murty MSRC, Sugiyama H (2004) Biol Pharm Bull 27:468–474Google Scholar
  10. 10.
    (a) Herman DM, Turner JM, Baird EE, Dervan PB (1999) J Am Chem Soc 121:1121–1129; (b) Melander C, Herman DM, Dervan PB (2000) Chem Eur J 6:4487–4497; (c) Morinaga H, Bando T, Takagaki T, Yamamoto H, Hashiya K, Sugiyama H (2011) J Am Chem Soc 133:18924–18930; (d) Li BC, Montgomery DC, Puckett JW, Dervan PB (2013) J Org Chem 78:124–133Google Scholar
  11. 11.
    (a) Herman DM, Baird EE, Dervan PB (1999) Chem Eur J 5:975–983; (b) Kers I, Dervan PB (2002) Bioorg Med Chem 10:3339–3349; (c) Schaal TD, Mallet WG, McMinn DL, Nguyen NV, Sopko MM, John S, Parekh BS (2003) Nucleic Acids Res 31:1282–1291; (d) Sasaki S, Bando T, Minoshima M, Shinohara K, Sugiyama H (2008) Chem Eur J 14:864–870Google Scholar
  12. 12.
    Maeshima K, Janssen S, Laemmli UK (2001) EMBO J 20:3218–3228CrossRefGoogle Scholar
  13. 13.
    (a) Bando T, Narita A, Saito I, Sugiyama H (2003) J Am Chem Soc 125:3471–3485; (b) Bando T, Sugiyama H (2006) Acc Chem Res 39:935–944; (c) Bando T, Sasaki S, Minoshima M, Dohno C, Shinohara K, Narita A, Sugiyama H (2006) Bioconjugate Chem 17:715–720. (d) Takagaki T, Bando T, Sugiyama H (2012) J Am Chem Soc 134:13074–13081Google Scholar
  14. 14.
    (a) Vaijayanthi T, Bando T, Pandian GN, Sugiyama H (2012) ChemBioChem 13:2170–2185; (b) Vaijayanthi T, Bando T, Hashiya K, Pandian GN, Sugiyama H (2013) Bioorg Med Chem 21:852–855; (c) Su W, Bagshaw CR, Burley GA (2013) Sci Rep 3:1883Google Scholar
  15. 15.
    (a) Ohtsuki A, Kimura MT, Minoshima M, Suzuki T, Ikeda M, Bando T, Nagase H, Shinohara K, Sugiyama H (2009) Tetrahedron Lett 50:7288–7292; (b) Pandian GN, Shinohara K, Ohtsuki A, Nakano Y, Minoshima M, Bando T, Nagase H, Yamada Y, Watanabe A, Terada N, Sato S, Morinaga H, Sugiyama H (2011) ChemBioChem 12:2822–2828. (c) Pandian GN, Ohtsuki A, Bando T, Sato S, Hashiya K, Sugiyama H (2012) Bioorg Med Chem 20:2656–2660; (d) Pandian GN, Nakano Y, Sato S, Morinaga H, Bando T, Nagase H, Sugiyama H (2012) Sci Rep 2:544Google Scholar
  16. 16.
    Fujimoto J, Bando T, Minoshima M, Kashiwazaki G, Nishijima S, Shinohara K, Sugiyama H (2008) Bioorg Med Chem 16:9741–9744CrossRefGoogle Scholar
  17. 17.
    (a) Takahashi R, Bando T, Sugiyama H (2003) Bioorg Med Chem 11:2503–2509; (b) Sasaki S, Bando T, Minoshima M, Shimizu T, Shinohara K, Takaoka T, Sugiyama H (2006) J Am Chem Soc 128, 12162–12168; (c) Kashiwazaki G, Bando T, Shinohara K, Minoshima M, Nishijima, S, Sugiyama S (2009) Bioorg Med Chem 17:1393–1397; (d) Kashiwazaki G, Bando T, Shinohara K, Minoshima M, Kumamoto H, Nishijima S, Sugiyama H (2010) Bioorg Med Chem 18:2887–2893Google Scholar
  18. 18.
    Wurtz NR, Turner JM, Baird EE, Dervan PB (2001) Org Lett 3:1201–1203CrossRefGoogle Scholar
  19. 19.
    (a) Rucker VC, Foister S, Melander C, Dervan PB (2003) J Am Chem Soc 125:1195–1202. (b) Rucker VC, Dunn AR, Sharma S, Dervan PB, Gray HB (2004) J Phys Chem B 108:7490–7494Google Scholar
  20. 20.
    (a) Pilch DS, Poklar N, Gelfand CA, Law SM, Breslauer KJ, Baird EE, Dervan PB (1996) Proc Natl Acad Sci USA 93:8306–8311; (b) Muzikar KA, Meier JL, Gubler DA, Raskatov JA, Dervan PB (2011) Org Lett 13:5612–5615Google Scholar
  21. 21.
    Kumar S, Xue L, Arya DP (2011) J Am Chem Soc 133:7361–7375CrossRefGoogle Scholar
  22. 22.
    (a) Herman DM, Baird EE, Dervan PB (1998) J Am Chem Soc 120:1382–1391; (b) Dose C, Farkas ME, Chenoweth DM, Dervan PB (2008) J Am Chem Soc 130:6859–6866Google Scholar
  23. 23.
    Aubert G, Hills M, Lansdorp PM (2012) Mutat Res 730:59–67CrossRefGoogle Scholar
  24. 24.
    Yoshida I (2002) Cytogenet. Genome Res 99:44–51CrossRefGoogle Scholar
  25. 25.
    Maeshima K, Laemmli UK (2003) Dev Cell 4:467–480CrossRefGoogle Scholar
  26. 26.
    Maeshima K, Yahata K, Sasaki Y, Nakatomi R, Tachibana T, Hashikawa T, Imamoto F, Imamoto N (2006) J Cell Sci 119:4442–4451CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.Department of Chemistry and BiochemistryUniversity of CaliforniaSan Diego, La JollaUSA

Personalised recommendations