Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Focus Review
  • Published:

Application of naphthalene diimide in biotechnology

Polymer Journal volume 53, pages 415–427 (2021)Cite this article

Subjects

Abstract

Naphthalene diimide (NDI) is an electron-deficient, robust, and planar molecule. These characteristics make it highly applicable to electronic devices that take advantage of their electric character, for imide group-based supramolecular materials that utilize hydrogen bonding, or for sensing materials with a combination of functional groups. Water-soluble NDI binds to a DNA duplex via the threading intercalation mode. Such NDI has enabled the development of unique DNA analytical techniques, functional DNA polymers, and supramolecular polymers. A ferrocene-containing NDI, possessing electrochemically active sites, has been applied to an electrochemical gene detection system and utilized in the precision analysis of genes and single nucleotide polymorphisms. Recently, a DNA quadruplex was identified as one of the noncanonical DNA structures formed by a guanine quartet (G4). The latter serves as one of the control units of gene expression and is associated with cancer development. A stable complex was formed between electron-deficient NDI and the electron-rich G4 planes. Since the G4 stabilizer is recognized as an anticancer agent with relatively few side effects, NDI derivatives may serve as potential candidates for anticancer therapeutics or for designing a unique cancer-detection system.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  1. Bhosale SV, Jani CH, Langford SJ. Chemistry of naphthalene diimides. Chem Soc Rev. 2008;37:331–42.

    CAS  PubMed  Google Scholar 

  2. Kobaisi MA, Bhosale SV, Latham K, Raynor AM, Bhosale SV. Functional naphthalene diimides: synthesis, properties, and applications. Chem Rev. 2016;116:11685–796.

    CAS  PubMed  Google Scholar 

  3. Das A, Ghosh S. H-bonding directed programmed supramolecular assembly of naphthalene-diimide (NDI) derivatives. Chem Commun. 2016;52:6860–72.

    CAS  Google Scholar 

  4. Yen SF, Gabbay EJ, Wilson WD. Interaction of aromatic imides with deoxyribonucleic acid. Spectrophotometric and viscometric studies. Biochemistry. 1982;21:2070–6.

    CAS  PubMed  Google Scholar 

  5. Tanious FA, Yen S-F, Wilson WD. Kinetic and equilibrium analysis of a threading intercalation mode: DNA sequence and ion effects. Biochemistry. 1991;30:1813–9.

    CAS  PubMed  Google Scholar 

  6. Ou T, Lu Y, Tan J, Huang Z, Wong KY, Gu L. G-Quadruplexes: targets in anticancer drug design. ChemMedChem. 2008;3:690–713.

    CAS  PubMed  Google Scholar 

  7. Yang D, Okanoto K. Structural insights into G-quadruplexes: towards new anticancer drugs. Future Med Chem. 2010;2:619–46.

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Pirota V, Nadai M, Doria F, Richter S. Naphthalene diimides as multimodal G-quadruplex-selective ligands. Molecules. 2019;24:426.

    PubMed Central  Google Scholar 

  9. Gawronski J, Brzostowska M, Kacprzak K, Kolbon H, Skowronek P. Chirality of aromatic bis-imides from their circular dichroism spectra. Chirality. 2000;12:263–8.

    CAS  PubMed  Google Scholar 

  10. Green S, Fox A. Intramolecular photoinduced electron transfer from nitroxyl radicals. J Phys Chem. 1995;99:14752–7.

    CAS  Google Scholar 

  11. Salerno F, Berrocal JA, Haedler AT, Zinna F, Meijer EW, Bari LD. Highly circularly polarized broad-band emission from chiral naphthalene diimide-based supramolecular aggregates. J Mater Chem C. 2017;5:3609–15.

    CAS  Google Scholar 

  12. Andric G, Boas JF, Bond AM, Fallon GD, Ghiggino KP, Hogan CF et al. Spectroscopy of naphthalene diimides and their anion radicals. Aut J Chem. 2004;57:1011–9.

    CAS  Google Scholar 

  13. Chu Y, Hoffman DW, Iverson BL. A pseudocatenane structure formed between DNA and A cyclic bisintercalator. J Am Chem Soc. 2009;131:3499–508.

    CAS  PubMed  PubMed Central  Google Scholar 

  14. McGhee JD, von Hippel PH. Theorical aspects of DNA-protyein interaction: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J Mol Biol. 1974;86:469–89.

    CAS  PubMed  Google Scholar 

  15. McKnight RE, Gleason AB, Keyes JA, Sahabi S. Binding mode and affinity studies of DNA-binding agents using topoisomerase I DNA unwinding assay. Bioorg Med Chem Lett.2007;17:1013–7.

    CAS  PubMed  Google Scholar 

  16. Wilson WD, Jones RL. Intercalation in biological systems. Intercalation Chemistry, Whittingham MS, Jacobson AJ, editors. New York: Academic Press; 1982, pp. 445–510.

  17. Takenaka S, Yamashita K, Takagi M, Uto Y, Kondo H. DNA sensing on a DNA probe-modified electrode using ferrocenylnaphthalene diimide as the electrochemically active ligand. Anal Chem. 2000;72:1334–41.

    CAS  PubMed  Google Scholar 

  18. Yamashita K, Takagi M, Kondo H, Takenaka S. Electrochemical detection of nucleic base mismatches with ferrocenyl naphthalene diimide. Anal Biochem. 2002;306:188–96.

    CAS  PubMed  Google Scholar 

  19. Miyahara H, Yamashita K, Kanai M, Uchida K, Takagi M, Kondo H et al. Electrochemical analysis of single nucleotide polymorphisms of p53 gene. Talanta. 2002;56:829–35.

    CAS  PubMed  Google Scholar 

  20. Nojima T, Yamashita K, Takagi A, Takagi M, Ikeda Y, Kondo H et al. Electrochemical analysis of single nucleotide polymorphisms of p53 gene. Anal Sci. 2003;19:79–83.

    CAS  PubMed  Google Scholar 

  21. Nojima T, Yamashita K, Takagi A, Ikeda Y, Kondo H, Takenaka S. Genotyping of human lipoprotein lipase gene by ferrocenylnaphthalene diimide-based electrochemical hybridization assay. Anal Sci. 2005;21:1437–41.

    CAS  PubMed  Google Scholar 

  22. Sato S, Hokazono K, Irie T, Ueki T, Waki M, Nojima T et al. Ferrocenylnaphthalene diimide-based electrochemical detection of methylated gene. Anal Chim Acta. 2006;578:82–7.

    CAS  PubMed  Google Scholar 

  23. Ishikawa N, Miya T, Mizumoto K, Ohuchida K, Nagai E, Yamaguchi K et al. Rapid and sensitive assay of K-ras mutations in pancreatic cancer by electrochemical detection with ferrocenyl-naphthalene-diimide. Cancer Genomics Proteom. 2006;3:47–54.

    CAS  Google Scholar 

  24. Sato S, Tsueda M, Kanezaki Y, Takenaka S. Detection of an aberrant methylation of CDH4 gene in PCR product by ferrocenylnaphthalene diimide-based electrochemical hybridization assay. Anal Chim Acta. 2012;715:42–8.

    CAS  PubMed  Google Scholar 

  25. Harahuchi K, Sato S, Habu M, Yada N, Hayakawa M, Takahashi O et al. Oral cancer screening based on methylation frequency detection in hTERT gene using electrochemical hybridization assay via a multi-electrode chip coupled with ferrocenylnaphthalene diimide. Electroanalysis. 2017;29:1596–601.

    Google Scholar 

  26. Sato S, Saeki T, Tanaka T, Kanezaki Y, Hayakawa M, Haraguchi K et al. Ferrocenylnaphthalene diimide-based electrochemical detection of aberrant methylation in hTERT gene. Appl Biochem Biotechnol. 2014;174:869–79.

    CAS  PubMed  Google Scholar 

  27. Sato S, Takenaka S. Linker effect of ferrocenylnaphthalene diimide ligands in the interaction with double stranded DNA. J Organomet Chem. 2008;693:1177–85.

    CAS  Google Scholar 

  28. Sato S, Tsueda M, Takenaka S. Electrochemical detection of aberrant methylated gene using naphthalene diimide derivative carrying four ferrocene moieties. J Origanomet Chem. 2010;695:1858–62.

    CAS  Google Scholar 

  29. Sato S, Nojima T, Waki M, Takenaka S. Supramolecular complex formation by β-cyclodextrin and ferrocenylnaphthalene diimide-intercalated double stranded DNA and improved electrochemical gene detection. Molecules. 2005;10:693–707.

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Sato S, Nojima T, Takenaka S. Electrochemical gene detection based on supramolecular complex formation by ferrocenyl-b-cyclodextrin and adamantylnaphthalene diimide bound to double stranded DNA. J Organomet Chem. 2004;689:4722–8.

    CAS  Google Scholar 

  31. Takenaka H, Sato S, Takenaka S. Electrochemical detection of duplex DNA using intercalation-triggered decomplexation of ferrocene with b-cyclodextrin. Electroanalysis. 2013;25:1827–30.

    CAS  Google Scholar 

  32. Watanabe S, Sato S, Ohsuka K, Takenaka S. Electrochemical DNA analysis with a supramolecular assembly of naphthalene diimide, ferrocene, and β-cyclodextrin. Anal Chem. 2011;83:7290–6.

    CAS  PubMed  Google Scholar 

  33. Komizo K, Ikeda H, Sato S, Takenaka S. Metallization of double-stranded DNA triggered by bound galactose-modified naphthalene diimide. Bioconjugate Chem. 2014;25:1547–55.

    CAS  Google Scholar 

  34. Ohtsuka K, Komizo K, Takenaka S. Synthesis and DNA binding behavior of a naphthalene diimide derivative carrying two dicobalt hexacarbonyl complexes as an infrared DNA probe. J Organomet Chem. 2010;695:1281–6.

    CAS  Google Scholar 

  35. Himuro T, Araki R, Sato S, Takenaka S, Yasuda T. Specific metallization of double-stranded DNA using reducing group-labeled intercalator. IEEJ Trans Sens Micromachines. 2016;36:425–31.

    Google Scholar 

  36. Sato S, Umeda Y, Fujii S, Takenaka S. Cooperative binding of ferrocenylnaphthalene diimide carrying β-cyclodextrin converts double-stranded DNA to a rod-like structure. Bioconjugate Chem. 2015;26:379–82.

    CAS  Google Scholar 

  37. Steel AB, Heme TM, Tarlov MJ. Electrochemical quantitation of DNA immobilized on gold. Anal Chem. 1998;70:4670–7.

    CAS  PubMed  Google Scholar 

  38. Sato S, Hirano A, Takenaka S. Selective immobilization of double stranded DNA on a gold surface through threading intercalation of a naphthalene diimide having dithiolane moieties. Anal Chim Acta. 2010;665:91–97.

    CAS  PubMed  Google Scholar 

  39. Sato S, Yamamura K, Takenaka S. Naphthalene diimide carrying two cysteine termini at both imide linkers as a molecular staple. Electroanalysis. 2013;25:1831–9.

    CAS  Google Scholar 

  40. Tian T, Chen YQ, Wang SR, Zhou X. G-Quadruplex: a regulator of gene expression and its chemical targeting. Chem. 2018;4:1314–44.

    CAS  Google Scholar 

  41. Spiegel J, Adhikari S, Balasubramanian S. The structure and function of DNA G-quadruplexes. Trends Chem. 2020;2:123–36.

    CAS  PubMed  PubMed Central  Google Scholar 

  42. O’Hagan MP, Morales JC, Galan MC. Binding and beyond: what else can G-quadruplex ligands do? Eur J Org Chem. 2019;31–2: 4995–5017.

  43. Parkinson GN, Cuenca F, Neidle S. Topology conservation and loop flexibility in quadruplex–drug recognition: crystal structures of inter- and intramolecular telomeric DNA quadruplex–drug complexes. J Mol Biol. 2008;381:1145–56.

    CAS  PubMed  Google Scholar 

  44. Sato S, Kondo H, Nojima T, Takenaka S. Electrochemical telomerase assay with ferrocenylnaphthalene diimide as a tetraplex DNA-specific binder. Anal Chem. 2005;77:7304–9.

    CAS  PubMed  Google Scholar 

  45. Sato S, Takenaka S. Ferrocenyl naphthalene diimides as tetraplex DNA binders. J Inorg Biochem. 2017;167:21–6.

    CAS  PubMed  Google Scholar 

  46. Mori K, Sato S, Kodama M, Habu M, Takahashi O, Nishihara T et al. Oral cancer diagnosis via a ferrocenylnaphthalene diimide–based electrochemical telomerase assay. Clin Chem. 2013;59:289–95.

    CAS  PubMed  Google Scholar 

  47. Hayakawa M, Sato S, Diala I, Kodama M, Tomoeda-Mori K, Haraguchi K et al. Screening for oral cancer using electrochemical telomerase assay. Electroanalysis. 2016;28:503–7.

    CAS  Google Scholar 

  48. Marchetti C, Zyner KG, Ohnmacht SA, Robson M, Haider SM, Morton JP et al. Targeting multiple effector pathways in pancreatic ductal adenocarcinoma with a G‑quadruplex-binding small molecule. J Med Chem. 2018;61:2500–17.

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Sato S, Kajima A, Hamanaka H, Takenaka S. Naphthalene diimide carrying four ferrocenyl substitutes as an electrochemical indicator of tetraplex DNA aiming at cancer diagnosis. J Organomet Chem. 2019;897:107–13.

    CAS  Google Scholar 

  50. Esaki Y, Islam MM, Fujii S, Sato S, Takenaka S. Design of tetraplex specific ligands: cyclic naphthalene diimide. Chem Commun. 2014;50:5967–9.

    CAS  Google Scholar 

  51. Vasimalla S, Sato S, Takenaka F, Kurose Y, Takenaka S. Cyclic perylene diimide: selective ligand for tetraplex DNA binding over double stranded DNA. Bioorg Med Chem. 2017;25:6404–11.

    CAS  PubMed  Google Scholar 

  52. Kaneyoshi S, Zou T, Ozaki S, Takeuchi R, Udou A, Nakahara T et al. Cyclic naphthalene diimide with a ferrocene moiety as a redox-active tetraplex-DNA ligand. Chem Eur J. 2020;26:139–42.

    CAS  PubMed  Google Scholar 

  53. Takeuchi R, Zou T, Wakahara D, Nakano Y, Sato S, Takenaka S. Cyclic naphthalene diimide dimer with a strengthened ability to stabilize dimeric G-quadruplex. Chem Eur J. 2019;25:8691–5.

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

ST appreciates the significant contribution made by the researchers who appear in the reference papers of Takenaka’s group. ST thanks Dr. Zou Tingting for preparing a conceptual diagram of figures according to his idea and thanks Dr. Satoshi Fujii for the molecular modeling simulation of the threading intercalation complex in Fig. 2c, d. Finally, ST thanks Dr. Shinobu Sato for engaging in discussion and support.

Author information

Authors and Affiliations

  1. Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, 804-8550, Japan

    Shigeori Takenaka

Authors
  1. Shigeori Takenaka
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Shigeori Takenaka.

Ethics declarations

Conflict of interest

The author declares no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Takenaka, S. Application of naphthalene diimide in biotechnology. Polym J 53, 415–427 (2021). https://doi.org/10.1038/s41428-020-00434-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41428-020-00434-2

Search

Advanced search

Quick links