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Targeting human c-Myc promoter duplex DNA with actinomycin D by use of multi-way analysis of quantum-dot-mediated fluorescence resonance energy transfer

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Abstract

Actinomycin D (Act D), an oncogenic c-Myc promoter binder, interferes with the action of RNA polymerase. There is great demand for high-throughput technology able to monitor the activity of DNA-binding drugs. To this end, binding of 7-aminoactinomycin D (7AAD) to the duplex c-Myc promoter was investigated by use of 2D-photoluminescence emission (2D-PLE), and the resulting data were subjected to analysis by use of convenient and powerful multi-way approaches. Fluorescence measurements were performed by use of the quantum dot (QD)-conjugated c-Myc promoter. Intercalation of 7AAD within duplex base pairs resulted in efficient energy transfer from drug to QD via fluorescence resonance energy transfer (FRET). Multi-way analysis of the three-way data array obtained from titration experiments was performed by use of restricted Tucker3 and hard trilinear decomposition (HTD). These techniques enable analysis of high-dimensional and complex data from nanobiological systems which include several spectrally overlapped structures. It was almost impossible to obtain robust and meaningful information about the FRET process for such high overlap data by use of classical analysis. The soft approach had the important advantage over univariate classical methods of enabling us to investigate the source of variance in the fluorescence signal of the DNA–drug complex. It was established that hard trilinear decomposition analysis of FRET-measured data overcomes the problem of rank deficiency, enabling calculation of concentration profiles and pure spectra for all species, including non-fluorophores. The hard modeling approach was also used for determination of equilibrium constants for the hybridization and intercalation equilibria, using nonlinear fit data analysis. The intercalation constant 3.6 × 106 mol−1 L and hybridization stability 1.0 × 108 mol−1 L obtained were in good agreement with values reported in the literature. The analytical concentration of the QD-labeled DNA was determined by use of nonlinear fitting, without using external standard calibration samples. This study was a successful application of multi-way chemometric methods to investigation of nano-biotechnological systems where several overlapped species coexist in solution.

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References

  1. Lutz W, Leon J, Eilers M (2002) Contributions of Myc to tumorigenesis. Biochim Biophys Acta (BBA) Rev Cancer 1602(1):61–71

    Article  CAS  Google Scholar 

  2. Vita M, Henriksson M (2006) The Myc oncoprotein as a therapeutic target for human cancer. Semin Cancer Biol 16(4):318–330

    Article  CAS  Google Scholar 

  3. Simonsson T, Kubista M, Pecinka P (1998) DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res 26(5):1167–1172

    Article  CAS  Google Scholar 

  4. Siddiqui-Jain A, Grand CL, Bearss DJ, Hurley LH (2002) Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc Natl Acad Sci 99(18):11593–11598

    Article  CAS  Google Scholar 

  5. Wadkins RM, Vladu B, Tung C-S (1998) Actinomycin D binds to metastable hairpins in single-stranded DNA. Biochemistry 37(34):11915–11923

    Article  CAS  Google Scholar 

  6. Vaquero A, Portugal J (1998) Modulation of DNA-protein interactions in the P1 and P2 c-myc promoters by two intercalating drugs. Eur J Biochem 251(1–2):435–442

    Article  CAS  Google Scholar 

  7. Kang H-J, Park H-J (2009) Novel molecular mechanism for actinomycin D activity as an oncogenic promoter G-quadruplex binder. Biochemistry 48(31):7392–7398

    Article  CAS  Google Scholar 

  8. Wadkins RM, Jovin TM (1991) Actinomycin D and 7-aminoactinomycin D binding to single-stranded DNA. Biochemistry 30(39):9469–9478

    Article  CAS  Google Scholar 

  9. Wang L-R, Qu N, Guo L-H (2008) Electrochemical displacement method for the investigation of the binding interaction of polycyclic organic compounds with DNA. Anal Chem 80(10):3910–3914

    Article  CAS  Google Scholar 

  10. Wang S, Peng T, Yang CF (2003) Investigation on the interaction of DNA and electroactive ligands using a rapid electrochemical method. J Biochem Biophys Methods 55(3):191–204

    Article  CAS  Google Scholar 

  11. Yuan J, Guo W, Yang X, Wang E (2008) Anticancer drug−DNA interactions measured using a photoinduced electron-transfer mechanism based on luminescent quantum dots. Anal Chem 81(1):362–368

    Article  Google Scholar 

  12. Kumar P, Kanchan K, Gargallo R, Chowdhury S (2005) Application of multivariate curve resolution for the study of folding processes of DNA monitored by fluorescence resonance energy transfer. Anal Chim Acta 536(1–2):135–143

    Article  CAS  Google Scholar 

  13. Rauf S, Gooding JJ, Akhtar K, Ghauri MA, Rahman M, Anwar MA, Khalid AM (2005) Electrochemical approach of anticancer drugs–DNA interaction. J Pharm Biomed Anal 37(2):205–217

    Article  CAS  Google Scholar 

  14. Cardullo RA, Agrawal S, Flores C, Zamecnik PC, Wolf DE (1988) Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer. Proc Natl Acad Sci 85(23):8790–8794

    Article  CAS  Google Scholar 

  15. Aoki T, Imamura T, Ozaki H, Ideuchi H, Tsuchida S, Watabe H (2006) Fluorescence resonance energy transfer-based assay for DNA-binding protein tagged by green fluorescent protein. Biosci Biotechnol Biochem 70(8):1921–1927

    Article  CAS  Google Scholar 

  16. Leung C-H, Chan DS-H, He H-Z, Cheng Z, Yang H, Ma D-L (2012) Luminescent detection of DNA-binding proteins. Nucleic Acids Res 40(3):941–955

    Article  CAS  Google Scholar 

  17. Mergny J-L (1999) Fluorescence energy transfer as a probe for tetraplex formation: the i-Motif. Biochemistry 38(5):1573–1581

    Article  CAS  Google Scholar 

  18. Bruchez M, Moronne M, Gin P, Weiss S, Alivisatos AP (1998) Semiconductor nanocrystals as fluorescent biological labels. Science 281(5385):2013–2016

    Article  CAS  Google Scholar 

  19. Chan WCW, Nie S (1998) Quantum dot bioconjugates for ultrasensitive nonisotopic detection. Science 281(5385):2016–2018

    Article  CAS  Google Scholar 

  20. Medintz IL, Uyeda HT, Goldman ER, Mattoussi H (2005) Quantum dot bioconjugates for imaging, labelling and sensing. Nat Mater 4(6):435–446

    Article  CAS  Google Scholar 

  21. Michalet X, Pinaud FF, Bentolila LA, Tsay JM, Doose S, Li JJ, Sundaresan G, Wu AM, Gambhir SS, Weiss S (2005) Quantum dots for live cells, in vivo imaging, and diagnostics. Science 307(5709):538–544

    Article  CAS  Google Scholar 

  22. Algar W, Krull U (2007) Towards multi-colour strategies for the detection of oligonucleotide hybridization using quantum dots as energy donors in fluorescence resonance energy transfer (FRET). Anal Chim Acta 581(2):193–201

    Article  CAS  Google Scholar 

  23. Zhang C-Y, Yeh H-C, Kuroki MT, Wang T-H (2005) Single-quantum-dot-based DNA nanosensor. Nat Mater 4(11):826–831

    Article  CAS  Google Scholar 

  24. Gill R, Willner I, Shweky I, Banin U (2005) Fluorescence resonance energy transfer in CdSe/ZnS−DNA conjugates: probing hybridization and DNA cleavage. J Phys Chem B 109(49):23715–23719

    Article  CAS  Google Scholar 

  25. Jaumot J, Eritja R, Tauler R, Gargallo R (2006) Resolution of a structural competition involving dimeric G-quadruplex and its C-rich complementary strand. Nucleic Acids Res 34(1):206–216

    Article  CAS  Google Scholar 

  26. Jaumot J, Escaja N, Gargallo R, González C, Pedroso E, Tauler R (2002) Multivariate curve resolution: a powerful tool for the analysis of conformational transitions in nucleic acids. Nucleic Acids Res 30(17):e92

    Article  Google Scholar 

  27. Akhlaghi Y, Kompany-Zareh M, Hormozi-Nezhad MR (2012) Multiway investigation of interaction between fluorescence labeled DNA strands and unmodified gold nanoparticles. Anal Chem 84(15):6603–6610

    Article  CAS  Google Scholar 

  28. del Toro M, Bucek P, Aviñó A, Jaumot J, González C, Eritja R, Gargallo R (2009) Targeting the G-quadruplex-forming region near the P1 promoter in the human BCL-2 gene with the cationic porphyrin TMPyP4 and with the complementary C-rich strand. Biochimie 91(7):894–902

    Article  Google Scholar 

  29. Ghasemi Moghaddam F, Kompany-Zareh M, Gholami S (2012) Study of neutral red interaction with DNA by resolution of rank deficient multi-way fluorescence data. J Pharm Biomed Anal 70:388–395

    Article  CAS  Google Scholar 

  30. Kukolka F, Schoeps O, Woggon U, Niemeyer CM (2007) DNA-directed assembly of supramolecular fluorescent protein energy transfer systems. Bioconjug Chem 18(3):621–627

    Article  CAS  Google Scholar 

  31. Smilde AK, Wang Y, Kowalski BR (1994) Theory of medium-rank second-order calibration with restricted-Tucker models. J Chemom 8(1):21–36

    Article  CAS  Google Scholar 

  32. Kiers HAL, Smilde AK (1998) Constrained three-mode factor analysis as a tool for parameter estimation with second-order instrumental data. J Chemom 12(2):125–147

    Article  CAS  Google Scholar 

  33. Smilde AK, Tauler R, Henshaw JM, Burgess LW, Kowalski BR (1994) Multicomponent determination of chlorinated hydrocarbons using a reaction-based chemical sensor. 3. Medium-rank second-order calibration with restricted Tucker models. Anal Chem 66(20):3345–3351

    Article  CAS  Google Scholar 

  34. Neuhold Y-M, Maeder M (2002) Hard-modelled trilinear decomposition (HTD) for an enhanced kinetic multicomponent analysis. J Chemom 16(5):218–227

    Article  CAS  Google Scholar 

  35. Mitchell GP, Mirkin CA, Letsinger RL (1999) Programmed assembly of DNA functionalized quantum dots. J Am Chem Soc 121(35):8122–8123

    Article  CAS  Google Scholar 

  36. Smilde AK, Bro R, Geladi P (2004) Multi-way analysis with applications in the chemical sciences. Wiley, J, Hoboken

    Book  Google Scholar 

  37. Buet P, Lewitzki E, Grell E, Albrecht-Gary AM, Wannowius KJ, Mass F, Elias H, Mundt AA, Dupont Y (2001) Concentration jump experiments for the precise determination of rate constants of reverse reactions in the millisecond time range. Anal Chem 73(5):857–863

    Article  CAS  Google Scholar 

  38. Bugnon P, Chottard J-C, Jestin J-L, Jung B, Laurenczy G, Maeder M, Merbach AE, Zuberbühler AD (1994) Second-order globalisation for the determination of activation parameters in kinetics. Anal Chim Acta 298(2):193–201

    Article  CAS  Google Scholar 

  39. Bijlsma S, Smilde AK (1999) Application of curve resolution based methods to kinetic data. Anal Chim Acta 396(2–3):231–240

    Article  CAS  Google Scholar 

  40. Maeder M, Neuhold YM (2007) Practical data analysis in chemistry. Elsevier Science

  41. Bailey SA, Graves DE, Rill R (1994) Binding of actinomycin D to the T(G)nT motif of double-stranded DNA: determination of the guanine requirement in nonclassical, non-GpC binding sites. Biochemistry 33(38):11493–11500

    Article  CAS  Google Scholar 

  42. Bailey SA, Graves DE, Rill R, Marsch G (1993) Influence of DNA base sequence on the binding energetics of actinomycin D. Biochemistry 32(22):5881–5887

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran

    Somayeh Gholami & Mohsen Kompany-Zareh

  2. Department of Food Science, Faculty of Life Sciences, University of Copenhagen, Rolighedsvej 30, 1958, Frederiksberg C, Denmark

    Mohsen Kompany-Zareh

Authors
  1. Somayeh Gholami
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  2. Mohsen Kompany-Zareh
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Correspondence to Mohsen Kompany-Zareh.

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Gholami, S., Kompany-Zareh, M. Targeting human c-Myc promoter duplex DNA with actinomycin D by use of multi-way analysis of quantum-dot-mediated fluorescence resonance energy transfer. Anal Bioanal Chem 405, 6271–6280 (2013). https://doi.org/10.1007/s00216-013-7041-8

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  • DOI: https://doi.org/10.1007/s00216-013-7041-8

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