297
Views
8
CrossRef citations to date
0
Altmetric
Research Article

Retained binding mode of various DNA-binding molecules under molecular crowding condition

, , , &
Pages 3035-3046 | Received 23 Jul 2017, Accepted 22 Aug 2017, Published online: 18 Sep 2017

References

  • Adali, T., Bentaleb, A., Elmarzuqi, N., & Hamza, A. M. (2013). PEG-calf thymus DNA interactions: Conformational, morphological and spectroscopic thermal studies. International Journal of Biological Macromolecules, 61, 373–378.10.1016/j.ijbiomac.2013.07.024
  • Cavatorta, P., Masotti, L., & Szabo, A. G. (1985). A time-resolved fluorescence study of 4′,6′-diamidine-2-phenylindole dihydrochloride binding to polynucleotides. Biophysical Chemistry, 22, 11–16.10.1016/0301-4622(85)80021-1
  • Chatterjee, S., & Kumar, S. (2016). Binding of fluorescent acridine dyes acridine orange and 9-aminoacridine to hemoglobin: Elucidation of their molecular recognition by spectroscopy, calorimetry and molecular modeling techniques. Journal of Photochemistry and Photobiology B, 159, 169–178.10.1016/j.jphotobiol.2016.03.045
  • Daisuke, M., Akihiro, N., & Naoki, S. (2002). Molecular crowding regulates the structural switch of the DNA G-quadruplex. Biochemistry, 41, 15017–15024.
  • Daisuke, M., Hisae, K., & Naoki, S. (2006). Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. Journal of American Chemistry Society, 128, 7957–7963.
  • Ellis, R. J. (2001). Macromolecular crowding: Obvious but underappreciated. Trends Biochemical Sciences, 26, 597–604.10.1016/S0968-0004(01)01938-7
  • Fiel, R. J. (1979). Interaction of DNA with a porphyrin ligand: Evidence for intercalation. Nucleic Acid Research, 6, 3093–3118.10.1093/nar/6.9.3093
  • Froehlich, E., Mandeville, J. S., Arnold, D., Kreplak, L., & Tajmir-Riahi, H. A. (2011). PEG and mPEG-Anthracene induce DNA condensation and particle formation. The Journal of Physical Chemistry B, 115, 9873–9879.10.1021/jp205079u
  • Goobes, R., & Minsky, A. (2001). Thermodynamic aspects of triplex DNA formation in crowded environments. Journal of American Chemistry Society, 123, 12692–12693.10.1021/ja016577d
  • Hansen, J. B., Koch, T., Buchardt, O., Nielsen, P. E., Wirth, P. M., & Norden, B. (1983). Acridine-psoralen amines and their interaction with deoxyribonucleic acid. Biochemistry, 21, 4878–4886.10.1021/bi00290a003
  • Houssier, C., Hardy, B., & Fredericq, E. (1974). Interaction of ethidium bromide with DNA. Optical and Electrooptical study. Biopolymers, 13, 1141–1160.10.1002/(ISSN)1097-0282
  • Ismail, M. A., Rodger, P. M., & Rodger, A. (2000). Drug self-assembly on DNA: Sequence effects with trans-bis -(4- N -methylpyridiniumyl) diphenyl Porphyrin and Hoechst 33258. Journal of Biomolecular Structure & Dynamics, 11, 335–348.10.1080/07391102.2000.10506639
  • Izbicka, E., Wheelhouse, R. T., Raymond, E., Davidson, K. K., Lawrence, R. A., Sun, D., … Von Hoff, D. D. (1999). Effects of cationic porphyrins as G-quadruplex interactive agents in human tumor cells. Cancer Research, 59, 639–644.
  • Jeppesen, C., & Nielsen, P. E. (1989). Photofootprinting of drug-binding sites on DNA using diazo- and azido-9-aminoacridine derivatives. European Journal of Biochemistry, 182, 437–444.10.1111/ejb.1989.182.issue-2
  • Jin, B., Lee, H. M., Lee, Y.-A., Ko, J. H., Kim, C., & Kim, S. K. (2005). Simultaneous binding of meso-tetrakis (N-methylpyridinium-4-yl) porphyrin and 4′,6-diamidino-2-phenylindole at the minor grooves of poly (dA)·poly (dT) and Poly[d(A-T)2]: Fluorescence resonance energy transfer between DNA bound drugs. Journal of American Chemistry Society, 127, 2417–2424.10.1021/ja044555w
  • Johnson, I. M., Bhuvan Kumar, S. G., & Malathi, R. (2012). De-intercalation of ethidium bromide and acridine orange by xanthine derivatives and their modulatory effect on anticancer agents: A study of DNA-directed toxicity enlightened by time correlated single photon counting. Journal of Biomolecular Structure and Dynamics, 20, 677–685.
  • Karimata, H., Nakano, S.-I., Ohmichi, T., Kawakami, J., & Sugimoto, N. (2004). Stabilization of a DNA duplex under molecular crowding conditions of PEG. Nucleic Acids Symposium Series, 48, 107–108.10.1093/nass/48.1.107
  • Kim, H.-K., Cho, T.-S., & Kim, S. K. (1996). Ionic strength dependent binding mode of 9-aminoacridine to DNA. Bulletin of the Korean Chemical Society, 17, 358–362.
  • Kimpton, P., Corbitti, G., & Morris, D. J. (1990). Comparison of polyethylene glycol precipitation and ultracentrifugation for recovery of cytomegalovirus from urine prior to detection of DNA by dot-blot hybridisation. Journal of Virological Methods, 28, 141–145.10.1016/0166-0934(90)90028-E
  • Kubista, M., Aakerman, B., & Albinsson, Bo. (1989). Characterization of the electronic structure of 4′,6-diamidino-2-phenylindole. Journal of American Chemistry Society, 111, 7031–7035.10.1021/ja00200a020
  • Kubista, M., Akerman, B., & Norden, B. (1987). Characterization of interaction between DNA and 4′,6-diamidino-2-phenylindoleby optical spectroscopy. Biochemistry, 26, 4545–4553.10.1021/bi00388a057
  • Kuroda, R., & Tanaka, H. (1994). DNA–porphyrin interactions probed by induced CD spectroscopy. Journal of the Chemical Society, Chemical Communications Articles, 1575–1576.
  • Kuznetsova, I. M., Turoverov, K. K., & Uversky, V. N. (2014). What macromolecular crowding can do to a protein. International Journal of Molecular Sciences, 15, 23090–23140.10.3390/ijms151223090
  • Lee, M.-J., Jin, B., Lee, H. M., Jung, M. J., Kim, S. K., & Kim, J. M. (2008). Direct stacking of non-metawllic planar porphyrin to DNA. Bulletin of the Korean Chemical Society, 29, 1533–1538.
  • Lee, S., Jeon, S. H., Kim, B. J., Han, S. W., Jang, H. G., & Kim, S. K. (2001). Classification of CD and absorption spectra in the Soret band of H2TMPyP bound to various synthetic polynucleotides. Biophysical Chemistry, 92, 35–45.10.1016/S0301-4622(01)00181-8
  • Lee, Y.-A., Cho, T.-S., Kim, C., Han, S. W., & Kim, S. K. (2002). Mode of meso-tetrakis (N-methylpyridinium-4-yl) porphyrin to poly [d(I-C)2]: Effect of amino group at the minor groove of poly [d(G-C)2] on the porphyrin-DNA interaction. Journal of Physical Chemistry B, 106, 11351–11355.10.1021/jp025924i
  • Lipscomb, L. A., Zhou, F. X., Presnell, S. R., Woo, R. J., Peek, M. E., Plaskon, R. R., & Williams, L. D. (1996). Structure of a DNA-porphyrin complex. Biochemistry, 35, 2818–2823.10.1021/bi952443z
  • Lis, J. T., & Schlief, R. (1975). Size fractionation of double-stranded DNA by precipitation with polyethylene glycol. Nucleic Acids Research, 2, 383–389.10.1093/nar/2.3.383
  • Marzilli, L. G. (1990). Medical aspects of DNA-porphyrin interactions. New Journal of Chemistry, 14, 409–420.
  • Marzilli, L. G., Banville, L. D., & Wilson, W. D. (1986). Pronounced proton and phosphorus-31 NMR spectral changes on meso-tetrakis (N-methylpyridinium-4-yl) porphyrin binding to poly [d(G-C)]·poly[d(G-C)] and to three tetradecaoligodeoxyribonucleotides: Evidence for symmetric, selective binding to 5′CG3′ sequences. Journal of American Chemistry Society, 108, 4188–4192.10.1021/ja00274a056
  • Minton, A. P. (2001). The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. The Journal of Biological Chemistry, 276, 10577–10580.10.1074/jbc.R100005200
  • Mocz, G., & Ross, J. A. (2013). Fluorescence techniques in analysis of protein–ligand interactions. Methods in Molecular Biology, 1008, 169–210.10.1007/978-1-62703-398-5
  • Nakano, S., Karimata, H., Ohmichi, T., Kawakami, J., & Sugimoto, N. J. (2004). The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability. Journal of American Chemistry Society, 126, 14330–14331.10.1021/ja0463029
  • Norden, B., Kubista, M., & Kurucsev, T. (1992). Linear dichroism spectroscopy of nucleic acids. Quarterly Reviews of Biophysics, 25, 51–170.10.1017/S0033583500004728
  • Orgis, M., Brunner, S., Schuller, S., Kircheis, R., & Wagner, E. (1999). PEGylated DNA/transferrin-PEI complexes: Reduced interaction with blood components, extended circulation in blood and potential for systemic gene delivery. Gene Therapy, 6, 595–605.
  • Pasternack, R. F. (2003). Circular dichroism and the interactions of water soluble porphyrins with DNA–A minireview. Chirality, 15, 329–332.10.1002/(ISSN)1520-636X
  • Pasternack, R. F., & Gibbs, E. J. (1996). Porphyrin and metalloporphyrin interactions with nucleic acids. In A. Sigel & H. Sigel (Eds.), Metal ions in biological systems (Vol. 33, pp. 367–397). New York, NY: Marcel Dekker.
  • Qiao, C., Bi, S., Sun, Y., Song, D., Zhang, H., & Zhou, W. (2008). Study of interactions of anthraquinones with DNA using ethidium bromide as a fluorescence probe. Spectrochimica Acta Part A, 70, 136–143.10.1016/j.saa.2007.07.038
  • Schneider, H. J., & Wang, M. (1994). DNA interactions with porphyrins bearing ammonium side chains. The Journal of Organic Chemistry, 59, 7473–7478.10.1021/jo00103a047
  • Sehlstedt, U., Kim, S. K., Carter, P., Goodisman, J., Vollano, J. K., Nordén, B., & Dabrowiak, J. C. (1994). Interaction of cationic porphyrins with DNA. Biochemistry, 33, 417–426.10.1021/bi00168a005
  • Spink, C. H., & Chaires, J. B. (1995). Selective stabilization of triplex DNA by poly (ethylene glycols). Journal of American Chemistry Society, 117, 12887–12888.10.1021/ja00156a038
  • Spink, C. H., & Chaires, J. B. (1999). Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA. Biochemistry, 38, 496–508.10.1021/bi9820154
  • Tuite, E., & Norden, B. (1995). Intercalative interactions of ethidium dyes with triplex structures. Bioorganic & Medicinal Chemistry, 3, 701–711.10.1016/0968-0896(95)00061-K
  • Ughetto, G., Wang, A. H., Quigley, G. J., Van der, M. G. A., Van Boom, J. H., & Rich, A. (1985). A comparison of the structure of echinomycin and triostin A complexed to a DNA fragment. Nucleic Acids Research, 13, 2305–2323.10.1093/nar/13.7.2305
  • Vardevanyan, P. O., Antonyan, A. P., Parsadanyan, M. A., Shahinyan, M. A., Hambardzumyan, L. A., Torosyan, M. A., & Karapetian, A. T. (2012). The influence of GC/AT composition on intercalating and semi-intercalating binding of ehtidium bromide to DNA. Journal of the Brazilian Chemical Society, 23, 2016–2020.10.1590/S0103-50532012005000076
  • Vardevanyan, P. O., Antonyan, A. P., Parsadanyan, M. A., Torosyan, M. A., & Karapetian, A. T. (2016). Joint interaction of ethidium bromide and methylene blue with DNA. The effect of ionic strength on binding thermodynamic parameter. Journal of Biomolecular Structure and Dynamics, 34, 1377–1382.10.1080/07391102.2015.1079557
  • Vardevanyan, P. O., Arakelyan, V. B., Parsadanyan, M. A., Antonyan, A. P., Hovhannisyan, G. G., & Shahinyan, M. A. (2014). Analysis of experimental binding curves of EtBr with single- and double-stranded DNA at small fillings. Modern Physics Letters B, 28, 1450178–1450188.10.1142/S0217984914501784
  • Wei, C., Jia, G., Yuan, J., Feng, Z., & Can, L. (2006). A spectroscopic study on the interactions of porphyrin with G-quadruplex DNAs. Biochemistry, 45, 6681–6691.10.1021/bi052356z
  • Wei, C., Jia, G., Zhou, J., Han, G., & Li, C. (2009). Evidence for the binding mode of porphyrins to G-quadruplex DNA. Physical Chemistry Chemical Physics, 11, 4025–4032.10.1039/b901027 k
  • Yun, B. H., Jeon, S. H., Cho, T.-S., Yi, Y., Sehlstedt, U., & Kim, S. K. (1998). Binding mode of porphyrins to poly [d(A-T)2] and poly [d(G-C)2]. Biophysical Chemistry, 70, 1–10.10.1016/S0301-4622(97)00031-8
  • Zhang, G., Hu, X., & Fu, P. (2012). Spectroscopic studies on the interaction between carbaryl and calf thymus DNA with the use of ethidium bromide as a fluorescence probe. Journal of Photochemistry and Photobiology B, 108, 53–61.10.1016/j.jphotobiol.2011.12.011
  • Zhou, H. X., Rivas, G., & Minton, A. P. (2008). Macromolecular crowding and confinement: Biochemical, biophysical, and potential physiological consequences. Annual Review of Biophyscis, 37, 375–397.10.1146/annurev.biophys.37.032807.125817

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.