Table of Contents
Retracted

This article has been retracted upon the authors’ request, as they have incorporated the studies of two oncogene promoter regions which form G-quadruplex complex (i.e., Bcl2 and KRAS), but the DNA considered for the studies was not from these regions. The DNA samples got mixed up, and they are from other regions of oncogene promoter. The complete ESI-MS (mass data) and the ITC (microcalorimetry data) were wrong. Since the mistake occurred at the fundamental level (i.e., at the DNA itself), the whole experiment gave wrong data. Additionally, the article was submitted for publication by the author Narayana Nagesh without the knowledge and approval of the other author Arumugam Ganesh Kumar.

ISRN Biophysics
Volume 2012 (2012), Article ID 786596, 12 pages
http://dx.doi.org/10.5402/2012/786596
Research Article

Interaction of TMPyP4, TMPyP3, and TMPyP2 with Intramolecular G-Quadruplex Formed by Promoter Region of Bcl2 and KRAS NHPPE

1Department of Medicinal Chemistry, Centre for Cellular and Molecular Biology, Hyderabad 500007, India
2Marine Biotechnology, National Institute of Ocean Technology, Chennai 600100, India

Received 5 September 2011; Accepted 2 October 2011

Academic Editors: M. P. Evstigneev and M. P. Ponomarenko

Copyright © 2012 Narayana Nagesh and Arumugam Ganesh Kumar. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. Gellert, M. N. Lipsett, and D. R. Davies, “Helix formation by guanylic acid,” Proceedings of the National Academy of Sciences of the United States of America, vol. 48, pp. 2013–2018, 1962. View at Google Scholar · View at Scopus
  2. J. E. Johnson, J. S. Smith, M. L. Kozak, and F. B. Johnson, “In vivo veritas: using yeast to probe the biological functions of G-quadruplexes,” Biochimie, vol. 90, no. 8, pp. 1250–1263, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. J. L. Huppert, “Hunting G-quadruplexes,” Biochimie, vol. 90, no. 8, pp. 1140–1148, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  4. N. Maizels, “Dynamic roles for G4 DNA in the biology of eukaryotic cells,” Nature Structural and Molecular Biology, vol. 13, no. 12, pp. 1055–1059, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  5. S. Burge, G. N. Parkinson, P. Hazel, A. K. Todd, and S. Neidle, “Quadruplex DNA: sequence, topology and structure,” Nucleic Acids Research, vol. 34, no. 19, pp. 5402–5415, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  6. J. Popiołkiewicz, K. Polkowski, J. S. Skierski, and A. P. Mazurek, “In vitro toxicity evaluation in the development of new anticancer drugs—Genistein glycosides,” Cancer Letters, vol. 229, no. 1, pp. 67–75, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  7. D. Gomez, N. Aouali, A. Londoño-Vallejo et al., “Resistance to the short term antiproliferative activity of the G-quadruplex ligand 12459 is associated with telomerase overexpression and telomere capping alteration,” Journal of Biological Chemistry, vol. 278, no. 50, pp. 50554–50562, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  8. P. L. Thao Tran, A. Virgilio, V. Esposito, G. Citarella, J. L. Mergny, and A. Galeone, “Effects of 8-methylguanine on structure, stability and kinetics of formation of tetramolecular quadruplexes,” Biochimie, vol. 93, no. 3, pp. 399–408, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  9. J. Seenisamy, S. Bashyam, V. Gokhale et al., “Design and synthesis of an expanded porphyrin that has selectivity for the c-MYC G-quadruplex structure,” Journal of the American Chemical Society, vol. 127, no. 9, pp. 2944–2959, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  10. I. M. Dixon, F. Lopez, J. P. Estève et al., “Porphyrin derivatives for telomere binding and telomerase inhibition,” ChemBioChem, vol. 6, no. 1, pp. 123–132, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  11. M. J. Carvlin and R. J. Fiel, “Intercalative and nonintercalative binding of large cationic porphyrin ligands to calf thymus DNA,” Nucleic Acids Research, vol. 11, no. 17, pp. 6121–6139, 1983. View at Publisher · View at Google Scholar · View at Scopus
  12. N. Nagesh, R. Buscaglia, J. M. Dettler, and E. A. Lewis, “Studies on the site and mode of TMPyP4 interactions with Bcl-2 promoter sequence G-quadruplexes,” Biophysical Journal, vol. 98, no. 11, pp. 2628–2633, 2010. View at Publisher · View at Google Scholar · View at PubMed
  13. R. D. Gray, L. Petraccone, R. Buscaglia, and J. B. Chaires, “2-aminopurine as a probe for quadruplex loop structures,” Methods in Molecular Biology, vol. 608, pp. 121–136, 2010. View at Google Scholar
  14. N. Nagesh, V. K. Sharma, A. Ganesh Kumar, and E. A. Lewis, “Effect of ionic strength on porphyrin drugs interaction with quadruplex DNA formed by the promoter region of C-myc and Bcl2 oncogenes,” Journal of Nucleic Acids, vol. 2010, Article ID 146418, 9 pages, 2010. View at Publisher · View at Google Scholar · View at PubMed
  15. Y. He, R. D. Neumann, and I. G. Panyutin, “Intramolecular quadruplex conformation of human telomeric DNA assessed with 125I-radioprobing,” Nucleic Acids Research, vol. 32, no. 18, pp. 5359–5367, 2004. View at Publisher · View at Google Scholar · View at PubMed
  16. J. Dai, T. S. Dexheimer, D. Chen et al., “An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution,” Journal of the American Chemical Society, vol. 128, no. 4, pp. 1096–1098, 2006. View at Publisher · View at Google Scholar · View at PubMed
  17. G. D. Fassman, “Nucleic acids,” in Handbook of Biochemistry and Molecular Biology, CRC Press, Cleveland, Ohio, USA, 1975. View at Google Scholar
  18. G.E. Plum, Determination of Oligonucleotide Molar Extinction Coefficients in Current Protocols in Nucleic Acid Chemistry, vol. 7.3, John Wiley & Sons, New York, NY, USA, 2000.
  19. R. F. Pasternack, P. R. Huber, P. Boyd et al., “On the aggregation of meso-substituted water-soluble porphyrins,” Journal of the American Chemical Society, vol. 94, no. 13, pp. 4511–4517, 1972. View at Google Scholar
  20. K. Kalyanasundaram, “Photochemistry of water-soluble porphyrins: comparative study of isomeric tetrapyridyl- and tetrakis(N-methylpyridiniumyl)porphyrins,” Inorganic Chemistry, vol. 23, no. 16, pp. 2453–2459, 1984. View at Google Scholar
  21. P. Hambright, T. Gore, and M. Burton, “Synthesis and characterization of new isomeric water-soluble porphyrins. Tetra(2-N-methylpyridyl)porphine and tetra(3-N-methylpyridyl)porphine,” Inorganic Chemistry, vol. 15, no. 9, pp. 2314–2315, 1976. View at Google Scholar
  22. L. R. Keating and V. A. Szalai, “Parallel-stranded guanine quadruplex interactions with a copper cationic porphyrin,” Biochemistry, vol. 43, no. 50, pp. 15891–15900, 2004. View at Publisher · View at Google Scholar · View at PubMed
  23. W. Likussar and D. F. Boltz, “Theory of continuous variations plots and a new method for spectrophotometric determination of extraction and formation constants,” Analytical Chemistry, vol. 43, no. 10, pp. 1265–1272, 1971. View at Google Scholar
  24. F. Rosu, E. De Pauw, and V. Gabelica, “Electrospray mass spectrometry to study drug-nucleic acids interactions,” Biochimie, vol. 90, no. 7, pp. 1074–1087, 2008. View at Publisher · View at Google Scholar · View at PubMed
  25. N. E. Mukundan, G. Pethö, D. W. Dixon, M. S. Kim, and L. G. Marzilli, “Interactions of an electron-rich tetracationic tentacle porphyrin with calf thymus DNA,” Inorganic Chemistry, vol. 33, no. 21, pp. 4676–4687, 1994. View at Google Scholar
  26. I. Haq, J. O. Trent, B. Z. Chowdhry, and T. C. Jenkins, “Intercalative G-tetraplex stabilization of telomeric DNA by a cationic porphyrin,” Journal of the American Chemical Society, vol. 121, no. 9, pp. 1768–1779, 1999. View at Publisher · View at Google Scholar
  27. N. V. Anantha, M. Azam, and R. D. Sheardy, “Porphyrin binding to quadruplexed T4G4,” Biochemistry, vol. 37, no. 9, pp. 2709–2714, 1998. View at Publisher · View at Google Scholar · View at PubMed
  28. R. F. Pasternack, E. J. Gibbs, and J. J. Villafranca, “Interactions of porphyrins with nucleic acids,” Biochemistry, vol. 22, no. 23, pp. 5409–5417, 1983. View at Google Scholar
  29. M. A. Sari, J. P. Battioni, D. Dupré, D. Mansuy, and J. B. Le Pecq, “Interaction of cationic porphyrins with DNA: importance of the number and position of the charges and minimum structural requirements for intercalation,” Biochemistry, vol. 29, no. 17, pp. 4205–4215, 1990. View at Google Scholar
  30. M. W. Freyer, R. Buscaglia, K. Kaplan, D. Cashman, L. H. Hurley, and E. A. Lewis, “Biophysical studies of the c-MYC NHE III1 promoter: model quadruplex interactions with a cationic porphyrin,” Biophysical Journal, vol. 92, no. 6, pp. 2007–2015, 2007. View at Publisher · View at Google Scholar · View at PubMed
  31. C. Wei, G. Jia, J. Yuan, Z. Feng, and C. Li, “A spectroscopic study on the interactions of porphyrin with G-quadruplex DNAs,” Biochemistry, vol. 45, no. 21, pp. 6681–6691, 2006. View at Publisher · View at Google Scholar · View at PubMed
  32. J. E. Ladbury and B. Z. Chowdhry, “Sensing the heat: the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions,” Chemistry and Biology, vol. 3, no. 10, pp. 791–801, 1996. View at Google Scholar · View at Scopus
  33. S. Cogoi, M. Paramasivam, V. Filichev, I. Géci, E. B. Pedersen, and L. E. Xodo, “Identification of a new G-quadruplex motif in the KRAS promoter and design of pyrene-modified G4-decoys with antiproliferative activity in pancreatic cancer cells,” Journal of Medicinal Chemistry, vol. 52, no. 2, pp. 564–568, 2009. View at Publisher · View at Google Scholar · View at PubMed
  34. T. S. Dexheimer, D. Sun, and L. H. Hurley, “Deconvoluting the structural and drug-recognition complexity of the G-quadruplex-forming region upstream of the bcl-2 P1 promoter,” Journal of the American Chemical Society, vol. 128, no. 16, pp. 5404–5415, 2006. View at Publisher · View at Google Scholar · View at PubMed
  35. E. M. Rezler, J. Seenisamy, S. Bashyam et al., “Telomestatin and diseleno sapphyrin bind selectively to two different forms of the human telomeric G-quadruplex structure,” Journal of the American Chemical Society, vol. 127, no. 26, pp. 9439–9447, 2005. View at Publisher · View at Google Scholar · View at PubMed
  36. H. Han, D. R. Langley, A. Rangan, and L. H. Hurley, “Selective interactions of cationic porphyrins with G-quadruplex structures,” Journal of the American Chemical Society, vol. 123, no. 37, pp. 8902–8913, 2001. View at Publisher · View at Google Scholar
  37. P. Weisman-Shomer, E. Cohen, I. Hershco et al., “The cationic porphyrin TMPyP4 destabilizes the tetraplex form of the fragile X syndrome expanded sequence d(CGG)n,” Nucleic Acids Research, vol. 31, no. 14, pp. 3963–3970, 2003. View at Publisher · View at Google Scholar
  38. R. F. Pasternack, E. J. Gibbs, and J. J. Villafranca, “Interactions of porphyrins with nucleic acids,” Biochemistry, vol. 22, no. 10, pp. 2406–2414, 1983. View at Google Scholar
  39. G. Dougherty, J. Pilbrow, A. Skorobogaty, and R. Kreilick, “EPR and ENDOR study of selected porphyrin- and phthalocyanine-copper complexes,” Journal of Physical Chemistry, vol. 96, no. 23, pp. 9132–9139, 1992. View at Google Scholar
  40. K. Kano, H. Minamizono, T. Kitae, and S. Negi, “Self-aggregation of cationic porphyrins in water. Can π-π stacking interaction overcome electrostatic repulsive force?” Journal of Physical Chemistry A, vol. 101, no. 34, pp. 6118–6124, 1997. View at Google Scholar
  41. Z. Chen, K. W. Zheng, Y. H. Hao, and Z. Tan, “Reduced or diminished stabilization of the telomere G-quadruplex and inhibition of telomerase by small chemical ligands under molecular crowding condition,” Journal of the American Chemical Society, vol. 131, no. 30, pp. 10430–10438, 2009. View at Publisher · View at Google Scholar · View at PubMed
  42. B. P. Hudson, J. Sou, D. J. Berger, and D. R. McMillin, “Luminescence studies of the intercalation of Cu(TMpyP4) into DNA,” Journal of the American Chemical Society, vol. 114, no. 23, pp. 8997–9002, 1992. View at Google Scholar
  43. J. H. Schneider, J. Odo, and K. Nakamoto, “Interactions of water-soluble metalloporphyrins with nucleic acids studied by resonance Raman spectroscopy,” Nucleic Acids Research, vol. 16, no. 21, pp. 10323–10338, 1988. View at Google Scholar
  44. W. R. Scheidt, “Stereochemistry of low-spin cobalt porphyrins. III. The crystal structure and molecular stereochemistry of bis(piperidine)-α,β,γ,δ-tetraphenylporphinatocobalt(II),” Journal of the American Chemical Society, vol. 96, no. 1, pp. 84–89, 1974. View at Google Scholar
  45. L. A. Lipscomb, F. X. Zhou, S. R. Presnell et al., “Structure of a DNA-porphyrin complex,” Biochemistry, vol. 35, no. 9, pp. 2818–2823, 1996. View at Publisher · View at Google Scholar · View at PubMed
  46. J. B. Chaires, “Analysis and interpretation of ligand—DNA binding isotherms,” Methods in Enzymology, vol. 340, pp. 3–22, 2001. View at Publisher · View at Google Scholar
  47. D. Suh and J. B. Chaires, “Criteria for the mode of binding of DNA binding agents,” Bioorganic and Medicinal Chemistry, vol. 3, no. 6, pp. 723–728, 1995. View at Publisher · View at Google Scholar
  48. J. Ren and J. B. Chaires, “Sequence and structural selectivity of nucleic acid binding ligands,” Biochemistry, vol. 38, no. 49, pp. 16067–16075, 1999. View at Publisher · View at Google Scholar
  49. K. M. Hyun, S. D. Choi, S. Lee, and S. K. Kim, “Can energy transfer be an indicator for DNA intercalation?” Biochimica et Biophysica Acta, vol. 1334, no. 2-3, pp. 312–316, 1997. View at Publisher · View at Google Scholar
  50. J. B. Chaires, “A thermodynamic signature for drug-DNA binding mode,” Archives of Biochemistry and Biophysics, vol. 453, no. 1, pp. 26–31, 2006. View at Publisher · View at Google Scholar · View at PubMed