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Research Articles

Effect of periphery cationic substituents of porphyrin on the B-Z transition of poly[d(A-T)2], poly[d(G-C)2] and their binding modes

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Pages 518-525 | Received 21 Oct 2019, Accepted 28 Dec 2019, Published online: 24 Feb 2020

References

  • Bacolla, A., & Wells, R. D. (2004). Non-B DNA conformations, genomic rearrangements, and human disease. Journal of Biological Chemistry, 279(46), 47411–47414. doi:10.1074/jbc.R400028200
  • Bae, S., Kim, D., Kim, K. K., Kim, Y.-G., & Hohng, S. (2011). Intrinsic Z-DNA Is Stabilized by the Conformational Selection Mechanism of Z-DNA-Binding Proteins. Journal of the American Chemical Society, 133(4), 668–671. doi:10.1021/ja107498y
  • Belotserkovskii, B. P., Mirkin, S. M., & Hanawalt, P. C. (2013). DNA sequences that interfere with transcription: Implications for genome function and stability. Chemical Reviews, 113(11), 8620–8637. doi:10.1021/cr400078y
  • Choi, J., & Majima, T. (2011). Conformational changes of non-B DNA. Chemical Society Reviews, 40(12), 5893–5909. doi:10.1039/c1cs15153c
  • Doluca, O., Withers, J. M., & Filichev, V. V. (2013). Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chemical Reviews, 113(5), 3044–3083. doi:10.1021/cr300225q
  • Ha, S. C., Choi, J., Hwang, H.-Y., Rich, A., Kim, Y.-G., & Kim, K. K. (2009). The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ alpha(ADAR1). Nucleic Acids Research, 37(2), 629–637. doi:10.1093/nar/gkn976
  • Ha, S. C., Lokanath, N. K., Van Quyen, D., Wu, C. A., Lowenhaupt, K., Rich, A., … Kim, K. K. (2004). A poxvirus protein forms a complex with left-handed Z-DNA: Crystal structure of a Yatapoxvirus Zalpha bound to DNA. Proceedings of the National Academy of Sciences, 101(40), 14367–14372. doi:10.1073/pnas.0405586101
  • Herbert, A., & Rich, A. (1996). The biology of left-handed Z-DNA. Journal of Biological Chemistry, 271(20), 11595–11598. doi:10.1074/jbc.271.20.11595
  • Jang, Y. J., Lee, C., & Kim, S. K. (2015). Formation of Poly[d(A-T)2] specific Z-DNA by a cationic porphyrin. Scientific Reports., 5, 9943. doi:10.1038/srep09943
  • Jin, B., Ahn, J. E., Ko, J. H., Wang, W., Han, S. W., & Kim, S. K. (2008). Effect of position and number of positive charges on the intercalation and stacking of porphyrin to poly[d(G-C)2], poly[d(A-T)2], and native DNA. The Journal of Physical Chemistry B, 112(49), 15875–15882. doi:10.1021/jp801274u
  • Jung, J.-A., Lee, S. H., Jin, B., Sohn, Y., & Kim, S. K. (2010). Effect of number and position of positive charges on the stacking of porphyrin along poly[d(A-T)2] at high binding densities. The Journal of Physical Chemistry B, 114(22), 7641–7648. doi:10.1021/jp1009687
  • Kwon, J. A., & Rich, A. (2005). Biological function of the vaccinia virus Z-DNA-binding protein E3L: Gene transactivation and antiapoptotic activity in HeLa cells. Proceedings of the National Academy of Sciences, 102(36), 12759–12764. doi:10.1073/pnas.0506011102
  • Lee, A.-R., Kim, N.-H., Seo, Y.-J., Choi, S.-R., & Lee, J.-H. (2018). Thermodynamic Model for B-Z Transition of DNA Induced by Z-DNA Binding Proteins. Molecules, 23(11), 2748–2760. doi:10.3390/molecules23112748
  • Lee, Y.-A., Kim, J.-O., Cho, T.-S., Song, R., & Kim, S. K. (2003). Binding of meso-tetrakis(N-methylpyridium-4-yl)porphyrin to triplex oligonucleotides: Evidence for the porphyrin stacking in the major groove. Journal of the American Chemical Society, 125(27), 8106–8107. doi:10.1021/ja034499j
  • Lee, Y.-M., Kim, H.-E., Park, C.-J., Lee, A.-R., Ahn, H.-C., Cho, S. J., … Lee, J.-H. (2012). NMR Study on the B–Z Junction Formation of DNA Duplexes Induced by Z-DNA Binding Domain of Human ADAR1. Journal of the American Chemical Society, 134(11), 5276–5283. doi:10.1021/ja211581b
  • Milo, M. L., Dmitry, S., & Ahmed, H. Z. (2009). Structural ultrafast dynamics of macromolecules: Diffraction of free DNA and effect of hydration. Physical Chemistry Chemical Physics., 11, 10619–10632.
  • Pasternack, R. F. (2003). Circular dichroism and the interactions of water soluble porphyrins with DNA-a minireview. Chirality, 15(4), 329–332. doi:10.1002/chir.10206
  • Pasternack, R. F., Giannetto, A., Pagano, P., & Gibbs, E. J. (1991). Self-assembly of porphyrins on nucleic acids and polypeptides. Journal of the American Chemical Society, 113(20), 7799–7800. doi:10.1021/ja00020a072
  • Pohl, F. M., & Jovin, T. M. (1972). Salt-induced co-operative conformational change of a synthetic DNA: Equilibrium and kinetic studies with poly(dG-dC). Journal of Molecular Biology., 67(3), 375–396. doi:10.1016/0022-2836(72)90457-3
  • Premilat, S., & Albiser, G. (2001). A new D-DNA form of poly(dA-dT)⋅poly(dA-dT): an A-DNA type structure with reversed Hoogsteen pairing. European Biophysics Journal., 30(6), 404–410. doi:10.1007/s002490100170
  • Rich, A., & Zhang, S. (2003). Z-DNA: The long road to biological function. Nature Reviews Genetics, 4(7), 566–572. doi:10.1038/nrg1115
  • Schwartz, T., Behlke, J., Lowenhaupt, K., Heinemann, U., & Rich, A. (2001). Structure of the DLM-1 − Z-DNA complex reveals a conserved family of Z-DNA-binding proteins. Nature Structural Biology, 8(9), 761–765.
  • Shin, J. H., Hwang, Y. M., Jang, Y. J., & Kim, S. K. (2016). Length and sequence effect on the B-Z transition of [d(A-T)n]2 oligonucleotide induced by a cationic porphyrin. Biophysical Chemistry., 219, 38–42. doi:10.1016/j.bpc.2016.06.007
  • Wang, A. H. J., Quigley, G. J., Kolpak, F. J., Crawford, J. L., Van Boom, J. H., Van Der Marel, G., & Rich, A. (1979). Molecular structure of left-handed double helical DNA fragment at atomic resolution. Nature, 282(5740), 680–686. doi:10.1038/282680a0

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