A conformational B-Z DNA study monitored with phosphatemethylated DNA as a model for epigenetic dynamics focused on 5-(hydroxy)methylcytosine

Henk M. Buck

Kasteel Twikkelerf 94, Tilburg, The Netherlands.

DOI: 10.4236/jbpc.2013.42005                

Abstract

This study was directed on the B- into Z-DNA isomerization with alternating CG sequences monitored with artificial DNA model-systems based on methylation of the phosphate backbone. The chemical concept for this transition wherein shielding of the oxygen anions of the backbone phosphates plays an essential role, resulted in the preparation of the phosphatemethylated d(CpG). Even on this primitive level of only two base pair long, the B-Z conformational aspects of this self-complementary duplex could be described in solution with nuclear magnetic resonance (NMR) and circular dichroism (CD) measurements. The exclusivity of this choice became clear after synthesizing phosphatemethylated DNA with longer alternating CG fragments. It could be shown that conflicting conformational effects of the CG and GC fragments resulted in an overall B structure of the phosphatemethylated tetramer d(C_PG_PC_PG). From our model considerations, it is clear that the internal stress introduced by the alternating CG sequences will be promoted by a complete shielding of the phosphate backbone. Elimination of this effect may be realized by a site-specific phosphate shielding. The role of the anti-syn isomerization of G in the CG fragments is clarified by methylation of the phosphate group. This anti-syn transition is absent in corresponding methylphosphonates, suggesting an exclusive role for base-backbone coordination via hydrogen bonding. In addition, we propose that the B- into Z-DNA interconversion may offer a mechanistic view for differences in dynamics between cytosine and its epigenetic derivative 5-methylcytosine. This mechanism has been extended to the demethylation of 5-methylcytosine and the exchange of information between the new epigenetic base, 5-hydroxymethylcytosine and the DNA backbone via an intramolecular phosphorylation. The role of 5-hydroxymethylcytosine in Alzheimer disease has been briefly discussed. In our opinion, this study can be considered as a new dynamic concept for epigenetics based on the dynamics of the B-Z transition in natural and phosphatemethylated DNA.

Keywords

B-Z DNA Transition; Artificial DNA’s; Epigenetics; Phosphorylation-Demethylation; Alzheimer

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Eryazici, I., Yildirim, I., Schatz, G.C. and Nguyen, S.T. (2012) Enhancing the melting properties of small molecule-DNA hybrids through designed hydrophobic interactions: An experimental-computational study. Journal of the American Chemistry Society, 134, 7450-7458. doi:10.1021/ja300322a
[2]	Koole, L.H., van Genderen, M.H.P., Reiniers, R.G. and Buck, H.M. (1987) Enhanced stability of Watson & Crick duplex structure by methylation of the phosphates groups in one strand. Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen, 90, 41-46.
[3]	Moody, M.R., van Genderen, M.H.P. and Buck, H.M. (1990) Thermodynamics of polymer duplexes between phosphate-methylated DNA and natural DNA. Biopolymers, 30, 609-618. doi:10.1002/bip.360300513
[4]	van Genderen, M.H.P., Koole, L.H. and Buck, H.M. (1988) Duplex stability of hybrids between phosphatemethylated DNA and natural RNA. Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen, 91, 53-57.
[5]	van Genderen, M.H.P. (1989) Structure and stability of phosphate-methylated DNA duplexes: model systems for specific DNA-protein interaction and conformational transmission. Thesis, Eindhoven University of Technology, Eindhoven.
[6]	van Genderen, M.H.P., Koole, L.H. and Buck, H.M. (1989) Hybridization of phosphatemethylated DNA and natural oligonucleotides. Implications for protein-induced DNA duplex destabilization. Recueil Travaux Chimiques des Pays-Bas, 108, 28-35. doi:10.1002/recl.19891080106
[7]	Buck, H.M. (1996) Phosphate-methylated DNA: A unique oligodeoxynucleotide as compared with other modified DNAs. Proceedings of the Koninklijke Nederlandse Akademie van Wetenschappen, 99, 145-153.
[8]	Buck, H.M. (2004) The chemical and biochemical properties of methylphosphotriester DNA. Nucleosides, Nucleotides and Nucleic Acids, 23, 1833-1847. doi:10.1081/NCN-200040620
[9]	Buck, H.M. (2007) The chemical and biochemical properties of methylphosphotriester DNA and RNA in comparison with their corresponding methylphosphonates. A dynamic model description. Nucleosides, Nucleotides and Nucleic Acids, 26, 205-222. doi:10.1080/15257770601112812
[10]	Beaucage, S.L. and Caruthers, M.H. (1981) Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Letters, 22, 1859-1862. doi:10.1016/S0040-4039(01)90461-7
[11]	Koole, L.H., Moody, H.M., Broeders, N.L.H.L., Quaedflieg, P.J.L.M., Kuijpers, W.H.A., van Genderen, M.H.P., Coenen, A.J.J.M., van der Wal, S. and Buck, H.M. (1989) Synthesis of phosphate-methylated DNA fragments using 9-fluorenylmethoxycarbonyl as transient base protecting group. Journal of Organic Chemistry, 54, 1657-1664. doi:10.1021/jo00268a030
[12]	Koole, L.H., van Genderen, M.H.P. and Buck, H.M. (1987) A parallel right handed duplex of the hexamer d(TPTPTPTPTPT) with phosphate triester linkages. Journal of the American Chemistry Society, 109, 3916-3921. doi:10.1021/ja00247a015
[13]	Maruyama, Y., Yoshida, N. and Hirata, F., (2010) Revisiting the salt-induced conformational change of DNA with 3D-RISM theory. Journal of Physical Chemistry B, 114, 6464-6471. doi:10.1021/jp912141u
[14]	Kastenholz, M.A., Schwartz, T.U. and Hünenberger, P.H. (2006) The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation. Biophysical Journal, 91, 2976-2990. doi:10.1529/biophysj.106.083667
[15]	Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G. and Rich, A. (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature, 282, 680-686. doi:10.1038/282680a0
[16]	van Lier, J.J.C., Smits, M.T. and Buck, H.M. (1983) B-Z Transition in methylated DNA: A quantum-chemical study. European Journal of Biochememistry, 132, 55-62. doi:10.1111/j.1432-1033.1983.tb07324.x
[17]	Ha, S.C., Lowenhaupt, K., Rich, A., Kim, Y.-G. and Kim, K.K. (2005) Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature, 437, 1183-1186. doi:10.1038/nature04088
[18]	Quaedflieg, P.J.L.M., Koole, L.H., van Genderen, M.H.P. and Buck, H.M. (1989) A structural study of phosphatemethylated d(CPG)n and d(GPC)n DNA oligomers. Implication of phosphate shielding for the isomerization of B-DNA into Z-DNA. Recueil Travaux Chimiques des Pays-Bas, 108, 421-423. doi:10.1002/recl.19891081107
[19]	Shimada, N., Yamamoto, M., Kano, A. and Maruyama A. (2010) Cationic graft copolymer as a DNA B-Z transition inducer: Effect of copolymer structure. Biomacromolecules, 11, 3043-3048. doi:10.1021/bm100870b
[20]	Gong, L., Jang, Y.J., Kim, J. and Kim, S.K. (2012) Z-form DNA specific binding geometry of Zn(II) mesotetrakis (N-methylpyridinium-4-yl) porphyrin probed by linear dichroism spectroscopy. Journal of Physical Chemistry B, 116, 9619-9626. doi:10.1021/jp3041346
[21]	Ramakrishnan, B. and Viswamitra, M.A. (1988) Crystal and molecular structure of the ammonium salt of the dinucleoside monophosphate d(CPG). Journal of Biomolecular Structure & Dynamics, 6, 511-523. doi:10.1080/07391102.1988.10506504
[22]	Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., van der Marel, G., van Boom, J.H. and Rich, A. (1981) Left-handed double helical DNA: Variations in the backbone conformation. Science, 211, 171-176. doi:10.1126/science.7444458
[23]	Koole, L.H., Buck, H.M., Kanters, J.A. and Schouten, A. (1988) Molecular conformation of 2’-deoxy-3’,5’-di-O-acetyl guanosine. Crystal structure and high resolution proton nuclear magnetic resonance investigations. Canadian Journal of Chemistry, 66, 2634-2639. doi:10.1139/v88-413
[24]	Koole, L.H., de Boer, H., de Haan, J.W., Haasnoot, C.A.G., van Dael, P. and Buck, H.M. (1986) Intramolecular basebackbone association in 8-bromo-2’,3’-O-isopropylidene-adenosine. Detection of an O(5’)-H???N(3) spin-spin coupling. Journal of the Chemical Society, Chemical Communications, 4, 362-364. doi:10.1039/c39860000362
[25]	Fujii, S., Fujiwara, T. and Tomita, K. (1976) Structural studies on the two forms of 8-bromo-2’,3’-O-isopropylide- neadenosine. Nucleic Acids Research, 3, 1985-1996. doi:10.1093/nar/3.8.1985
[26]	Callahan, L., Han, F.-S., Watt, W., Duchamp, D., Kézdy, F.J. and Agarwal, K. (1986) B-to Z-DNA transition probed by oligonucleotides containing methylphosphonates. Proceedings of the National Academy of Sciences USA, 83, 1617-1621. doi:10.1073/pnas.83.6.1617
[27]	Rijkers, D. (1990) Synthesis of model systems for B-Z transition of DNA. Graduate Study, Eindhoven University of Technology, Eindhoven.
[28]	Lee, Y.-M., Kim, H.-E., Park, C.-J., Lee, A.-R., Ahn, H.- C., Cho, S.J., Choi, K.-H., Choi, B.-S. and 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 Chemistry Society, 134, 5276-5283. doi:10.1021/ja211581b
[29]	Shi, Y., Lan, F., Matson, C., Mulligan, P., Whetstine, J.R., Cole, P.A., Casero, R.A. and Shi, Y. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell, 119, 941-953. doi:10.1016/j.cell.2004.12.012
[30]	Viré, E., Brenner, C., Deplus, R., Blanchon, L., Fraga, M., Didelot, C., Morey, L., van Eynde, A., Bernard, D., Vanderwinden, J.-M., Bollen, M., Esteller, M., Di Croce, L., de Launoit, Y. and Fuks, F. (2006) The polycomb group protein EZH2 directly controls DNA methylation. Nature, 439, 871-874. doi:10.1038/nature04431
[31]	Chang, Y., Sun, L., Kokura, K., Horton, J.R., Fukuda, M., Espejo, A., Izumi, V., Koomen, J.M., Bedford, M.T., Zhang, X., Shinkai, Y., Fang, J. and Cheng, X. (2011) MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/ G9a. Nature Communications, 2, 533. doi:10.1038/ncomms1549
[32]	Buck, H.M. (2011) DNA systems for B-Z transition and their significance as epigenetic model: The fundamental role of the methyl group. Nucleosides, Nucleotides and Nucleic Acids, 30, 918-944. doi:10.1080/15257770.2011.620580
[33]	Fujii, S., Wang, A.H.-J., van der Marel, G., van Boom, J.H. and Rich, A. (1982) Molecular structure of (m5dC-dG)3: The role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA. Nucleic Acids Research, 10, 7879-7892. doi:10.1093/nar/10.23.7879
[34]	Mayer-Jung, C., Moras, D. and Timsit, Y. (1998) Hydra- tion and recognition of methylated CPG steps in DNA. European Molecular Biology Organization Journal, 17, 2709-2718.
[35]	Ho, K.L., McNae, I.W., Schmiedeberg, L., Klose, R.J., Bird, A.P. and Walkinshaw, M.D. (2008) MeCP2 binding to DNA depends upon hydration at methyl-CPG. Molecular Cell, 29, 525-531. doi:10.1016/j.molcel.2007.12.028
[36]	McEwen, K.R. and Ferguson-Smith, A.C. (2010) Distinguishing epigenetic marks of developmental and imprenting regulation. Epigenetics & Chromatin, 3, 2. doi:10.1186/1756-8935-3-2
[37]	Van Loenhout, M.T.J., de Grunt, M.V. and Dekker, C. (2012) Dynamics of DNA supercoils. Science, 338, 94-97. doi:10.1126/science.1225810
[38]	Blackledge, N.P., Zhou, J.C., Tolstorukov, M.Y., Farcas, A.M., Park, P.J. and Klose, R.J. (2010) CPG islands recruit a histone H3 lysine 36 demethylase. Molecular Cell, 38, 179-190. doi:10.1016/j.molcel.2010.04.009
[39]	Li, F., Martienssen, R. and Can, W.Z. (2011) Coordination of DNA replication and histone modification by the Rik1-Dos2 complex. Nature, 475, 244-248. doi:10.1038/nature10161
[40]	Jin, S.G., Wu, X., Li, A.X. and Pfeifer, G.P. (2011) Genomic mapping of 5-hydroxymethylcytosine in the hu- man brain. Nucleic Acids Research, 39, 5015-5024. doi:10.1093/nar/gkr120
[41]	Ito, S., Shen, L., Dai, Q., Wu, S.C., Collins, L.B., Swenberg, J.A., He, C. and Zhang, Y. (2011) Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science, 333, 1300-1303. doi:10.1126/science.1210597
[42]	Chouliaras, L., van den Hove, D.L.A., Kennis, G., Keitel, S., Hof, P.R., van Os, J., Steinbusch, H.W.M., Schmitz, C. and Rutten, B.P.F. (2012) Age-related increase in levels of 5-hydroxymethylcytosine in mouse hippocampus is prevented by caloric restriction. Current Alzheimer Research, 9, 536-544.
[43]	van den Hove, D.L.A., Chouliaras, L. and Rutten B.P.F. (2012) The role of 5-hydroxymethylcytosine in aging and Alzheimer’s disease: Current status and prospects for the future studies. Current Alzheimer Research, 9, 545-549.
[44]	Tahiliani, M., Koh, K.P., Shen, Y., Pastor, W.A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L.M., Liu, D.R., Aravind, L. and Rao, A. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science, 324, 930-935. doi:10.1126/science.1170116
[45]	Frauer, C., Hoffmann, T., Bultmann, S., Casa, V., Cardoso, C., Antes, I. and Leonhardt, H. (2011) Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS One, 6, e21306. doi:10.1371/journal.pone.0021306
[46]	Castelijns, M.M.C.F., Schipper, P., van Aken, D. and Buck, H.M. (1981) Dynamic equilibriums between pentavalent protonated oxyphosphoranes and their isomeric tetravalent enol phosphonium ions via inter-and intramolecular proton transfer. Journal of Organic Chemistry, 46, 47-53. doi:10.1021/jo00314a010
[47]	Nie, C.L., Wei, Y., Chen, X., Liu, Y.Y., Dui, W., Liu, Y. Davies, M.C., Tendler, S.J. and He, R.G. (2007) Formaldehyde at low concentration induces protein tau into globular amyloid-like aggregates in vitro and in vivo. PloS One, 2, Article ID: e629. doi:10.1371/journal.pone.0000629