DNA-Like Duplex Structures Derived from Chemistry Based on 2’-Deoxy-Cytidine: A New Model for Base-Specific Inhibition of G and C on DNA and RNA Level — Oak Academic Publishing
Research ArticleOpen AccessGoogle Scholar indexed
DNA-Like Duplex Structures Derived from Chemistry Based on 2’-Deoxy-Cytidine: A New Model for Base-Specific Inhibition of G and C on DNA and RNA Level
The new epigenetic elements 5-hydroxymethyl-dC, 5-formyl-dC, and 5-car - boxy-dC may be considered as intermediates of an active demethylation process. A comprehensive mechanistic model is given for the C-C bond cleavage focused on the chemistry within the DNA duplex structure. In addition we register spin-off chemistry of this process in evaluating new duplex systems closely related to natural DNA and RNA concerning their hydrogen-bond symmetrization. A model is composed for a base-specific inhibition of G and C on the DNA and RNA level. C-G combinations are of general importance in controlling the dynamics of gene expression. In some way the suggested model systems are related to antisense oligonucleotides (ASOs).
KeywordsActive DemethylationDNA CatalysisSymmetry Elements(Anti)Parallel Modified DNA and RNAInhibition of Genetic Information
Buck, H.M. (2011) DNA Systems for B-Z Transitions and Their Significance as Epigenetic Model: The Fundamental Role of the Methyl Group. Nucleosides, Nucleotides and Nucleic Acids, 30, 918-944. https://doi.org/10.1080/15257770.2011.620580
Kriaucionis, S. and Heintz, N. (2009) The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain. Science, 324, 929-93. https://doi.org/10.1126/science.1169786
Globisch, D., Münzel, M., Müller, M., Michalakis, S., Wager, M., Koch, S., Brückl, T., Biel, M. and Carell, T. ( 2010) Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates. PLoS ONE, 5, e15367. https://doi.org/10.1371/journal.pone.0015367
Münzel, M., Globisch, D. and Carell, T. (2011) 5-Hydroxymethyl-Cytosine, the Sixth Base of the Genome. Angewandte Chemie International Edition, 50, 6460-6468. https://doi.org/10.1002/anie.201101547
Wang, S.R., Long, Y.L., Wang, J.Q., Ge, Y.S., Guo, P., Liu, Y., Tian, T. and Zhou, X. (2014) Systematic Investigations of Different Cytosine Modifications on CpG Dinucleotide Sequences: The Effects on the B-Z Transition. Journal of the American Chemical Society, 136, 56-59. https://doi.org/10.1021/ja4107012
Raiber, E.-A., Murat, P., Chirgadze, D.Y., Beraldi, D., Luisi, B.F. and Balasubramanian, S. (2015) 5-Formylcytosine Alters the Structure of the DNA Double Helix. Nature Structural & Molecular Biology, 22, 44-49. https://doi.org/10.1038/nsmb.2936
Buck, H.M. (2004) The Chemical and Biochemical Properties Methylphosphotriester DNA. Nucleos. Nucleotides and Nucleic Acids, 23, 1833-1847. https://doi.org/10.1081/NCN-200040620
Pfaffeneder, T., Hackner, B., Truss, M., Müller, M., Deiml, C.A., Hagemeier, C. and Carell, T. (2011) The Discovery of 5-Formylcytosine in Embryonic Stem Cell DNA. Angewandte Chemie International Edition, 50, 7008-7012. https://doi.org/10.1002/anie.201103899
Iwan, K., Rahimoff, R., Kirchner, A., Spada, F., Schroder, A.S. ,Kosmatchev, O., Ferizai, S., Steinbacher, J., Parsa, E., Müller, M. and Carell, T. (2018) 5-Formylcytosine to Cytosine Conversion by C-C Bond Cleavage in Vivo. Nature Chemical Biology, 14, 72-78. https://doi.org/10.1038/nchembio.2531
Buck, H.M. (2013) A Conformational B-Z DNA Study Monitored with Phosphatemethylated DNA as a Model for Epigenetic Dynamics Focused on 5-(Hydroxy) Methylcytosine. Journal of Biophysical Chemistry, 4, 37-46. https://doi.org/10.4236/jbpc.2013.42005
Fonseca Guerra, C. (2000) Structure and Bonding of DNA. Ph.D. Thesis, Free University of Amsterdam, Amsterdam.
Schiesser, S., Pfaffeneder, T., Sadeghian, K., Hackner, B., Steigenberger, B., Schroder, A.S., Steinbacher, J., Kashiwazaki, G., Hofner, G., Wanner, K.T., Ochsenfeld, C. and Carell, T. (2013) Deamination, Oxidation, and C-C Bond Cleavage Reactivity of 5-Hydroxymethylcytosine, 5-Formylcytosine, and 5-Carboxycytosine. Journal of the American Chemical Society, 135, 14593-14599. https://doi.org/10.1021/ja403229y
Fonseca Guerra, C., Bickelhaupt, F.M., Snijders, J.G. and Baerends, E.-J. (2000) Hydrogen Bonding in DNA Base Pairs. Reconciliation of Theory and experiment. Journal of the American Chemical Society, 122, 4117-4128. https://doi.org/10.1021/ja993262d
Buck, H.M. (2016) Modified RNA with a Phosphate-Methylated Backbone. A Serious Omission in Our (Retracted) Study at HIV-1 RNA Loops and Integrated DNA. Specific Properties of the (Modified) RNA and DNA Dimers. Journal of Biophysical Chemistry, 7, 30-44. https://doi.org/10.4236/jbpc.2016.71003
Van Genderen, M.H., Hilbers, M.P., Koole, L.H. and Buck, H.M. (1990) Peptide-Induced Parallel DNA Duplexes for Oligopyrimidines. Stereospecificity in Complexation for Oligo(L-Lysine) and Oligo(L-Ornitine). Biochemistry, 29, 7838-7845. https://doi.org/10.1021/bi00486a009
Corey, D.R. (2017) Nusinersen, an Antisence Oligonucleotide Drug for Spinal Muscular Atrophy. Nature Neuroscience, 20, 497-499. https://doi.org/10.1038/nn.4508
Lin, Q.-Y., Mason, J.A., Li, Z., Zhou, W., O’Brien, M.N., Brown, K.A., Jones, M.R., Butun, S., Lee, B., Dravid, V.P., Avdin, K. and Mirkin, C.A. (2018) Building Superlattices from Individual Nanoparticles via Template-Confined DNA-Mediated Assembly. Science, 359, 669-672. https://doi.org/10.1126/science.aaq0591
Tardy-Planechaud, S., Fujimoto, J., Lin, S.S. and Sowers, L.C. (1997) Solid Phase Synthesis and Restriction Endonuclease Cleavage of Oligodeoxynucleotides Containing 5-(Hydroxymethyl)-Cytosine. Nucleic Acids Research, 25, 553-559. https://doi.org/10.1093/nar/25.3.553
Dai, Q. and He, C. (2011) Synthesis of 5-Formyl- and 5-Carboxyl-dC Containing DNA Oligos as Potential Oxidation Products of 5-Hydroxymethylcytosine in DNA. Organic Letters, 13, 3446-3449. https://doi.org/10.1021/ol201189n
Münzel, M., Lischke, U., Stathis, D., Pfaffeneder, T., Gnerlich, F.A., Deiml, C.A., Koch, S.C., Karaghiosoff, K. and Carell, T. (2011) Improved Synthesis and Mutagenicity of Oligonucleotides Containing 5-Hydroxymethylcytosine, 5-Formylcytosine and 5-Carboxylcytosine. Chemistry: A European Journal, 17, 13782-13788. https://doi.org/10.1002/chem.201102782
Steigenberger, B., Schiesser, S., Hackner, B., Brandmayr, C., Laube, S.K., Steinbacher, J., Pfaffeneder, T. and Carell, T. (2013) Synthesis of 5-Hydroxymethyl-, 5-Formyl-, and 5-Carboxycytidine-Triphosphates and Their Incorporation into Oligonucleotides by Polymerase Chain Reaction. Organic Letters, 15, 366-369. https://doi.org/10.1021/ol3033219
Schiesser, S., Hackner, B., Pfaffeneder, T., Müller, M., Hagemeier, C., Truss, M. and Carell, T. (2012) Mechanism and Stem-Cell Activity of 5-Carboxycytosine Decarboxylation Determined by Isotope Tracing. Angewandte Chemie International Edition, 51, 6516-6520. https://doi.org/10.1002/anie.201202583
Errea, I., Calandra, M., Pickard, C.J., Nelson, J.R., Needs, R.J., Li, Y., Liu, H., Zhang, Y., Ma, Y. and Mauri, F. (2016) Quantum Hydrogen-Bond Symmetrization in the Superconducting Hydrogen Sulfide System. Nature, 532, 81-84. https://doi.org/10.1038/nature17175
Buck, H.M. (2017) A Molecular Description of Superconductivity of Sulfur Hydride and Related Systems under High-Pressure Conditions. Open Journal of Physical Chemistry, 7, 9-25. https://doi.org/10.4236/ojpc.2017.71002
Wang, R., Luo, Z., He, K., Delaney, M.O., Chen, D. and Sheng, J. (2016) Base Pairing and Structural Insights into 5-Formylcytosine in RNA Duplex. Nucleic Acids Research, 44, 4968-4977. https://doi.org/10.1093/nar/gkw235
Buck, H.M. (2008) A Combined Experimental, Theoretical, and Van’t Hoff Model Study for Identity, Methyl, Proton, Hydrogen Atom, and Hydride Exchange Reactions. International Journal of Quantum Chemistry, 108, 1601-1614. https://doi.org/10.1002/qua.21683
Sarma, M.H., Gupta, G. and Sarma, R.H. (1986) A Cytosine-Cytosine Base Paired Parallel DNA Double Helix with Thymine-Thymine Bulges. FEBS Letters, 205, 223-229. https://doi.org/10.1016/0014-5793(86)80902-4
Quaedflieg, P.J.L.M., Broeders, N.L.H.L., Koole, L.H., van Genderen, M.H.P. and Buck, H.M. (1990) Conformation of the Phosphate-Methylated DNA Dinucleotides d(CPG) and d(TPC). Formation of a Parallel Miniduplex Exclusively for the S Configuration at Phosphorus. The Journal of Organic Chemistry, 55, 122-127. https://doi.org/10.1021/jo00288a025
Gehring, K., Leroy, J.-L. and Guéron, M. (1993) A Tetrameric DNA Structure with Protonated Cytosine-Cytosine Base Pairs. Nature, 363, 561-565. https://doi.org/10.1038/363561a0
Lieblein, A.L., Kramer, M., Dreuw, A., Fürtig, B. and Schwalbe, H. (2012) The Nature of Hydrogen Bonds in Cytidine H+ Cytidine DNA Base Pairs. Angewandte Chemie International Edition in English, 51, 4067-4077. https://doi.org/10.1002/anie.201200549
Zeraati, M., Langley, D.B., Schofield, P., Moye, A.L., Rouet, R., Hughes, W.E., Bryan, T.M., Dinger, M.E. and Christ, D. (2018) I-motif DNA Structures Are Formed in the Nuclei of Human Cells. Nature Chemistry, 10, 631-637. https://doi.org/10.1038/s41557-018-0046-3
Beijer, F.H., Kooijman, H., Spek, A.L., Sijbesma, R.P. and Meijer, E.W. (1998) Self-Complementarity Achieved through Quadruple Hydrogen Bonding. Angewandte Chemie International Edition in English, 37, 75-78. https://doi.org/10.1002/(SICI)1521-3773(19980202)37:1/2 3.0.CO;2-R
Mo, Y. (2006) Probing the Nature of Hydrogen Bonds in DNA Base Pairs. Journal of Molecular Modeling, 13, 665-672. https://doi.org/10.1007/s00894-005-0021-y