全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...

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

DOI: 10.4236/jbpc.2018.93003, PP. 23-40

Keywords: Active Demethylation, DNA Catalysis, Symmetry Elements, (Anti)Parallel Modified DNA and RNA, Inhibition of Genetic Information

Full-Text   Cite this paper   Add to My Lib

Abstract:

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).

References

[1]  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
[2]  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
[3]  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
[4]  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
[5]  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
[6]  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
[7]  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
[8]  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
[9]  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
[10]  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
[11]  Fonseca Guerra, C. (2000) Structure and Bonding of DNA. Ph.D. Thesis, Free University of Amsterdam, Amsterdam.
[12]  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
[13]  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
[14]  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
[15]  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
[16]  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
[17]  Knouse, K.W., deGruyter, J.N., Schmidt, M.A., Zheng, B., Vantourout, J.C., Kingston, C., Mercer, S.E., Mcdonald, I.M., Olson, R.E., Zhu, Ye., et al. (2018) Unlocking P(V): Reagents for Chiral Phosphorothioate Synthesis. Science, 361, 1234-1238.
https://doi.org/10.1126/science.aau3369
[18]  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
[19]  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
[20]  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
[21]  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
[22]  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
[23]  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
[24]  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
[25]  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
[26]  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
[27]  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
[28]  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
[29]  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
[30]  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
[31]  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
[32]  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
[33]  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<75::AID-ANIE75>3.0.CO;2-R
[34]  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

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133