Structure and Function of Noncanonical Nucleobases
Abstract
DNA and RNA contain, next to the four canonical nucleobases, a number of modified nucleosides that extend their chemical information content. RNA is particularly rich in modifications, which is obviously an adaptation to their highly complex and variable functions. In fact, the modified nucleosides and their chemical structures establish a second layer of information which is of central importance to the function of the RNA molecules. Also the chemical diversity of DNA is greater than originally thought. Next to the four canonical bases, the DNA of higher organisms contains a total of four epigenetic bases: m5dC, hm5dC, f5dC und ca5dC. While all cells of an organism contain the same genetic material, their vastly different function and properties inside complex higher organisms require the controlled silencing and activation of cell‐type specific genes. The regulation of the underlying silencing and activation process requires an additional layer of epigenetic information, which is clearly linked to increased chemical diversity. This diversity is provided by the modified non‐canonical nucleosides in both DNA and RNA.
Number of times cited: 72
- Joanna Skiba, Qing Yuan, Alexander Hildebrandt, Heinrich Lang, Damian Trzybiński, Krzysztof Woźniak, Ria K. Balogh, Béla Gyurcsik, Valerije Vrček and Konrad Kowalski, Ferrocenyl GNA Nucleosides: A Bridge between Organic and Organometallic Xeno‐nucleic Acids , ChemPlusChem, 83, 2, (77-86), (2018).
- Christina Schneider, Sidney Becker, Hidenori Okamura, Antony Crisp, Tynchtyk Amatov, Michael Stadlmeier and Thomas Carell, Noncanonical RNA Nucleosides as Molecular Fossils of an Early Earth—Generation by Prebiotic Methylations and Carbamoylations, Angewandte Chemie International Edition, 57, 20, (5943-5946), (2018).
- Christina Schneider, Sidney Becker, Hidenori Okamura, Antony Crisp, Tynchtyk Amatov, Michael Stadlmeier and Thomas Carell, , Angewandte Chemie, 130, 20, (6050-6054), (2018).
- Will McIntyre, Rachel Netzband, Gaston Bonenfant, Jason M Biegel, Clare Miller, Gabriele Fuchs, Eric Henderson, Manoj Arra, Mario Canki, Daniele Fabris and Cara T Pager, Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection, Nucleic Acids Research, (2018).
- Sidney Becker, Christina Schneider, Hidenori Okamura, Antony Crisp, Tynchtyk Amatov, Milan Dejmek and Thomas Carell, Wet-dry cycles enable the parallel origin of canonical and non-canonical nucleosides by continuous synthesis, Nature Communications, 9, 1, (2018).
- Pieter van Delft, Alper Akay, Sabrina M. Huber, Christoph Bueschl, Konrad L. M. Rudolph, Tomás Di Domenico, Rainer Schuhmacher, Eric A. Miska and Shankar Balasubramanian, The Profile and Dynamics of RNA Modifications in Animals, ChemBioChem, 18, 11, (979-984), (2017).
- Elena Eremeeva, Michail Abramov, Lia Margamuljana and Piet Herdewijn, Base‐Modified Nucleic Acids as a Powerful Tool for Synthetic Biology and Biotechnology, Chemistry – A European Journal, 23, 40, (9560-9576), (2017).
- Sebastian Mai, Brennan Ashwood, Philipp Marquetand, Carlos E. Crespo-Hernández and Leticia González, Solvatochromic Effects on the Absorption Spectrum of 2-Thiocytosine, The Journal of Physical Chemistry B, 121, 20, (5187), (2017).
- Daisuke Koyama, Matthew J. Milner and Andrew J. Orr-Ewing, Evidence for a Double Well in the First Triplet Excited State of 2-Thiouracil, The Journal of Physical Chemistry B, 10.1021/acs.jpcb.7b06917, 121, 39, (9274-9280), (2017).
- Iacovos N. Michaelides, Nobuhiro Tago, Bastien Viverge and Thomas Carell, Synthesis of RNA Containing 5‐Hydroxymethyl‐, 5‐Formyl‐, and 5‐Carboxycytidine, Chemistry – A European Journal, 23, 63, (15894-15898), (2017).
- Carlos Crespo-Hernández, Photorelaxation and Photorepair Processes in Nucleic and Amino Acid Derivatives, Molecules, 22, 12, (2203), (2017).
- Michał A. Kochman, Andrzej Bil and R. J. Dwayne Miller, Mechanism Underlying the Nucleobase-Distinguishing Ability of Benzopyridopyrimidine (BPP), The Journal of Physical Chemistry A, 10.1021/acs.jpca.7b08334, 121, 43, (8267-8279), (2017).
- Heidelinde Glasner, Christian Riml, Ronald Micura and Kathrin Breuker, Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry, Nucleic Acids Research, 10.1093/nar/gkx470, 45, 13, (8014-8025), (2017).
- M.J. Mayoral, C. Montoro-García and D. González-Rodríguez, Self-Assembled Systems via Nucleobase Pairing, Comprehensive Supramolecular Chemistry II, 10.1016/B978-0-12-409547-2.12536-3, (191-257), (2017).
- Hiromu Kashida, Ayako Kurihara, Hayato Kawai and Hiroyuki Asanuma, Orientation-dependent FRET system reveals differences in structures and flexibilities of nicked and gapped DNA duplexes, Nucleic Acids Research, 45, 11, (e105), (2017).
- Lukas Trixl, Thomas Amort, Alexandra Wille, Manuela Zinni, Susanne Ebner, Clara Hechenberger, Felix Eichin, Hanna Gabriel, Ines Schoberleitner, Anming Huang, Paolo Piatti, Roxana Nat, Jakob Troppmair and Alexandra Lusser, RNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity, Cellular and Molecular Life Sciences, (2017).
- Thomas Amort and Alexandra Lusser, Detection of 5-Methylcytosine in Specific Poly(A) RNAs by Bisulfite Sequencing, RNA Methylation, 10.1007/978-1-4939-6807-7_8, (107-121), (2017).
- Takaaki Kurinomaru, Naoshi Kojima and Ryoji Kurita, An alkylating immobilization linker for immunochemical epigenetic assessment, Chemical Communications, 53, 59, (8308), (2017).
- Ville Väre, Emily Eruysal, Amithi Narendran, Kathryn Sarachan and Paul Agris, Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function, Biomolecules, 7, 1, (29), (2017).
- Indrajit Deb, Rupak Pal, Joanna Sarzynska and Ansuman Lahiri, Reparameterizations of the χ Torsion and Lennard‐Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines, Journal of Computational Chemistry, 37, 17, (1576-1588), (2016).
- Biswajit Samanta, Jan Seikowski and Claudia Höbartner, , Angewandte Chemie, 128, 5, (1946-1950), (2015).
- Meng Su, Angie Kirchner, Samuele Stazzoni, Markus Müller, Mirko Wagner, Arne Schröder and Thomas Carell, 5‐Formylcytosine Could Be a Semipermanent Base in Specific Genome Sites, Angewandte Chemie International Edition, 55, 39, (11797-11800), (2016).
- You Xu, Kenno Vanommeslaeghe, Alexey Aleksandrov, Alexander D. MacKerell and Lennart Nilsson, Additive CHARMM force field for naturally occurring modified ribonucleotides, Journal of Computational Chemistry, 37, 10, (896-912), (2016).
- Meng Su, Angie Kirchner, Samuele Stazzoni, Markus Müller, Mirko Wagner, Arne Schröder and Thomas Carell, , Angewandte Chemie, 128, 39, (11974-11978), (2016).
- Biswajit Samanta, Jan Seikowski and Claudia Höbartner, Fluorogenic Labeling of 5‐Formylpyrimidine Nucleotides in DNA and RNA, Angewandte Chemie International Edition, 55, 5, (1912-1916), (2015).
- Sebastian Mai, Philipp Marquetand and Leticia González, Intersystem Crossing Pathways in the Noncanonical Nucleobase 2-Thiouracil: A Time-Dependent Picture, The Journal of Physical Chemistry Letters, 7, 11, (1978), (2016).
- Collin Wetzel and Patrick A. Limbach, Mass spectrometry of modified RNAs: recent developments, The Analyst, 141, 1, (16), (2016).
- Dennis Gillingham, Stefanie Geigle and O. Anatole von Lilienfeld, Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics, Chemical Society Reviews, 45, 9, (2637), (2016).
- Jean-Louis H. A. Duprey, Gemma A. Bullen, Zheng-yun Zhao, Dario M. Bassani, Anna F. A. Peacock, John Wilkie and James H. R. Tucker, Single Site Discrimination of Cytosine, 5-Methylcytosine, and 5-Hydroxymethylcytosine in Target DNA Using Anthracene-Tagged Fluorescent Probes, ACS Chemical Biology, 11, 3, (717), (2016).
- Djemel Hamdane, Henri Grosjean and Marc Fontecave, Flavin-Dependent Methylation of RNAs: Complex Chemistry for a Simple Modification, Journal of Molecular Biology, 10.1016/j.jmb.2016.10.031, 428, 24, (4867-4881), (2016).
- You Xu, Alexander D. MacKerell and Lennart Nilsson, Structural effects of modified ribonucleotides and magnesium in transfer RNAs, Bioorganic & Medicinal Chemistry, 10.1016/j.bmc.2016.06.037, 24, 20, (4826-4834), (2016).
- Hui Yu, Jose A. Sanchez-Rodriguez, Marvin Pollum, Carlos E. Crespo-Hernández, Sebastian Mai, Philipp Marquetand, Leticia González and Susanne Ullrich, Internal conversion and intersystem crossing pathways in UV excited, isolated uracils and their implications in prebiotic chemistry, Physical Chemistry Chemical Physics, 10.1039/C6CP01790H, 18, 30, (20168-20176), (2016).
- Yoshiaki Masaki, Hyugo Ito, Yuki Oda, Kazufumi Yamazaki, Nobuhiro Tago, Kentaro Ohno, Nozomi Ishii, Hirosuke Tsunoda, Takashi Kanamori, Akihiro Ohkubo, Mitsuo Sekine and Kohji Seio, Enzymatic synthesis and reverse transcription of RNAs incorporating 2′-O-carbamoyl uridine triphosphate, Chemical Communications, 10.1039/C6CC05796A, 52, 87, (12889-12892), (2016).
- Judit Morla‐Folch, Hai‐nan Xie, Patricia Gisbert‐Quilis, Sara Gómez‐de Pedro, Nicolas Pazos‐Perez, Ramon A. Alvarez‐Puebla and Luca Guerrini, Ultrasensitive Direct Quantification of Nucleobase Modifications in DNA by Surface‐Enhanced Raman Scattering: The Case of Cytosine, Angewandte Chemie, 127, 46, (13854-13858), (2015).
- Judit Morla‐Folch, Hai‐nan Xie, Patricia Gisbert‐Quilis, Sara Gómez‐de Pedro, Nicolas Pazos‐Perez, Ramon A. Alvarez‐Puebla and Luca Guerrini, Ultrasensitive Direct Quantification of Nucleobase Modifications in DNA by Surface‐Enhanced Raman Scattering: The Case of Cytosine, Angewandte Chemie International Edition, 54, 46, (13650-13654), (2015).
- Rune Ougland, Torbjørn Rognes, Arne Klungland and Elisabeth Larsen, Non-homologous functions of the AlkB homologs, Journal of Molecular Cell Biology, 7, 6, (494), (2015).
- Mohit Chawla, Romina Oliva, Janusz M. Bujnicki and Luigi Cavallo, An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies, Nucleic Acids Research, 43, 14, (6714), (2015).
- Kevin C. Baldridge, Jose Zavala, Jason Surratt, Kenneth G. Sexton and Lydia M. Contreras, Cellular RNA is chemically modified by exposure to air pollution mixtures, Inhalation Toxicology, 27, 1, (74), (2015).
- Leonid I. Belen'kii and Yu B. Evdokimenkova, The Literature of Heterocyclic Chemistry, Part XIII, 2012–2013, , 10.1016/bs.aihch.2015.04.002, (193-363), (2015).
- Liang Xu, Ying‐Chu Chen, Jenny Chong, Andrea Fin, Lisa S. McCoy, Jun Xu, Chao Zhang and Dong Wang, Pyrene‐Based Quantitative Detection of the 5‐Formylcytosine Loci Symmetry in the CpG Duplex Content during TET‐Dependent Demethylation, Angewandte Chemie, 126, 42, (11405-11409), (2014).
- Liang Xu, Ying‐Chu Chen, Jenny Chong, Andrea Fin, Lisa S. McCoy, Jun Xu, Chao Zhang and Dong Wang, Pyrene‐Based Quantitative Detection of the 5‐Formylcytosine Loci Symmetry in the CpG Duplex Content during TET‐Dependent Demethylation, Angewandte Chemie International Edition, 53, 42, (11223-11227), (2014).
- Kevin C. Baldridge and Lydia M. Contreras, Functional implications of ribosomal RNA methylation in response to environmental stress, Critical Reviews in Biochemistry and Molecular Biology, 49, 1, (69), (2014).
- Zuzana Vaníková and Michal Hocek, Polymerase Synthesis of Photocaged DNA Resistant against Cleavage by Restriction Endonucleases, Angewandte Chemie International Edition, 53, 26, (6734-6737), (2014).
- Massimiliano Clamer, Lajos Höfler, Ellina Mikhailova, Gabriella Viero and Hagan Bayley, Detection of 3′-End RNA Uridylation with a Protein Nanopore, ACS Nano, 10.1021/nn4050479, 8, 2, (1364-1374), (2013).
- Indrajit Deb, Joanna Sarzynska, Lennart Nilsson and Ansuman Lahiri, Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields, Journal of Chemical Information and Modeling, 10.1021/ci400582a, 54, 4, (1129-1142), (2014).
- Felix Spenkuch, Gerald Hinze, Stefanie Kellner, Christoph Kreutz, Ronald Micura, Thomas Basché and Mark Helm, Dye label interference with RNA modification reveals 5-fluorouridine as non-covalent inhibitor, Nucleic Acids Research, 10.1093/nar/gku908, 42, 20, (12735-12745), (2014).
- Jean Cadet and J. Richard Wagner, TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine, Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 764-765, (18), (2014).
- Arne Klungland and John Arne Dahl, Dynamic RNA modifications in disease, Current Opinion in Genetics & Development, 26, (47), (2014).
- Zuzana Vaníková and Michal Hocek, Polymerase Synthesis of Photocaged DNA Resistant against Cleavage by Restriction Endonucleases, Angewandte Chemie, 126, 26, (6852-6855), (2014).
- Liang Xu, Ying-Chu Chen, Satoshi Nakajima, Jenny Chong, Lanfeng Wang, Li Lan, Chao Zhang and Dong Wang, A chemical probe targets DNA 5-formylcytosine sites and inhibits TDG excision, polymerases bypass, and gene expression, Chem. Sci., 5, 2, (567), (2014).
- Raghuvaran Shanmugam, Muktak Aklujkar, Matthias Schäfer, Richard Reinhardt, Olaf Nickel, Gunter Reuter, Derek R. Lovley, Ann Ehrenhofer-Murray, Wolfgang Nellen, Serge Ankri, Mark Helm, Tomasz P. Jurkowski and Albert Jeltsch, The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu, Nucleic Acids Research, 10.1093/nar/gku256, 42, 10, (6487-6496), (2014).
- Shiliang He, Hang Zhao, Xiurong Guo, Xiaoping Xu, Xinglong Zhou, Jiang Liu, Zhihua Xing, Ling Ye, Lu Jiang, Qianming Chen and Yang He, The Readout of Base‐Pair Information in Adenine–Thymine α‐D‐Arabinonucleosides, Chemistry – A European Journal, 20, 47, (15473-15481), (2014).
- WeiShen Aik, John S. Scotti, Hwanho Choi, Lingzhi Gong, Marina Demetriades, Christopher J. Schofield and Michael A. McDonough, Structure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation, Nucleic Acids Research, 42, 7, (4741), (2014).
- Miki Nakano, Hisae Tateishi-Karimata, Shigenori Tanaka and Naoki Sugimoto, Affinity of Molecular Ions for DNA Structures Is Determined by Solvent-Accessible Surface Area, The Journal of Physical Chemistry B, 10.1021/jp505107g, 118, 32, (9583-9594), (2014).
- Marie W. Johannsen, Simon R. Gerrard, Tracy Melvin and Tom Brown, Triplex-mediated analysis of cytosine methylation at CpA sites in DNA, Chem. Commun., 10.1039/C3CC45917A, 50, 5, (551-553), (2014).
- Rafael Notario, Vladimir N. Emel'yanenko, María Victoria Roux, Francisco Ros, Sergey P. Verevkin, James S. Chickos and Joel F. Liebman, Thermochemistry of Uracils. Experimental and Computational Enthalpies of Formation of 5,6-Dimethyl-, 1,3,5-Trimethyl-, and 1,3,5,6-Tetramethyluracils, The Journal of Physical Chemistry A, 117, 1, (244), (2013).
- Liang Xu, Steven W. Plouffe, Jenny Chong, Jesper Wengel and Dong Wang, A Chemical Perspective on Transcriptional Fidelity: Dominant Contributions of Sugar Integrity Revealed by Unlocked Nucleic Acids, Angewandte Chemie International Edition, 52, 47, (12341-12345), (2013).
- Iwona E. Głowacka, Jan Balzarini and Andrzej E. Wróblewski, The synthesis, antiviral, cytostatic and cytotoxic evaluation of a new series of acyclonucleotide analogues with a 1,2,3-triazole linker, European Journal of Medicinal Chemistry, 10.1016/j.ejmech.2013.10.057, 70, (703-722), (2013).
- Simona Irrera and Gustavo Portalone, First X-ray diffraction and quantum chemical study of proton-acceptor and proton-donor forms of 5-carboxylcytosine, the last-discovered nucleobase, Journal of Molecular Structure, 10.1016/j.molstruc.2013.07.023, 1050, (140-150), (2013).
- Georgeta N. Basturea, Research Methods for Detection and Quantitation of RNA Modifications, Materials and Methods, 3, (2013).
- Antje Hienzsch, Christian Deiml, Veronika Reiter and Thomas Carell, Total Synthesis of the Hypermodified RNA Bases Wybutosine and Hydroxywybutosine and Their Quantification Together with Other Modified RNA Bases in Plant Materials, Chemistry – A European Journal, 19, 13, (4244-4248), (2013).
- Andro C. Rios and Yitzhak Tor, On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution, Israel Journal of Chemistry, 53, 6‐7, (469-483), (2013).
- Su Zhang and Dong Wang, Understanding the Molecular Basis of RNA Polymerase II Transcription, Israel Journal of Chemistry, 53, 6‐7, (442-449), (2013).
- Liang Xu, Steven W. Plouffe, Jenny Chong, Jesper Wengel and Dong Wang, A Chemical Perspective on Transcriptional Fidelity: Dominant Contributions of Sugar Integrity Revealed by Unlocked Nucleic Acids, Angewandte Chemie, 125, 47, (12567-12571), (2013).
- Malte Winnacker and Eric T. Kool, Künstliche genetische Systeme bestehend aus vergrößerten Basenpaaren, Angewandte Chemie, 125, 48, (12728), (2013).
- , Ryoji‐Noyori‐Preis: M. Shibasaki / New Year Honours: C. V. Robinson und S. E. Gibson / Clara‐Immerwahr‐Preis: J. K. Edwards / Clemens‐Winkler‐Medaille: Otto S. Wolfbeis / Kuratorium der Volkswagenstiftung: T. Carell / AkzoNobel North America Science Award: K. Matyjaszewski, Angewandte Chemie, 125, 12, (3391-3392), (2013).
- Malte Winnacker and Eric T. Kool, Artificial Genetic Sets Composed of Size-Expanded Base Pairs, Angewandte Chemie International Edition, 52, 48, (12498), (2013).
- , Ryoji Noyori Prize: M. Shibasaki / New Year Honours: C. V. Robinson and S. E. Gibson / Clara Immerwahr Award: J. K. Edwards / Clemens Winkler Medal: Otto S. Wolfbeis / Board of Trustees, Volkswagen Foundation: T. Carell / AkzoNobel North America Science Award: K. Matyjaszewski, Angewandte Chemie International Edition, 52, 12, (3309-3310), (2013).
- Thomas Carell, Caterina Brandmayr, Antje Hienzsch, Markus Mueller, David Pearson, Veronika Reiter, Ines Thoma, Peter Thumbs and Mirko Wagner, ChemInform Abstract: Structure and Function of Noncanonical Nucleobases, ChemInform, 43, 47, (2012).
- Stefano D'Errico, Giorgia Oliviero, Nicola Borbone, Jussara Amato, Daniele D'Alonzo, Vincenzo Piccialli, Luciano Mayol and Gennaro Piccialli, A Facile Synthesis of 5'-Fluoro-5'-deoxyacadesine (5'-F-AICAR): A Novel Non-phosphorylable AICAR Analogue, Molecules, 10.3390/molecules171113036, 17, 12, (13036-13044), (2012).
- Sebastian Mai, Marvin Pollum, Lara Martínez-Fernández, Nicholas Dunn, Philipp Marquetand, Inés Corral, Carlos E. Crespo-Hernández and Leticia González, The origin of efficient triplet state population in sulfur-substituted nucleobases, Nature Communications, 10.1038/ncomms13077, 7, (13077), (2016).
- Miki Nakano, Hisae Tateishi-Karimata, Shigenori Tanaka, Florence Tama, Osamu Miyashita, Shu-ichi Nakano and Naoki Sugimoto, Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory, Nucleic Acids Research, 10.1093/nar/gkv1133, (gkv1133), (2015).




