Warum Pentose‐ und nicht Hexose‐Nucleinsäuren??. Teil V*. (Purin‐Purin)‐Basenpaarung in der homo‐DNS‐Reihe: Guanin, Isoguanin, 2,6‐Diaminopurin und Xanthin
Teile I‐IV der Reihe ‘Warum Pentose‐ und nicht Hexose‐Nucleinsäuren?’, vgl. [1–4]. Die vorliegende Arbeit gilt als 9. Mitteilung in der Reihe ‘Chemie von α‐Aminonitrilen’ 8. Mitteilung dieser Reihe vgl. [4]. Teile der hier publizierten Ergebnisse sind von J. H. an der Herbstversammlung der Schweizerischen Chemischen Gesellschaft in Bern am 16.10.1991 vorgetragen sowie in mehreren von A. E. gehaltenen und im Druck erschienenen Vorträgen erwähnt worden; vgl. [5–8].
Abstract
Why Pentose‐ and Not Hexose‐Nucleic Acids? Purine‐Purine Pairing in homo‐DNA: Guanine,Isoguanine, 2,6‐Diaminopurine, and Xanthine
This paper concludes the series of reports in this journal [1–4] on the chemistry of homo‐DNA, the constitutionally simplifie dmodel system of hexopyranosyl‐(6′ → 4′)‐oligonucleotide systems stidued in our laboratory as potentially natural‐nucleic‐acid alternatives in the context of a chemical aetiology of nucleic‐acid structure. The report describes the synthesis and pairing properties of homo‐DNA oligonucleotides which contain as nucleobases exclusively purines, and gives, together with part III of the series [3], a survey of what we know today about purine‐purine pairingin homo‐DNA. In addition, the paper discusses those aspects of the chemistry of homo‐DNA which, we think, influence the way how some of the structural features of DNA (and RNA) are to be interpreted on a qualitative level.
Purine‐purine pairing occurs in the homo‐DNA domain in great variety. Most prominent is a novel tridentate Watson‐Crick pair between guanine and isoguanine, as well as one between 2,6‐diaminopurine and xanthinone, both giving rise to very stable duplexes containing the all‐purine strands in antiparallel orientation. For the guanine‐isoguanine pair, constitutional assignment is based on temperature‐dependent UV and CD spectroscopy of various guanine‐ and isoguanine‐containg duplexes in comparison with duplexes known to be paired in the reverse guanine is replaced by 7‐carbauguanine. Isoguanine and 2,6‐diaminopurine also have the capability of self‐pariring in the reverse‐Hoogsteen mode, as previously observed for adenine and guanine [3]. In this type of pairing, the interchangeably. Fig. 36 provides an overall survey of the relative strength of pairing in all possible purine‐purine combinations.
Watson‐Crick pairing of isoguanine with guanine demands the former to participate in its 3H‐tautomeric form; hitherto this specific tautomer had not been considered in the pairing chemistry of isoguanine. Whereas (cumulative) purine‐purine pairing in DNA (reverse‐Hoogsten or Hoogsteen) seems to occur in triplexes and tetrapalexes only, its occurrence in duplexes in a characteristic feature of homo‐DNA chemistry. The occurrence of purine‐purine Watson‐Crick base pairs is probably a consequence of homo‐DNA's quasi‐linear ladder structure [1][4]. In a double helix, the distance between the two sugar C‐atoms, on which a base pair is anchored, is expected to be constrained by the dimensions of the helix; in a linear duplex, however, there would be no restrictions with regard to base‐pair length. Homo‐DNA's ladder‐like model also allows one to recognize one of the reasons why nucleic‐acid duplexes prefer to pair in antiparallel, rather than parallel strand orientation: in homo‐DNA duplexes, (averaged) backbone and base pair axes are strongly inclined toward one another [4]; the stronger this inclination, the higher the preference for antiparallel strand orientation is expected to be (Fig. 16).
In retrospect, homo‐DNA turns out to be one of the first artificial oligonucleotide systems (cf. Footnote 65) to demonstrate in a comprehensive way that informational base pairing involving purines and pyrimidines is not a capability unique to ribofuranosyl systems. Stability and helical shape of pairing complexes are not necessary conditions of one another; it is the potential for extensive conformational cooperativity of hte backbone structure with respect to the constellational demands of base pairing and base stacking that determines whether or nor a given type of base‐carrying backbone structure is an informational pairing system. From the viewpoint of the chemical aetiology of nucleic‐acid structure, which inspired our investigations on hexopyranosyl‐(6′ → 4′)‐oligonucleotide systems in the first place, the work on homo‐DNA is only an extensive model study, because homo‐DNA is not to be considered a potential natural‐nucleic‐acid altenratie. In retrospect, it seems fortunate that the model study was carried out, because without it we could hardly have comprehended the pairing behavior of the proper nucleic‐acid alternatives which we have studied later and which will be discussed in Part VI of this series.
The English footnotes to Fig. 1–49 provide an extension of this summary.
Number of times cited: 59
- Damien Evéquoz and Christian J. Leumann, Probing the Backbone Topology of DNA: Synthesis and Properties of 7′,5′‐Bicyclo‐DNA, Chemistry – A European Journal, 23, 33, (7953-7968), (2017).
- C. Li, B. J. Cafferty, S. C. Karunakaran, G. B. Schuster and N. V. Hud, Formation of supramolecular assemblies and liquid crystals by purine nucleobases and cyanuric acid in water: implications for the possible origins of RNA, Physical Chemistry Chemical Physics, 10.1039/C6CP03047E, 18, 30, (20091-20096), (2016).
- Brian J. Cafferty and Nicholas V. Hud, Was a Pyrimidine‐Pyrimidine Base Pair the Ancestor of Watson‐Crick Base Pairs? Insights from a Systematic Approach to the Origin of RNA, Israel Journal of Chemistry, 55, 8, (891-905), (2015).
- Kunihiko Morihiro, Hidekazu Hoshino, Osamu Hasegawa, Yuuya Kasahara, Kohsuke Nakajima, Masayasu Kuwahara, Shin-ichi Tsunoda and Satoshi Obika, Polymerase incorporation of a 2′-deoxynucleoside-5′-triphosphate bearing a 4-hydroxy-2-mercaptobenzimidazole nucleobase analogue, Bioorganic & Medicinal Chemistry Letters, 10.1016/j.bmcl.2015.05.075, 25, 15, (2888-2891), (2015).
- Junya Chiba and Masahiko Inouye, Synthesis of Nonnatural Oligonucleotides Made Exclusively of Alkynyl C‐Nucleosides with Nonnatural Bases, Current Protocols in Nucleic Acid Chemistry, 61, 1, (4.62.1-4.62.22), (2015).
- Pei Zhou, Chong Wang, Qi-ming Qiu, Jian-feng Yao, Chuan-fang Sheng and Hui Li, Controllable synthesis of nucleotide complex based on pH control: a small-molecule fluorescent probe as an auxiliary ligand to indicate the pre-organization of the nucleotide complex in solution, Dalton Trans., 10.1039/C5DT02624E, 44, 40, (17810-17818), (2015).
- Jian-Jun Li and Xing-Xing Gui, l-ProT catalyzed highly regioselective N-alkoxyalkylation of purine rings with vinyl ethers, Chinese Chemical Letters, 10.1016/j.cclet.2014.04.023, 25, 10, (1341-1345), (2014).
- Zahra Aliakbar Tehrani and Zahra Jamshidi, Watson–Crick versus imidazopyridopyrimidine base pairs: theoretical study on differences in stability and hydrogen bonding strength, Structural Chemistry, 10.1007/s11224-014-0397-3, 25, 4, (1271-1280), (2014).
- Malte Winnacker and Eric T. Kool, Künstliche genetische Systeme bestehend aus vergrößerten Basenpaaren, Angewandte Chemie, 125, 48, (12728-12739), (2013).
- Malte Winnacker and Eric T. Kool, Artificial Genetic Sets Composed of Size‐Expanded Base Pairs, Angewandte Chemie International Edition, 52, 48, (12498-12508), (2013).
- Zahra Aliakbar Tehrani, Mehdi Shakourian-Fard and Alireza Fattahi, Computational investigation of thermochemical properties of non-natural C-nucloebases: different hydrogen-bonding preferences for non-natural Watson–Crick base pairs, Structural Chemistry, 10.1007/s11224-012-0115-y, 24, 4, (1015-1025), (2012).
- Osman Doluca, Jamie M. Withers and Vyacheslav V. Filichev, Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes, Chemical Reviews, 10.1021/cr300225q, 113, 5, (3044-3083), (2013).
- Nicholas V. Hud, Brian J. Cafferty, Ramanarayanan Krishnamurthy and Loren Dean Williams, The Origin of RNA and “My Grandfather’s Axe”, Chemistry & Biology, 20, 4, (466), (2013).
- Ramanarayanan Krishnamurthy, Role of p K a of Nucleobases in the Origins of Chemical Evolution , Accounts of Chemical Research, 10.1021/ar200262x, 45, 12, (2035-2044), (2012).
- Albert Eschenmoser, Ätiologie potentiell primordialer Biomolekül‐Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens – ein Rückblick, Angewandte Chemie, 123, 52, (12618-12681), (2011).
- Albert Eschenmoser, Etiology of Potentially Primordial Biomolecular Structures: From Vitamin B12 to the Nucleic Acids and an Inquiry into the Chemistry of Life’s Origin: A Retrospective, Angewandte Chemie International Edition, 50, 52, (12412-12472), (2011).
- Albert Eschenmoser, Searching for Nucleic Acid Alternatives, Chemical Synthetic Biology, (5-45), (2011).
- Junya Chiba and Masahiko Inouye, Exotic DNAs Made of Nonnatural Bases and Natural Phosphodiester Bonds, Chemistry & Biodiversity, 7, 2, (259-282), (2010).
- E. D. Horowitz, A. E. Engelhart, M. C. Chen, K. A. Quarles, M. W. Smith, D. G. Lynn and N. V. Hud, Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world, Proceedings of the National Academy of Sciences, 10.1073/pnas.0914172107, 107, 12, (5288-5293), (2010).
- Marc‐Olivier Ebert and Bernhard Jaun, Oligonucleotides with Sugars Other Than Ribo‐ and 2′‐Deoxyribofuranose in the Backbone: the Solution Structures Determined by NMR in the Context of the ‘Etiology of Nucleic Acids’ Project of Albert Eschenmoser, Chemistry & Biodiversity, 7, 9, (2103-2128), (2010).
- Xuejun Zhang and Ramanarayanan Krishnamurthy, Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligo‐dipeptides Tagged with Orotic Acid Derivatives as Recognition Elements, Angewandte Chemie, 121, 43, (8268-8272), (2009).
- Daniele D'Alonzo, Arthur Van Aerschot, Annalisa Guaragna, Giovanni Palumbo, Guy Schepers, Stefania Capone, Jef Rozenski and Piet Herdewijn, Synthesis and Base Pairing Properties of 1′,5′‐Anhydro‐L‐Hexitol Nucleic Acids (L‐HNA), Chemistry � A European Journal, 15, 39, (10121-10131), (2009).
- Xuejun Zhang and Ramanarayanan Krishnamurthy, Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligo‐dipeptides Tagged with Orotic Acid Derivatives as Recognition Elements, Angewandte Chemie International Edition, 48, 43, (8124-8128), (2009).
- Benjamin D. Heuberger and Christopher Switzer, An Alternative Nucleobase Code: Characterization of Purine–Purine DNA Double Helices Bearing Guanine–Isoguanine and Diaminopurine 7‐Deaza‐Xanthine Base Pairs, ChemBioChem, 9, 17, (2779-2783), (2008).
- Gopi Kumar Mittapalli, Yazmin M. Osornio, Miguel A. Guerrero, Kondreddi Ravinder Reddy, Ramanarayanan Krishnamurthy and Albert Eschenmoser, Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligodipeptides Tagged with 2,4‐Disubstituted 5‐Aminopyrimidines as Recognition Elements, Angewandte Chemie, 119, 14, (2530-2536), (2006).
- Gopi Kumar Mittapalli, Yazmin M. Osornio, Miguel A. Guerrero, Kondreddi Ravinder Reddy, Ramanarayanan Krishnamurthy and Albert Eschenmoser, Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligodipeptides Tagged with 2,4‐Disubstituted 5‐Aminopyrimidines as Recognition Elements, Angewandte Chemie International Edition, 46, 14, (2478-2484), (2006).
- Koen Nauwelaerts, Eveline Lescrinier and Piet Herdewijn, Structure of the α‐Homo‐DNA:RNA Duplex and the Function of Twist and Slide To Catalogue Nucleic Acid Duplexes, Chemistry – A European Journal, 13, 1, (90-98), (2006).
- Khalil I. Shaikh, Peter Leonard and Frank Seela, 7-Deaza-2′-Deoxyxanthosine: Nucleobase Protection and Base Pairing of Oligonucleotides, Nucleosides, Nucleotides and Nucleic Acids, 26, 6-7, (737), (2007).
- Christoph Arenz and Oliver Seitz, DNA Made of Purines Only, Chemistry & Biology, 10.1016/j.chembiol.2007.05.001, 14, 5, (467-469), (2007).
- Albert Eschenmoser, The search for the chemistry of life's origin, Tetrahedron, 10.1016/j.tet.2007.10.012, 63, 52, (12821-12844), (2007).
- Pradeep S. Pallan, Paolo Lubini, Martin Bolli and Martin Egli, Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing, Nucleic Acids Research, 35, 19, (6611), (2007).
- Thomas R. Battersby, Maria Albalos and Michel J. Friesenhahn, An Unusual Mode of DNA Duplex Association: Watson-Crick Interaction of All-Purine Deoxyribonucleic Acids, Chemistry & Biology, 10.1016/j.chembiol.2007.03.012, 14, 5, (525-531), (2007).
- Frank Seela and Khalil I. Shaikh, Oligonucleotides Containing 7‐Deaza‐2′‐deoxyxanthosine: Synthesis, Base Protection, and Base‐Pair Stability, Helvetica Chimica Acta, 89, 11, (2794-2814), (2006).
- Sanjeeva R. Guppi, Maoquan Zhou and George A. O'Doherty, De Novo Asymmetric Synthesis of Homoadenosine via a Palladium-CatalyzedN-Glycosylation, Organic Letters, 8, 2, (293), (2006).
- Frank Seela and Khalil I. Shaikh, pH-Independent triplex formation: hairpin DNA containing isoguanine or 9-deaza-9-propynylguanine in place of protonated cytosine, Organic & Biomolecular Chemistry, 4, 21, (3993), (2006).
- Jianmin Gao, Haibo Liu and Eric T. Kool, Assembly of the Complete Eight‐Base Artificial Genetic Helix, xDNA, and Its Interaction with the Natural Genetic System, Angewandte Chemie, 117, 20, (3178-3182), (2005).
- Trixie Wagner, Bo Han, Guido Koch, Ramanarayanan Krishnamurthy and Albert Eschenmoser, Tautomerism in 5,8‐Diaza‐7,9‐dicarbaguanine (‘Alloguanine’), Helvetica Chimica Acta, 88, 7, (1960-1968), (2005).
- Jianmin Gao, Haibo Liu and Eric T. Kool, Assembly of the Complete Eight‐Base Artificial Genetic Helix, xDNA, and Its Interaction with the Natural Genetic System, Angewandte Chemie International Edition, 44, 20, (3118-3122), (2005).
- Jeffery T. Davis, , Angewandte Chemie, 116, 6, (684-716), (2004).
- Alexander Heckel, A New DNA Analogue with Expanded Size and Scope, ChemBioChem, 5, 6, (765-767), (2004).
- Bo Han, Bernhard Jaun, Ramanarayanan Krishnamurthy and Albert Eschenmoser, Mannich-Type C-Nucleosidations in the 5,8-Diaza-7,9-dicarba-purine Family1, Organic Letters, 6, 21, (3691), (2004).
- Jeffery T. Davis, G‐Quartets 40 Years Later: From 5′‐GMP to Molecular Biology and Supramolecular Chemistry, Angewandte Chemie International Edition, 43, 6, (668-698), (2004).
- Orgel Leslie E., Prebiotic Chemistry and the Origin of the RNA World, Critical Reviews in Biochemistry and Molecular Biology, 10.1080/10409230490460765, 39, 2, (99-123), (2010).
- Stefan Pitsch, Sebastian Wendeborn, Ramanarayanan Krishnamurthy, Armin Holzner, Mark Minton, Martin Bolli, Christian Miculca, Norbert Windhab, Ronald Micura, Michael Stanek, Bernhard Jaun and Albert Eschenmoser, Pentopyranosyl Oligonucleotide Systems. 9th Communication, Helvetica Chimica Acta, 86, 12, (4270-4363), (2003).
- C.Ronald Geyer, Thomas R. Battersby and Steven A. Benner, Nucleobase Pairing in Expanded Watson-Crick-like Genetic Information Systems, Structure, 11, 12, (1485), (2003).
- DÓNALL A. Mac DÓNAILL and DENISE BROCKLEBANK, Anab initioquantum chemical investigation of the error-coding model of nucleotide alphabet composition, Molecular Physics, 101, 17, (2755), (2003). 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society IEMBS-03 Cancun, Mexico 17-21 Sept. 2003 Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE Cat. No.03CH37439) IEEE , (2003). 0-7803-7789-3 D.A. Mac Donaill The role of error-coding in shaping the nucleotide alphabet: nature's choice of A,U, C and G 3850 3853 , 10.1109/IEMBS.2003.1281003 http://ieeexplore.ieee.org/document/1281003/
- Kai‐Uwe Schöning, Peter Scholz, Xiaolin Wu, Sreenivasulu Guntha, Guillermo Delgado, Ramanarayanan Krishnamurthy and Albert Eschenmoser, The α‐L‐Threofuranosyl‐(3′→2′)‐oligonucleotide System (‘TNA'): Synthesis and Pairing Properties, Helvetica Chimica Acta, 85, 12, (4111-4153), (2003).
- Mangmang Cai, Xiaodong Shi, Vladimir Sidorov, Daniele Fabris, Yiu-fai Lam and Jeffery T Davis, Cation-directed self-assembly of lipophilic nucleosides: the cation's central role in the structure and dynamics of a hydrogen-bonded assembly, Tetrahedron, 10.1016/S0040-4020(01)01101-2, 58, 4, (661-671), (2002).
- F. Seela and H. Debelak, 8-AZA-7-DEAZAADENINE AND 7-DEAZAGUANINE: SYNTHESIS AND PROPERTIES OF NUCLEOSIDES AND OLIGONUCLEOTIDES WITH NUCLEOBASES LINKED AT POSITION-8, Nucleosides, Nucleotides and Nucleic Acids, 20, 4-7, (577), (2001).
- Christopher Switzer and John C. Chaput, Probing Structure and Function with Alternative Nucleic Acids Bearing 2′,5′-Linked, Zwitterionic, and Isocytosine·Isoguanine Components, Methods, 23, 2, (141), (2001).
- NICHOLAS V HUD and FRANK A.L ANET, Intercalation-Mediated Synthesis and Replication: A New Approach to the Origin of Life, Journal of Theoretical Biology, 205, 4, (543), (2000).
- Yong Ju, Jian-Jun Hu and Yu-Fen Zhao, Reaction of Carbohydrates and Pentacoordinate Oxaphosphorane and Their Biomimetic Mechanism, Phosphorus, Sulfur, and Silicon and the Related Elements, 167, 1, (93), (2000).
- Frank Seela and Alexander Melenewski, 5‐Aza‐7‐deaza‐2′‐deoxyguanosine: Oligonucleotide Duplexes with Novel Base Pairs, Parallel Chain Orientation and Protonation Sites in the Core of a Double Helix, European Journal of Organic Chemistry, 1999, 2, (485-496), (1999).
- Ronald Micura, René Kudick, Stefan Pitsch and Albert Eschenmoser, Die gegensätzliche Orientierung der Rückgratneigung in Pyranosyl‐RNA und homo‐DNA korreliert mit einer entsprechend gegensätzlichen Orientierung von Duplexeigenschaften, Angewandte Chemie, 111, 5, (715-718), (1999).
- Kyeong-Eun Jung, Kichul Kim, Mirim Yang, Kwangjun Lee and Hong Lim, Synthesis and hybridization properties of oligonucleotides containing 6-membered azasugar nucleotides, Bioorganic & Medicinal Chemistry Letters, 9, 24, (3407), (1999).
- Ulf Diederichsen and Harald W. Schmitt, β‐Homoalanyl‐PNA: A Special Case of β‐Peptides with β‐Sheet‐Like Backbone Conformation; Organization in Higher Ordered Structures, European Journal of Organic Chemistry, 1998, 5, (827-835), (1998).
- K. GROEBKE, J. HUNZIKER, W. FRASER, L. PENG, U. DIEDERICHSEN, K. ZIMMERMANN, A. HOLZNER, C. LEUMANN and A. ESCHENMOSER, ChemInform Abstract: Why Pentose‐ and Not Hexose‐Nucleic Acids? Purine‐Purine Pairing in homo‐DNA: Guanine, Isoguanine, 2,6‐Diaminopurine, and Xanthine., ChemInform, 29, 23, (2010).
- Ana Gomez, Fernando Lobo, Silvia Miranda and J. Lopez, A Survey of Recent Synthetic Applications of 2,3-Dideoxy-Hex-2-enopyranosides, Molecules, 10.3390/molecules20058357, 20, 5, (8357-8394), (2015).
