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Research Articles

Substituent effects on indole universal bases in DNA

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Pages 1187-1204 | Received 23 Apr 2022, Accepted 25 Jun 2022, Published online: 03 Aug 2022

References

  • Varani, G.; McClain, W. H. The G·U Wobble Base Pair. EMBO Rep. 2000, 1, 18–23. DOI: 10.1093/embo-reports/kvd001.
  • Crick, F. H. C. Codon-Anticodon Pairing: The Wobble Hypothesis. J. Mol. Biol. 1966, 19, 548–555. DOI: 10.1016/S0022-2836(66)80022-0.
  • Srinivasan, S.; Torres, A. G.; Ribas de Pouplana, L. Inosine in Biology and Disease. Genes 2021, 12, 600. DOI: 10.3390/genes12040600.
  • Too, K.; Loakes, D. Universal Base Analogues and Their Applications to Biotechnology. In Modified Nucleosides: In Biochemistry, Biotechnology and Medicine. Herdewijn, P., Ed. Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany, 2008; pp. 277–303.
  • Millican, T. A.; Mock, G. A.; Chauncey, M. A.; Patel, T. P.; Eaton, M. A. W.; Gunning, J.; Cutbush, S. D.; Neidle, S.; Mann, J. Synthesis and Biophysical Studies of Short Oligodeoxynucleotides with Novel Modifications: A Possible Approach to the Problem of Mixed Base Oligodeoxynucleotide Synthesis. Nucleic Acids Res. 1984, 12, 7435–7453. DOI: 10.1093/nar/12.19.7435.
  • Loakes, D.; Brown, D. M. 5-Nitroindole as an Universal Base Analog. Nucleic Acids Res. 1994, 22, 4039–4043. DOI: 10.1093/nar/22.20.4039.
  • Wheaton, C. A.; Dobrowolski, S. L.; Millen, A. L.; Wetmore, S. D. Nitrosubstituted Aromatic Molecules as Universal Nucleobases: Computational Analysis of Stacking Interactions. Chem. Phys. Lett. 2006, 428, 157–166. DOI: 10.1016/j.cplett.2006.07.051.
  • Zhang, X.; Motea, E.; Lee, I.; Berdis, A. J. Replication of a Universal Nucleobase Provides Unique Insight into the Role of Entropy during DNA Polymerization and Pyrophosphorolysis. Biochemistry 2010, 49, 3009–3023. DOI: 10.1021/bi901523y.
  • Leonard, P.; Ming, X.; Jawalekar, A. M.; Thür, W.; Heindl, D.; Seela, F. Universal Bases: Base Pairing and Duplex Stability of Oligonucleotides Containing Pyrrolo[2,3-d]Pyrimidines and 5-Nitroindole Nucleosides. Collect. Symp. Ser. 2005, 7, 429–431. DOI: 10.1135/css200507429.
  • Reineks, E. Z.; Berdis, A. J. Evaluating the Contribution of Base Stacking during Translesion DNA Replication. Biochemistry 2004, 43, 393–404. DOI: 10.1021/bi034948s.
  • Zhang, X.; Lee, I.; Berdis, A. J. Evaluating the Contributions of Desolvation and Base-Stacking during Translesion DNA Synthesis. Org. Biomol. Chem. 2004, 2, 1703–1711. DOI: 10.1039/b401732c.
  • Zhang, X.; Lee, I.; Berdis, A. J. The Use of Nonnatural Nucleotides to Probe the Contributions of Shape Complementarity and π-Electron Surface Area during DNA Polymerization. Biochemistry 2005, 44, 13101–13110. DOI: 10.1021/bi050585f.
  • Zhang, X.; Donnelly, A.; Lee, I.; Berdis, A. J. Rational Attempts to Optimize Non-Natural Nucleotides for Selective Incorporation opposite an Abasic Site. Biochemistry 2006, 45, 13293–13303. DOI: 10.1021/bi060418v.
  • Zhang, X.; Lee, I.; Zhou, X.; Berdis, A. J. Hydrophobicity, Shape, and π-Electron Contributions during Translesion DNA Synthesis. J. Am. Chem. Soc. 2006, 128, 143–149. DOI: 10.1021/ja0546830.
  • Vineyard, D.; Zhang, X.; Donnelly, A.; Lee, I.; Berdis, A. J. Optimization of Non-Natural Nucleotides for Selective Incorporation opposite Damaged DNA. Org. Biomol. Chem. 2007, 5, 3623–3630. DOI: 10.1039/b712480e.
  • Barluenga, J.; Rodriguez, M. A.; Campos, P. J. Electrophilic Additions of Positive Iodine to Alkynes through an Iodonium Mechanism. J. Org. Chem. 1990, 55, 3104–3106. DOI: 10.1021/jo00297a027.
  • Hoffer, M. α-Thymidin. Chem. Ber. 1960, 93, 2777–2781. DOI: 10.1002/cber.19600931204.
  • Bhat, C. C. 2-Deoxy-3,5-Di-O-Toluoyl-D-Erythro-Pentosyl Chloride. In Synthetic Procedures in Nucleic Acid Chemistry, Zorbach, W. W.; Tipson, R. S., Eds. John Wiley Interscience: New York, 1968; Vol. 1, pp. 521–522.
  • Ezquerra, J.; Pedregal, C.; Lamas, C.; Barluenga, J.; Pérez, M.; García-Martín, M. A.; González, J. M. Efficient Reagents for the Synthesis of 5-, 7-, and 5,7-Substituted Indoles Starting from Aromatic Amines: Scope and Limitations. J. Org. Chem. 1996, 61, 5804–5812. DOI: 10.1021/jo952119+.
  • Parmentier, J.-G.; Poissonnet, G.; Goldstein, S. Practical Syntheses of 5-Trifluoromethyl-1H-Indoles. Heterocycles 2002, 57, 465–476. DOI: 10.3987/COM-01-9411.
  • Schlosser, M.; Ginanneschi, A.; Leroux, F. In Search of Simplicity and Flexibility: A Rational Access to Twelve Fluoroindolecarboxylic Acids. Eur. J. Org. Chem. 2006, 2006, 2956–2969. DOI: 10.1002/ejoc.200600118.
  • Girgis, N. S.; Cottam, H. B.; Robins, R. K. Synthesis of 2′-Deoxyribofuranosyl Indole Nucleosides Related to the Antibiotics SF-2140 and Neosidomycin. J. Heterocyclic Chem. 1988, 25, 361–366. DOI: 10.1002/jhet.5570250202.
  • Lai, J. S.; Kool, E. T. Selective Pairing of Polyfluorinated DNA Bases. J. Am. Chem. Soc. 2004, 126, 3040–3041. DOI: 10.1021/ja039571s.
  • Božilović, J.; Bats, J. W.; Engels, J. W. Synthesis and Structure of Fluoroindole Nucleosides. Can. J. Chem. 2007, 85, 283–292. DOI: 10.1139/v07-020.
  • Loakes, D.; Hill, F.; Brown, D. M.; Ball, S.; Reeve, M. A.; Robinson, P. S. 5'-Tailed Octanucleotide Primers for Cycle Sequencing. Nucleosides Nucleotides 1999, 18, 2685–2695. DOI: 10.1080/07328319908044634.
  • Maniatis, T.; Sambrook, J.; Fritsch, E. F. Molecular Cloning: A Laboratory Manual 2nd ed.; Cold Spring Harbor Laboratory: Cold Spring Harbor, New York, 1989, p. 1130.
  • McDowell, J. A.; Turner, D. H. Investigation of the Structural Basis for Thermodynamic Stabilities of Tandem GU Mismatches: Solution Structure of (rGAGGUCUC)2 by Two-Dimensional NMR and Simulated Annealing. Biochemistry 1996, 35, 14077–14089. DOI: 10.1021/bi9615710.
  • Hansch, C.; Leo, A.; Taft, R. W. A Survey of Hammett Substituent Constants and Resonance and Field Parameters. Chem. Rev. 1991, 91, 165–195. DOI: 10.1021/cr00002a004.
  • Gallego, J.; Loakes, D. Solution Structure and Dynamics of DNA Duplexes Containing the Universal Base Analogues 5-Nitroindole and 5-Nitroindole 3-Carboxamide. Nucleic Acids Res. 2007, 35, 2904–2912. DOI: 10.1093/nar/gkm074.

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