Communication
Highly Precise Shape Mimicry by a Difluorotoluene Deoxynucleoside, a Replication‐Competent Substitute for Thymidine*
*
This research was supported by the National Institutes of Health (GM 52956). We thank Prof. T. R. Krugh for helpful discussions, Prof. W. D. Jones and Dr. R. Lachicotte for assistance with the crystallographic data, and Dr. J. Perlstein for assistance with the graphics.
Abstract
Large differences in the electrostatic properties of nucleosides can have surprisingly small effects on DNA replication. Size and shape appear to be more important, as structural studies of difluorotoluene deoxynucleoside 1, an isostere of thymidine (2), prove. The two nucleosides have virtually the same aromatic ring, almost identical sugar puckers, and very similar glycosidic angles (see the structural formulas). Hydrogen‐bonding capacity is apparently not crucial for templating in DNA replication.
Citing Literature
Number of times cited: 41
- Yajun Jian, Egle Maximowitsch, Degang Liu, Surya Adhikari, Lei Li and Tatiana Domratcheva, Indications of 5′ to 3′ Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog, Chemistry – A European Journal, 23, 31, (7526-7537), (2017).
- Richard B. Silverman and Mark W. Holladay, DNA-Interactive Agents, The Organic Chemistry of Drug Design and Drug Action, 10.1016/B978-0-12-382030-3.00006-4, (275-331), (2014).
- Marina Kovaliov, Chaim Wachtel, Eylon Yavin and Bilha Fischer, Synthesis and evaluation of a photoresponsive quencher for fluorescent hybridization probes, Org. Biomol. Chem., 10.1039/C4OB01185F, 12, 39, (7844-7858), (2014).
- Malte Winnacker and Eric T. Kool, Artificial Genetic Sets Composed of Size‐Expanded Base Pairs, Angewandte Chemie International Edition, 52, 48, (12498-12508), (2013).
- Degang Liu and Lei Li, Examining the base stacking interaction in a dinucleotide context via reversible cyclobutane dimer analogue formation under UV irradiation, RSC Advances, 3, 42, (19545), (2013).
- Malte Winnacker and Eric T. Kool, Künstliche genetische Systeme bestehend aus vergrößerten Basenpaaren, Angewandte Chemie, 125, 48, (12728-12739), (2013).
- A. K. Jissy, Sukanya Konar and Ayan Datta, Molecular Switching Behavior in Isosteric DNA Base Pairs, ChemPhysChem, 14, 6, (1219-1226), (2013).
- Omid Khakshoor, Steven E. Wheeler, K. N. Houk and Eric T. Kool, Measurement and Theory of Hydrogen Bonding Contribution to Isosteric DNA Base Pairs, Journal of the American Chemical Society, 134, 6, (3154), (2012).
- Shuangluo Xia, Soo Hyun Eom, William H. Konigsberg and Jimin Wang, Structural Basis for Differential Insertion Kinetics of dNMPs Opposite a Difluorotoluene Nucleotide Residue, Biochemistry, 51, 7, (1476), (2012).
- Degang Liu, Yan Zhou, Jingzhi Pu and Lei Li, Expanding the Horizon of the Thymine Isostere Biochemistry: Unique Cyclobutane Dimers Formed by Photoreaction between a Thymine and a Toluene Residue in the Dinucleotide Framework, Chemistry – A European Journal, 18, 25, (7823-7833), (2012).
- Travis J. Lund, Nisha A. Cavanaugh, Nicolas Joubert, Milan Urban, Jennifer N. Patro, Michal Hocek and Robert D. Kuchta, B Family DNA Polymerases Asymmetrically Recognize Pyrimidines and Purines, Biochemistry, 50, 33, (7243), (2011).
- Hidehito Urata, Eriko Yamaguchi, Yasunari Nakamura and Shun-ichi Wada, Pyrimidine–pyrimidine base pairs stabilized by silver( i ) ions , Chem. Commun., 10.1039/C0CC04091F, 47, 3, (941-943), (2011).
- Kenneth A. Johnson, The kinetic and chemical mechanism of high-fidelity DNA polymerases, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1804, 5, (1041), (2010).
- Hidehito Urata, Eriko Yamaguchi, Tatsuya Funai, Yuriko Matsumura and Shun‐ichi Wada, Incorporation of Thymine Nucleotides by DNA Polymerases through T–HgII–T Base Pairing, Angewandte Chemie International Edition, 49, 37, (6516-6519), (2010).
- Hidehito Urata, Eriko Yamaguchi, Tatsuya Funai, Yuriko Matsumura and Shun‐ichi Wada, Incorporation of Thymine Nucleotides by DNA Polymerases through T–HgII–T Base Pairing, Angewandte Chemie, 122, 37, (6666-6669), (2010).
- Donald E. Bergstrom, Unnatural Nucleosides with Unusual Base Pairing Properties, Current Protocols in Nucleic Acid Chemistry, 37, 1, (1.4.1-1.4.32), (2009).
- Sarah K. Jarchow-Choy, Elena Sjuvarsson, Herman O. Sintim, Staffan Eriksson and Eric T. Kool, Nonpolar Nucleoside Mimics as Active Substrates for Human Thymidine Kinases, Journal of the American Chemical Society, 131, 15, (5488), (2009).
- Harold R. Lee, Sandra A. Helquist, Eric T. Kool and Kenneth A. Johnson, Importance of Hydrogen Bonding for Efficiency and Specificity of the Human Mitochondrial DNA Polymerase, Journal of Biological Chemistry, 283, 21, (14402), (2008).
- Eric T. Kool, Modified DNA Bases: Probing Base‐Pair Recognition by Polymerases, Modified Nucleosides, (49-74), (2008).
- Eric T. Kool and Herman O. Sintim, The difluorotoluene debate—a decade later, Chem. Commun., 10.1039/B605414E, 35, (3665-3675), (2006).
- Alvaro Somoza, Jijumon Chelliserrykattil and Eric T. Kool, The Roles of Hydrogen Bonding and Sterics in RNA Interference, Angewandte Chemie, 118, 30, (5116-5119), (2006).
- Alvaro Somoza, Jijumon Chelliserrykattil and Eric T. Kool, The Roles of Hydrogen Bonding and Sterics in RNA Interference, Angewandte Chemie International Edition, 45, 30, (4994-4997), (2006).
- Kentaro Tanaka and Mitsuhiko Shionoya, Bio-inspired Programmable Self-assembly on DNA Templates, Chemistry Letters, 10.1246/cl.2006.694, 35, 7, (694-699), (2006).
- Mitsuhiko Shionoya and Kentaro Tanaka, Artificial metallo-DNA: a bio-inspired approach to metal array programming, Current Opinion in Chemical Biology, 8, 6, (592), (2004).
- Tae Woo Kim and Eric T. Kool, A Set of Nonpolar Thymidine Nucleoside Analogues with Gradually Increasing Size, Organic Letters, 10.1021/ol048487u, 6, 22, (3949-3952), (2004).
- Richard B. Silverman, DNA-Interactive Agents, The Organic Chemistry of Drug Design and Drug Action, 10.1016/B978-0-08-051337-9.50011-0, (323-403), (2004).
- Natasha Paul, Vishal C. Nashine, Geoffrey Hoops, Peiming Zhang, Jie Zhou, Donald E. Bergstrom and V.Jo Davisson, DNA Polymerase Template Interactions Probed by Degenerate Isosteric Nucleobase Analogs, Chemistry & Biology, 10, 9, (815), (2003).
- Eric T. Kool, Active Site Tightness and Substrate Fit in DNA Replication, Annual Review of Biochemistry, 71, 1, (191), (2002).
- Célia Fonseca Guerra and F. Matthias Bickelhaupt, Orbitalwechselwirkungen in starken und schwachen Wasserstoffbrücken sind essentiell für die DNA‐Replikation, Angewandte Chemie, 114, 12, (2194-2197), (2002).
- Donald E. Bergstrom, Unnatural Nucleosides with Unusual Base Pairing Properties, Current Protocols in Nucleic Acid Chemistry, 5, 1, (1.4.1-1.4.13), (2001).
- Eric T. Kool, Hydrogen Bonding, Base Stacking, and Steric Effects in DNA Replication, Annual Review of Biophysics and Biomolecular Structure, 30, 1, (1), (2001).
- E Kool, Synthetically modified DNAs as substrates for polymerases, Current Opinion in Chemical Biology, 4, 6, (602), (2000).
- Eric T. Kool, Juan C. Morales and Kevin M. Guckian, Einsichten in Stabilität und Replikation der DNA durch Nachahmung ihrer Struktur und Funktion, Angewandte Chemie, 112, 6, (1046-1068), (2000).
- B. David Silverman, Mike C. Pitman and Daniel E. Platt, Molecular Moment Similarity Between Several Nucleoside Analogs of Thymidine and Thymidine, Journal of Biomolecular Structure and Dynamics, 16, 6, (1169), (1999).
- Tim Searls and Larry W. McLaughlin, Synthesis of the analogue nucleoside 3-deaza-2′-deoxycytidine and its template activity with DNA polymerase, Tetrahedron, 55, 41, (11985), (1999).
- Gholamreza Sheikhnejad, Adam Brank, Judith K. Christman, Amanda Goddard, Estela Alvarez, Harry Ford, Victor E. Marquez, Canio J. Marasco, Janice R. Sufrin, Margaret O’Gara and Xiaodong Cheng, Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine 1 1Edited by R. Huber, Journal of Molecular Biology, 10.1006/jmbi.1998.2426, 285, 5, (2021-2034), (1999).
- Ulf Diederichsen, Selektivität der DNA‐Replikation: Basenpaargeometrie wichtiger als Wasserstoffbrücken, Angewandte Chemie, 110, 12, (1745-1747), (1999).
- Kevin M. Guckian, Thomas R. Krugh and Eric T. Kool, Solution structure of a DNA duplex containing a replicable difluorotoluene–adenine pair, Nature Structural Biology, 5, 11, (954), (1998).
- Juan C. Morales and Eric T. Kool, Efficient replication between non-hydrogen-bonded nucleoside shape analogs, Nature Structural Biology, 5, 11, (950), (1998).
- Eric T. Kool, Replication of non‐hydrogen bonded bases by DNA polymerases: A mechanism for steric matching, Biopolymers, 48, 1, (3-17), (1999).
- Dongyu Liu, Sean Moran and Eric T. Kool, Bi-stranded, multisite replication of a base pair between difluorotoluene and adenine: confirmation by ‘inverse’ sequencing, Chemistry & Biology, 10.1016/S1074-5521(97)90300-8, 4, 12, (919-926), (1997).
