Efforts toward Expansion of the Genetic Alphabet: DNA Polymerase Recognition of a Highly Stable, Self-Pairing Hydrophobic Base

Dustin L. McMinn, Anthony K. Ogawa, Yiqin Wu, Jianquan Liu, Peter G. Schultz*, and Floyd E. Romesberg*

Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037

J. Am. Chem. Soc., 1999, 121 (49), pp 11585–11586

DOI: 10.1021/ja9925150

Publication Date (Web): November 25, 1999

Cite this:J. Am. Chem. Soc. 121, 49, 11585-11586

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Site-Specific Functional Labeling of Nucleic Acids by In Vitro Replication and Transcription using Unnatural Base Pair Systems
Michiko Kimoto, Yasushi Hikida, Ichiro Hirao
Israel Journal of Chemistry 2013 , n/a-n/a
A quantum chemistry study of Ds-Pa unnatural DNA base pair
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International Journal of Quantum Chemistry 2013 113 (10.1002/qua.v113.4), 504-509
The Selective Synthesis of Metallanucleosides and Metallanucleotides: A New Tool for the Functionalization of Nucleic Acids
Mamen Martín-Ortíz, Mar Gómez-Gallego, Carmen Ramírez de Arellano, Miguel A. Sierra
Chemistry - A European Journal 2012 18, 12603-12608
Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet
Denis A. Malyshev, Kirandeep Dhami, Henry T. Quach, Thomas Lavergne, Phillip Ordoukhanian, Ali Torkamani, Floyd E. Romesberg
Proceedings of the National Academy of Sciences 2012 109 (30), 12005-12010
AgI Ion Mediated Formation of a C-A Mispair by DNA Polymerases
Tatsuya Funai, Yuki Miyazaki, Megumi Aotani, Eriko Yamaguchi, Osamu Nakagawa, Shun-ichi Wada, Hidetaka Torigoe, Akira Ono, Hidehito Urata
Angewandte Chemie 2012 124 (10.1002/ange.v124.26), 6570-6572
AgI Ion Mediated Formation of a C-A Mispair by DNA Polymerases
Tatsuya Funai, Yuki Miyazaki, Megumi Aotani, Eriko Yamaguchi, Osamu Nakagawa, Shun-ichi Wada, Hidetaka Torigoe, Akira Ono, Hidehito Urata
Angewandte Chemie International Edition 2012 51 (10.1002/anie.v51.26), 6464-6466
KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry
Karin Betz, Denis A Malyshev, Thomas Lavergne, Wolfram Welte, Kay Diederichs, Tammy J Dwyer, Phillip Ordoukhanian, Floyd E Romesberg, Andreas Marx
Nature Chemical Biology 2012 8, 612-614
Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma
Ichiro HIRAO, Michiko KIMOTO
Proceedings of the Japan Academy, Series B 2012 88, 345-367
Matthew B. Coppock, Mary Elizabeth Williams
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Nucleobases with Designed Patterns of Hydrogen Bonding
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Solution structure of S-DNA formed by covalent base pairing involving a disulfide bond
Akihiko Hatano, Munehiro Okada, Gota Kawai
Organic & Biomolecular Chemistry 2012 10, 7327
Synthetic Nucleotides as Probes of DNA Polymerase Specificity
Jason M. Walsh, Penny J. Beuning
Journal of Nucleic Acids 2012 2012, 1-17
Major Groove Substituents and Polymerase Recognition of a Class of Predominantly Hydrophobic Unnatural Base Pairs
Thomas Lavergne, Denis A. Malyshev, Floyd E. Romesberg
Chemistry - A European Journal 2011 , n/a-n/a
Unnatural base pair systems for sensing and diagnostic applications
Michiko Kimoto, Robert Sidney Cox, Ichiro Hirao
Expert Review of Molecular Diagnostics 2011 11 (3), 321-331
Synthesis, Characterization, and Physical Properties of a Conjugated Heteroacene: 2-Methyl-1,4,6,7,8,9-hexaphenylbenz(g)isoquinolin-3(2H)-one (BIQ)
Qichun Zhang, Jinchong Xiao, Zongyou Yin, Hieu M. Duong, Fen Qiao, Freddy Boey, Xiao Hu, Hua Zhang, Fred Wudl
Chemistry - An Asian Journal 2011 6, 856-862
Alternative DNA base-pairs: from efforts to expand the genetic code to potential material applications
Filip Wojciechowski, Christian J. Leumann
Chemical Society Reviews 2011 40, 5669
Solution Structure, Mechanism of Replication, and Optimization of an Unnatural Base Pair
Denis A. Malyshev, Danielle A. Pfaff, Shannon I. Ippoliti, Gil Tae Hwang, Tammy J. Dwyer, Floyd E. Romesberg
Chemistry - A European Journal 2010 16 (10.1002/chem.v16:42), 12650-12659
Expansion of the Genetic Alphabet in Nucleic Acids by Creating New Base Pairs
Ichiro Hirao, Michiko Kimoto
2010,39-62
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Toward a designed genetic system with biochemical function: polymerase synthesis of single and multiple size-expanded DNA base pairs
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Organic & Biomolecular Chemistry 2010 8, 2704
Genetic Incorporation of Unnatural Amino Acids into Proteins
Angela R. Parrish, Lei Wang
2010,587-617
Structure and Replication of yDNA: A Novel Genetic Set Widened by Benzo-Homologation
Haige Lu, Stephen R. Lynch, Alex H. F. Lee, Eric T. Kool
ChemBioChem 2009 10 (10.1002/cbic.v10:15), 2530-2538
Major Groove Derivatization of an Unnatural Base Pair
Young Jun Seo, Floyd E. Romesberg
ChemBioChem 2009 10 (10.1002/cbic.v10:14), 2394-2400
The effects of unnatural base pairs and mispairs on DNA duplex stability and solvation
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Nucleic Acids Research 2009 37 (14), 4757-4763
Unnatural Nucleosides with Unusual Base Pairing Properties
Donald E. Bergstrom
2009,1.4.1-1.4.32
Hydrogen-bond self-assembly of DNA-base analogues — Experimental results
Felaniaina Rakotondradany, Hanadi Sleiman, M. A. Whitehead
Canadian Journal of Chemistry 2009 87 (5), 627-639
An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules
Michiko Kimoto, Rie Kawai, Tsuneo Mitsui, Shigeyuki Yokoyama, Ichiro Hirao
Nucleic Acids Research 2009 37 (2), e14-e14
An Alternative Nucleobase Code: Characterization of Purine-Purine DNA Double Helices Bearing Guanine-Isoguanine and Diaminopurine 7-Deaza-Xanthine Base Pairs
Benjamin D. Heuberger, Christopher Switzer
ChemBioChem 2008 9 (10.1002/cbic.v9:17), 2779-2783
Solution Structure of a DNA Duplex Containing a Biphenyl Pair
Zeena Johar, Alain Zahn, Christian J. Leumann, Bernhard Jaun
Chemistry - A European Journal 2008 14 (10.1002/chem.v14:4), 1080-1086
Recognition Properties of Donor- and Acceptor-Modified Biphenyl-DNA
Alain Zahn, Christian J. Leumann
Chemistry - A European Journal 2008 14 (10.1002/chem.v14:4), 1087-1094
Polymerase Recognition and Stability of Fluoro-Substituted Pyridone Nucleobase Analogues
Gil Tae Hwang, Aaron M. Leconte, Floyd E. Romesberg
ChemBioChem 2007 8 (10.1002/cbic.v8:13), 1606-1611
Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligodipeptides and Oligodipeptoids Tagged with Triazines as Recognition Elements
Gopi Kumar Mittapalli, Kondreddi Ravinder Reddy, Hui Xiong, Omar Munoz, Bo Han, Francesco De Riccardis, Ramanarayanan Krishnamurthy, Albert Eschenmoser
Angewandte Chemie 2007 119 (10.1002/ange.v119:14), 2522-2529
Mapping the Landscape of Potentially Primordial Informational Oligomers: Oligodipeptides and Oligodipeptoids Tagged with Triazines as Recognition Elements
Gopi Kumar Mittapalli, Kondreddi Ravinder Reddy, Hui Xiong, Omar Munoz, Bo Han, Francesco De Riccardis, Ramanarayanan Krishnamurthy, Albert Eschenmoser
Angewandte Chemie International Edition 2007 46 (10.1002/anie.v46:14), 2470-2477
A metallo base-pair incorporating a terpyridyl-like motif: bipyridyl-pyrimidinone·Ag(i)·4-pyridine
Dongwon Shin, Christopher Switzer
Chemical Communications 2007 , 4401
Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
Zunyi Yang, Daniel Hutter, Pinpin Sheng, A. Michael Sismour, Steven A. Benner
Nucleic Acids Research 2006 34 (21), 6095-6101
Stability and Polymerase Recognition of Pyridine Nucleobase Analogues: Role of Minor-Groove H-Bond Acceptors
Yoonkyung Kim, Aaron M. Leconte, Yoshiyuki Hari, Floyd E. Romesberg
Angewandte Chemie International Edition 2006 45 (10.1002/anie.v45:46), 7809-7812
Stability and Polymerase Recognition of Pyridine Nucleobase Analogues: Role of Minor-Groove H-Bond Acceptors
Yoonkyung Kim, Aaron M. Leconte, Yoshiyuki Hari, Floyd E. Romesberg
Angewandte Chemie 2006 118 (10.1002/ange.v118:46), 7973-7976
An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA
Ichiro Hirao, Michiko Kimoto, Tsuneo Mitsui, Tsuyoshi Fujiwara, Rie Kawai, Akira Sato, Yoko Harada, Shigeyuki Yokoyama
Nature Methods 2006 3 (9), 729-735
Bio-inspired Programmable Self-assembly on DNA Templates
Kentaro Tanaka, Mitsuhiko Shionoya
Chemistry Letters 2006 35 (7), 694-699
Efforts towards Expansion of the Genetic Alphabet: Pyridone and Methyl Pyridone Nucleobases
Aaron M. Leconte, Shigeo Matsuda, Gil Tae Hwang, Floyd E. Romesberg
Angewandte Chemie 2006 118 (10.1002/ange.v118:26), 4432-4435
Efforts towards Expansion of the Genetic Alphabet: Pyridone and Methyl Pyridone Nucleobases
Aaron M. Leconte, Shigeo Matsuda, Gil Tae Hwang, Floyd E. Romesberg
Angewandte Chemie International Edition 2006 45 (10.1002/anie.v45:26), 4326-4329
Placing Extra Components into RNA by Specific Transcription Using Unnatural Base Pair Systems
Ichiro Hirao
BioTechniques 2006 40 (6), 711-717
Exceptional Thermodynamic Stability of DNA Duplexes Modified by Nonpolar Base Analogues Is due to Increased Stacking Interactions and Favorable Solvation: Correlated Ab Initio Calculations and Molecular Dynamics Simulations
David Řeha, Michal Hocek, Pavel Hobza
Chemistry - A European Journal 2006 12 (10.1002/chem.v12:13), 3587-3595
Synthesis and Mechanistic Study of Isoquinolinones from Cinnamoyl Azides
Ta-Hsien Chuang, Pei-Lin Wu
Journal of the Chinese Chemical Society 2006 53 (10.1002/jccs.v53.2), 413-420
Orbital interactions and charge redistribution in weak hydrogen bonds: Watson-Crick GC mimic involving CH proton donor and F proton acceptor groups
Célia Fonseca Guerra, Evert Jan Baerends, F. Matthias Bickelhaupt
International Journal of Quantum Chemistry 2006 106 (10.1002/qua.v106:12), 2428-2443
Importance of 3′-Hydroxyl Group of the Nucleosides for the Reactivity of Thymidine Phosphorylase from Escherichia coli
Akihiko Hatano, Aiko Harano, Masayuki Kirihara
Chemistry Letters 2006 35 (2), 232-233
Computational Evaluation of Intermolecular Interactions of a Universal Base 3-Nitropyrrole in Stacked Dimers and DNA Duplexes
Kohji Seio, Hisashi Ukawa, Koh-ichiro Shohda, Mitsuo Sekine
Journal of Biomolecular Structure and Dynamics 2005 22, 735-746
Pentafluorophenyl-Phenyl Interactions in Biphenyl-DNA
Alain Zahn, Christine Brotschi, Christian J. Leumann
Chemistry - A European Journal 2005 11 (10.1002/chem.v11:7), 2125-2129
Bipyridyl- and Biphenyl-DNA: A Recognition Motif Based on Interstrand Aromatic Stacking
Christine Brotschi, G�rald Mathis, Christian J. Leumann
Chemistry - A European Journal 2005 11 (10.1002/chem.v11:6), 1911-1923
A Purine-like Nickel(II) Base Pair for DNA
Christopher Switzer, Surajit Sinha, Paul H. Kim, Benjamin D. Heuberger
Angewandte Chemie International Edition 2005 44 (10.1002/anie.v44:10), 1529-1532
A Purine-like Nickel(II) Base Pair for DNA
Christopher Switzer, Surajit Sinha, Paul H. Kim, Benjamin D. Heuberger
Angewandte Chemie 2005 117 (10.1002/ange.v117:10), 1553-1556
Synthesis and redox-active base-pairing properties of DNA incorporating mercapto C-nucleosides
Akihiko Hatano, Seiji Makita, Masayuki Kirihara
Tetrahedron 2005 61, 1723-1730
Forced Intercalation Probes (FIT Probes): Thiazole Orange as a Fluorescent Base in Peptide Nucleic Acids for Homogeneous Single-Nucleotide-Polymorphism Detection
Olaf Köhler, Dilip Venkatrao Jarikote, Oliver Seitz
ChemBioChem 2005 6 (10.1002/cbic.v6:1), 69-77
RNA duplexes with biphenyl substituents as base replacements are less stable than DNA duplexes
Christine Brotschi, Christian J. Leumann
Chemical Communications 2005 , 2023
A pyrimidine-like nickel(ii) DNA base pair
Christopher Switzer, Dongwon Shin
Chemical Communications 2005 , 1342
Fluorous Base-Pairing Effects in a DNA Polymerase Active Site
Jacob S. Lai, Eric T. Kool
Chemistry - A European Journal 2005 11 (10.1002/chem.v11:10), 2966-2971
Artificial metallo-DNA: a bio-inspired approach to metal array programming
Mitsuhiko Shionoya, Kentaro Tanaka
Current Opinion in Chemical Biology 2004 8, 592-597
yDNA: A New Geometry for Size-Expanded Base Pairs
Haige Lu, Kaizhang He, Eric T. Kool
Angewandte Chemie International Edition 2004 43 (10.1002/anie.v43:43), 5834-5836
yDNA: A New Geometry for Size-Expanded Base Pairs
Haige Lu, Kaizhang He, Eric T. Kool
Angewandte Chemie 2004 116 (10.1002/ange.v116:43), 5958-5960
Nonnucleosidic Base Surrogates: The Effect of 1,2-Disubstituted Phenanthrenes on DNA Duplex Stability
Damian Ackermann, Robert Häner
Helvetica Chimica Acta 2004 87, 2790-2804
Synthesis and characterization of a DNA analogue stabilized by mercapto C-nucleoside induced disulfide bonding
Akihiko Hatano, Seiji Makita, Masayuki Kirihara
Bioorganic & Medicinal Chemistry Letters 2004 14, 2459-2462
Unnatural base pairs mediate the site-specific incorporation of an unnatural hydrophobic component into RNA transcripts
Masayuki Endo, Tsuneo Mitsui, Taeko Okuni, Michiko Kimoto, Ichiro Hirao, Shigeyuki Yokoyama
Bioorganic & Medicinal Chemistry Letters 2004 14, 2593-2596
An unnatural hydrophobic base, 4-propynylpyrrole-2-carbaldehyde, as an efficient pairing partner of 9-methylimidazo[(4,5)- b ]pyridine
Tsuneo Mitsui, Michiko Kimoto, Akira Sato, Shigeyuki Yokoyama, Ichiro Hirao
Bioorganic & Medicinal Chemistry Letters 2003 13 (24), 4515-4518
DNA Polymerase Template Interactions Probed by Degenerate Isosteric Nucleobase Analogs
Natasha Paul, Vishal C. Nashine, Geoffrey Hoops, Peiming Zhang, Jie Zhou, Donald E. Bergstrom, V.Jo Davisson
Chemistry & Biology 2003 10, 815-825
Selective recognition of CG interruption by 2′,4′-BNA having 1-isoquinolone as a nucleobase in a pyrimidine motif triplex formation
Yoshiyuki Hari, Satoshi Obika, Mitsuaki Sekiguchi, Takeshi Imanishi
Tetrahedron 2003 59, 5123-5128
Orbital interactions and charge redistribution in weak hydrogen bonds: The Watson–Crick AT mimic adenine-2,4-difluorotoluene
Célia Fonseca Guerra, F. Matthias Bickelhaupt
The Journal of Chemical Physics 2003 119, 4262
Development of a Universal Nucleobase and Modified Nucleobases for Expanding the Genetic Code
Floyd E. Romesberg, Chengzhi Yu, Shigeo Matsuda, Allison A. Henry
2002,1.5.1-1.5.36
Active Site Tightness and Substrate Fit in DNA Replication
Eric T. Kool
Annual Review of Biochemistry 2002 71 (1), 191-219
2-Amino-7-deazaadenine forms stable base pairs with cytosine and thymine
Akimitsu Okamoto, Kazuo Tanaka, Isao Saito
Bioorganic & Medicinal Chemistry Letters 2002 12, 97-99
The origin of spontaneous point mutations in DNA via Löwdin mechanism of proton tunneling in DNA base pairs: Cure with covalent base pairing*
Eugene S. Kryachko
International Journal of Quantum Chemistry 2002 90 (2), 910-923
A Stable DNA Duplex Containing a Non-Hydrogen-Bonding and Non-Shape-Complementary Base Couple: Interstrand Stacking as the Stability Determining Factor
Christine Brotschi, Adrian Häberli, Christian J. Leumann
Angewandte Chemie International Edition 2001 40 (10.1002/1521-3773(20010817)40:16<>1.0.CO;2-A), 3012-3014
Ein stabiler DNA-Duplex mit einem nichtwasserstoffverbrückenden, nichtformkomplementären Basenpaar: Interstrang-Stapelwechselwirkungen als stabilitätsbestimmender Faktor
Christine Brotschi, Adrian Häberli, Christian J. Leumann
Angewandte Chemie 2001 113 (10.1002/1521-3757(20010817)113:16<>1.0.CO;2-6), 3101-3103
A Stable DNA Duplex Containing a Non-Hydrogen-Bonding and Non-Shape-Complementary Base Couple: Interstrand Stacking as the Stability Determining Factor
Christine Brotschi, Adrian Häberli, Christian J. Leumann
Angewandte Chemie International Edition 2001 40 (16), 3012-3014
Ein stabiler DNA-Duplex mit einem nichtwasserstoffverbrückenden, nichtformkomplementären Basenpaar: Interstrang-Stapelwechselwirkungen als stabilitätsbestimmender Faktor
Christine Brotschi, Adrian Häberli, Christian J. Leumann
Angewandte Chemie 2001 113 (16), 3101-3103
Unnatural Nucleosides with Unusual Base Pairing Properties
Donald E. Bergstrom
2001,1.4.1-1.4.13
Hydrogen Bonding, Base Stacking, and Steric Effects in DNA Replication
Eric T. Kool
Annual Review of Biophysics and Biomolecular Structure 2001 30 (1), 1-22
Unnatural base pairs for specific transcription
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Proceedings of the National Academy of Sciences 2001 98, 4922-4925
Synthesis and duplex stability of oligonucleotides containing 7-vinyl-7-deazaguanine as a strong electron-donating nucleobase
Akimitsu Okamoto, Toshiji Taiji, Kazuo Tanaka, Isao Saito
Tetrahedron Letters 2000 41, 10035-10039
Synthetically modified DNAs as substrates for polymerases
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Current Opinion in Chemical Biology 2000 4, 602-608
Stable and Selective Hybridization of Oligonucleotides with Unnatural Hydrophobic Bases
Markus Berger, Anthony K. Ogawa, Dustin L. McMinn, Yiqin Wu, Peter G. Schultz, Floyd E. Romesberg
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Stabile und selektive Hybridisierung von Oligonucleotiden unter Verwendung nichtnatürlicher hydrophober Basen
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Angewandte Chemie 2000 112 (16), 3069-3071
Stable and Selective Hybridization of Oligonucleotides with Unnatural Hydrophobic Bases
Markus Berger, Anthony K. Ogawa, Dustin L. McMinn, Yiqin Wu, Peter G. Schultz, Floyd E. Romesberg
Angewandte Chemie 2000 39 (16), 2940-2942
Roles of Watson-Crick and Minor Groove Hydrogen Bonds in DNA Replication
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Communication

Efforts toward Expansion of the Genetic Alphabet: DNA Polymerase Recognition of a Highly Stable, Self-Pairing Hydrophobic Base

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