Communication
Efficient Replication Bypass of Size‐Expanded DNA Base Pairs in Bacterial Cells*
*
We thank the U.S. National Institutes of Health (CA80024 to J.M.E. and GM63587 to E.T.K.) for support. J.G. and H.L. acknowledge Stanford Graduate Fellowships.
Abstract
Supersize me! Size‐expanded DNA bases (xDNA) are able to encode natural DNA sequences in replication. In vitro experiments with a DNA polymerase show nucleotide incorporation opposite the xDNA bases with correct pairing. In vivo experiments using E. coli show that two xDNA bases (xA and xC, see picture) encode the correct replication partners.
Citing Literature
Number of times cited: 35
- Peiwen Zhao and Yuxiang Bu, Azobenzene‐bridged diradical janus nucleobases with photo‐converted magnetic properties between antiferromagnetic and ferromagnetic couplings, Journal of Computational Chemistry, 39, 20, (1398-1405), (2018).
- Peiwen Zhao and Yuxiang Bu, Remarkable Differences in Spin Couplings for Various Self‐Paired Dimers of Ring‐Expansion‐Radicalized Uracil: A Basis for the Design of Magnetically Anisotropic Assemblies, ChemPhysChem, 19, 2, (208-219), (2018).
- Amit M. Jabgunde, Faten Jaziri, Omprakash Bande, Matheus Froeyen, Mikhail Abramov, Hoai Nguyen, Guy Schepers, Eveline Lescrinier, Vitor B. Pinheiro, Valérie Pezo, Philippe Marlière and Piet Herdewijn, Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo, Chemistry – A European Journal, 24, 48, (12695-12707), (2018).
- Subhendu Sekhar Bag and Suman Kalyan Das, Design, Synthesis and Photophysical Property of a Doubly Widened Fused‐Triazolyl‐Phenanthrene Unnatural Nucleoside, ChemistrySelect, 2, 12, (3577-3583), (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).
- Rania Abu El Asrar, Lia Margamuljana, Mikhail Abramov, Omprakash Bande, Stefano Agnello, Miyeon Jang and Piet Herdewijn, Enzymatic Incorporation of Modified Purine Nucleotides in DNA, ChemBioChem, 18, 24, (2408-2415), (2017).
- Wen-Jin Wu, Wei Yang and Ming-Daw Tsai, How DNA polymerases catalyse replication and repair with contrasting fidelity, Nature Reviews Chemistry, 1, 9, (0068), (2017).
- Indu Negi, Preetleen Kathuria, Purshotam Sharma and Stacey D. Wetmore, How do hydrophobic nucleobases differ from natural DNA nucleobases? Comparison of structural features and duplex properties from QM calculations and MD simulations, Physical Chemistry Chemical Physics, 10.1039/C7CP02576A, 19, 25, (16365-16374), (2017).
- Ruowen Wang, Cheng Jin, Xiaoyan Zhu, Liyi Zhou, Wenjing Xuan, Yuan Liu, Qiaoling Liu and Weihong Tan, Artificial Base zT as Functional “Element” for Constructing Photoresponsive DNA Nanomolecules, Journal of the American Chemical Society, 10.1021/jacs.7b02865, 139, 27, (9104-9107), (2017).
- Elena Eremeeva, Michail Abramov, Lia Margamuljana, Jef Rozenski, Valerie Pezo, Philippe Marlière and Piet Herdewijn, Chemical Morphing of DNA Containing Four Noncanonical Bases, Angewandte Chemie International Edition, 55, 26, (7515-7519), (2016).
- Elena Eremeeva, Michail Abramov, Lia Margamuljana, Jef Rozenski, Valerie Pezo, Philippe Marlière and Piet Herdewijn, Chemical Morphing of DNA Containing Four Noncanonical Bases, Angewandte Chemie, 128, 26, (7641-7645), (2016).
- Anaëlle Dumas, Guillaume Mata and Nathan W. Luedtke, Fluorescent Purine Analogs that Shed Light on DNA Structure and Function, Fluorescent Analogues of Biomolecular Building Blocks: Design and Applications, (242-275), (2016).
- Kalyanashis Jana and Bishwajit Ganguly, In silico studies with substituted adenines to achieve a remarkable stability of mispairs with thymine nucleobase, New Journal of Chemistry, 10.1039/C5NJ02311D, 40, 2, (1807-1816), (2016).
- Subhendu Sekhar Bag, Sangita Talukdar, Suman Kalyan Das, Manoj Kumar Pradhan and Soumen Mukherjee, Donor/acceptor chromophores-decorated triazolyl unnatural nucleosides: synthesis, photophysical properties and study of interaction with BSA, Organic & Biomolecular Chemistry, 10.1039/C6OB00500D, 14, 22, (5088-5108), (2016).
- Kalyanashis Jana and Bishwajit Ganguly, In Silico Studies to Explore the Mutagenic Ability of 5-Halo/Oxy/Li-Oxy-Uracil Bases with Guanine of DNA Base Pairs, The Journal of Physical Chemistry A, 118, 41, (9753), (2014).
- Malte Winnacker and Eric T. Kool, Künstliche genetische Systeme bestehend aus vergrößerten Basenpaaren, Angewandte Chemie, 125, 48, (12728-12739), (2013).
- Purshotam Sharma, Linda A. Lait and Stacey D. Wetmore, yDNA versus yyDNA pyrimidines: computational analysis of the effects of unidirectional ring expansion on the preferred sugar–base orientation, hydrogen-bonding interactions and stacking abilities, Physical Chemistry Chemical Physics, 10.1039/c2cp43910g, 15, 7, (2435), (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).
- Subhendu Sekhar Bag, Sangita Talukdar, Katsuhiko Matsumoto and Rajen Kundu, Triazolyl Donor/Acceptor Chromophore Decorated Unnatural Nucleosides and Oligonucleotides with Duplex Stability Comparable to That of a Natural Adenine/Thymine Pair, The Journal of Organic Chemistry, 10.1021/jo302033f, 78, 2, (278-291), (2012).
- Gevorg Sargsyan and Milan Balaz, Porphyrin–DNA conjugates: porphyrin induced adenine–guanine homoduplex stabilization and interduplex assemblies, Organic & Biomolecular Chemistry, 10.1039/c2ob25710f, 10, 29, (5533), (2012).
- Sascha Rollié, Michael Mangold and Kai Sundmacher, Designing biological systems: Systems Engineering meets Synthetic Biology, Chemical Engineering Science, 10.1016/j.ces.2011.10.068, 69, 1, (1-29), (2012).
- Yin Nah Teo and Eric T. Kool, DNA-Multichromophore Systems, Chemical Reviews, 10.1021/cr100351g, 112, 7, (4221-4245), (2012).
- Astrid Sigel, Bert P. Operschall and Helmut Sigel, Steric guiding of metal ion binding to a purine residue by a non-coordinating amino group: Examplified by 9-[(2-phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer of the antiviral nucleotide analogue 9-[(2-phosphonomethoxy)ethyl]adenine (PMEA), and by related compounds, Coordination Chemistry Reviews, 10.1016/j.ccr.2011.06.030, 256, 1-2, (260-278), (2012).
- John C. Chaput, Hanyang Yu and Su Zhang, The Emerging World of Synthetic Genetics, Chemistry & Biology, 10.1016/j.chembiol.2012.10.011, 19, 11, (1360-1371), (2012).
- José Ramón Blas, Oscar Huertas, Carolina Tabares, Bobby G. Sumpter, Miguel Fuentes-Cabrera, Modesto Orozco, Pablo Ordejón and F. Javier Luque, Structural, Dynamical, and Electronic Transport Properties of Modified DNA Duplexes Containing Size-Expanded Nucleobases, The Journal of Physical Chemistry A, 10.1021/jp205122c, 115, 41, (11344-11354), (2011).
- Omid Khakshoor and Eric T. Kool, Chemistry of nucleic acids: impacts in multiple fields, Chemical Communications, 10.1039/c1cc11021g, 47, 25, (7018), (2011).
- Filip Wojciechowski and Christian J. Leumann, Alternative DNA base-pairs: from efforts to expand the genetic code to potential material applications, Chemical Society Reviews, 10.1039/c1cs15027h, 40, 12, (5669), (2011).
- Sarah K. Jarchow-Choy, Andrew T. Krueger, Haibo Liu, Jianmin Gao and Eric T. Kool, Fluorescent xDNA nucleotides as efficient substrates for a template-independent polymerase, Nucleic Acids Research, 10.1093/nar/gkq853, 39, 4, (1586-1594), (2010).
- Jia Sheng, Abdalla E. A. Hassan, Wen Zhang, Jianfeng Zhou, Bingqian Xu, Alexei S. Soares and Zhen Huang, Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization, Nucleic Acids Research, 10.1093/nar/gkq1288, 39, 9, (3962-3971), (2011).
- Andrew T. Krueger, Larryn W. Peterson, Jijumon Chelliserry, Daniel J. Kleinbaum and Eric T. Kool, Encoding Phenotype in Bacteria with an Alternative Genetic Set, Journal of the American Chemical Society, 10.1021/ja208025e, 133, 45, (18447-18451), (2011).
- Haige Lu, Andrew T. Krueger, Jianmin Gao, Haibo Liu and Eric T. Kool, Toward a designed genetic system with biochemical function: polymerase synthesis of single and multiple size-expanded DNA base pairs, Organic & Biomolecular Chemistry, 10.1039/c002766a, 8, 12, (2704), (2010).
- Lilia Milanesi and Salvador Tomas, Bioinspired organic chemistry, Annual Reports Section "B" (Organic Chemistry), 10.1039/b927089m, 106, (447), (2010).
- , News in brief, Nature Methods, 6, 7, (483), (2009).
- Tatiana Kent, Timur D. Rusanov, Trung M. Hoang, Willem A. Velema, Andrew T. Krueger, William C. Copeland, Eric T. Kool and Richard T. Pomerantz, DNA polymerase θ specializes in incorporating synthetic expanded-size (xDNA) nucleotides, Nucleic Acids Research, 10.1093/nar/gkw721, (gkw721), (2016).
- Laura Albrecht, Katie Wilson and Stacey Wetmore, Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4, Molecules, 10.3390/molecules21070822, 21, 7, (822), (2016).
