1
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Le AV, Hartman MCT. Improved synthesis of the unnatural base NaM, and evaluation of its orthogonality in in vitro transcription and translation. RSC Chem Biol 2024:d4cb00121d. [PMID: 39279876 PMCID: PMC11389374 DOI: 10.1039/d4cb00121d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Accepted: 09/04/2024] [Indexed: 09/18/2024] Open
Abstract
Unnatural base pairs (UBP) promise to diversify cellular function through expansion of the genetic code. Some of the most successful UBPs are the hydrophobic base pairs 5SICS:NaM and TPT3:NaM developed by Romesberg. Much of the research on these UBPs has emphasized strategies to enable their efficient replication, transcription and translation in living organisms. These experiments have achieved spectacular success in certain cases; however, the complexity of working in vivo places strong constraints on the types of experiments that can be done to optimize and improve the system. Testing UBPs in vitro, on the other hand, offers advantages including minimization of scale, the ability to precisely control the concentration of reagents, and simpler purification of products. Here we investigate the orthogonality of NaM-containing base pairs in transcription and translation, looking at background readthrough of NaM codons by the native machinery. We also describe an improved synthesis of NaM triphosphate (NaM-TP) and a new assay for testing the purity of UBP containing RNAs.
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Affiliation(s)
- Anthony V Le
- Virginia Commonwealth University, Department of Chemistry 1001 W Main St. Richmond VA 23284 USA
- Virginia Commonwealth University, Massey Cancer Center 401 College St. Richmond VA 23219 USA
| | - Matthew C T Hartman
- Virginia Commonwealth University, Department of Chemistry 1001 W Main St. Richmond VA 23284 USA
- Virginia Commonwealth University, Massey Cancer Center 401 College St. Richmond VA 23219 USA
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2
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Sett A, Gadewar M, Babu MA, Panja A, Sachdeva P, Almutary AG, Upadhye V, Jha SK, Jha NK. Orchestration and theranostic applications of synthetic genome with Hachimoji bases/building blocks. Chem Biol Drug Des 2024; 103:e14378. [PMID: 38230795 DOI: 10.1111/cbdd.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 01/18/2024]
Abstract
Synthetic genomics is a novel field of chemical biology where the chemically modified genetic alphabets have been considered in central dogma of life. Tweaking of chemical compositions of natural nucleotide bases could be developed as novel building blocks of DNA/RNA. The modified bases (dP, dZ, dS, and dB etc.) have been demonstrated to be adaptable for replication, transcription and follow Darwinism law of evolution. With advancement of chemical biology especially nucleotide chemistry, synthetic genetic codes have been discovered and Hachimoji nucleotides are the most important and significant one among them. These additional nucleotide bases can form orthogonal base-pairing, and also follow Darwinian evolution and other structural features. In the Hachimoji base pairing, synthetic building blocks are formed using eight modified nucleotide (DNA/RNA) letters (hence the name "Hachimoji"). Their structural conformations, like polyelectrolyte backbones and stereo-regular building blocks favor thermodynamic stability and confirm Schrodinger aperiodic crystal. From the structural genomics aspect, these synthetic bases could be incorporated into the central dogma of life. Researchers have shown Hachimoji building blocks were transcribed to its RNA counterpart as a functional fluorescent Hachimoji aptamer. Apart from several unnatural nucleotide base pairs maneuvered into its in vitro and in vivo applications, this review describes future perspective towards the development and therapeutic utilization of the genetic codes, a primary objective of synthetic and chemical biology.
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Affiliation(s)
- Arghya Sett
- ERIN Department, Luxembourg Institute of Science and Technology, 5 Av. des Hauts-Fourneaux, Belval, 4362, Esch, Luxembourg
| | - Manoj Gadewar
- Department of Pharmacology, School of Medical and Allied Sciences, K R Mangalam University, Gurgaon, India
| | - M Arockia Babu
- Institute of Pharmaceutical Research, GLA University, Mathura, India
| | | | | | - Abdulmajeed G Almutary
- Department of Biomedical Sciences, College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Vijay Upadhye
- Centre of Research for Development (CR4D) and Department of Microbiology, Parul University, Vadodara, Gujarat, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Niraj Kumar Jha
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Centre of Research Impact and Outreach, Chitkara University Institute of Engineering and Technology, Chitkara University, Punjab, India
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, 144411, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, India
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3
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Wang R, Wang X, Xie S, Zhang Y, Ji D, Zhang X, Cui C, Jiang J, Tan W. Molecular elements: novel approaches for molecular building. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220024. [PMID: 36633277 PMCID: PMC9835600 DOI: 10.1098/rstb.2022.0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Classically, a molecular element (ME) is a pure substance composed of two or more atoms of the same element. However, MEs, in the context of this review, can be any molecules as elements bonded together into the backbone of synthetic oligonucleotides (ONs) with designed sequences and functions, including natural A, T, C, G, U, and unnatural bases. The use of MEs can facilitate the synthesis of designer molecules and smart materials. In particular, we discuss the landmarks associated with DNA structure and related technologies, as well as the extensive application of ONs, the ideal type of molecules for intervention therapy aimed at correcting disease-causing genetic errors (indels). It is herein concluded that the discovery of ON therapeutics and the fabrication of designer molecules or nanostructures depend on the ME concept that we previously published. Accordingly, ME will be our focal point as we discuss related research directions and perspectives in making molecules and materials. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Ruowen Wang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Xueqiang Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Sitao Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Yanyan Zhang
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Dingkun Ji
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China
| | - Weihong Tan
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, People's Republic of China,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Hangzhou, Zhejiang 310018, People's Republic of China,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People's Republic of China,Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, University of Florida Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
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4
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Miao S, Liang Y, Rundell S, Bhunia D, Devari S, Munyaradzi O, Bong D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers 2021; 112:e23399. [PMID: 32969496 PMCID: PMC7855516 DOI: 10.1002/bip.23399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Rundell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Shekar Devari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Oliver Munyaradzi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
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5
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Kimoto M, Hirao I. Genetic alphabet expansion technology by creating unnatural base pairs. Chem Soc Rev 2020; 49:7602-7626. [PMID: 33015699 DOI: 10.1039/d0cs00457j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advancements in the creation of artificial extra base pairs (unnatural base pairs, UBPs) are opening the door to a new research area, xenobiology, and genetic alphabet expansion technologies. UBPs that function as third base pairs in replication, transcription, and/or translation enable the site-specific incorporation of novel components into DNA, RNA, and proteins. Here, we describe the UBPs developed by three research teams and their application in PCR-based diagnostics, high-affinity DNA aptamer generation, site-specific labeling of RNAs, semi-synthetic organism creation, and unnatural-amino-acid-containing protein synthesis.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore.
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6
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Abstract
Chemical damage to DNA is a key initiator of adverse biological consequences due to disruption of the faithful reading of the genetic code. For example, O6-alkylguanine ( O6-alkylG) DNA adducts are strongly miscoding during DNA replication when the damaged nucleobase is a template for polymerase-mediated translesion DNA synthesis. Thus, mutations derived from O6-alkylG adducts can have severe adverse effects on protein translation and function and are an early event in the initiation of carcinogenesis. However, the low abundance of these adducts places significant limitations on our ability to relate their presence and biological influences with resultant mutations or disease risk. As a consequence, there is a critical need for novel tools to detect and study the biological role of alkylation adducts. Incorporating DNA bases with altered structures that are derived synthetically is a strategy that has been used widely to interrogate biological processes involving DNA. Such synthetic nucleosides have contributed to our understanding of DNA structure, DNA polymerase (Pol) and repair enzyme function, and to the expansion of the genetic alphabet. This Account describes our efforts toward creating and applying synthetic nucleosides directed at DNA adducts. We synthesized a variety of nucleosides with altered base structures that complement the altered hydrogen bonding capacity and hydrophilicity of O6-alkylG adducts. The heterocyclic perimidinone-derived nucleoside Per was the first of such adduct-directed synthetic nucleosides; it specifically stabilized O6-benzylguanine ( O6-BnG) in a DNA duplex. Structural variants of Per were used to determine hydrogen bonding and base-stacking contributions to DNA duplex stability in templates containing O6-BnG as well as O6-methylguanine ( O6-MeG) adducts. We created synthetic probes able to stabilize damaged over undamaged templates and established how altered hydrogen bonding or base-stacking properties impact DNA duplex stability as a function of adduct structures. This knowledge was then applied to devise a hybridization-based detection strategy involving gold nanoparticles that distinguish damaged from undamaged DNA by colorimetric changes. Furthermore, synthetic nucleosides were used as mechanistic tools to understand chemical determinants such as hydrogen bonding, π-stacking, and size and shape deviations that impact the efficiency and fidelity of DNA adduct bypass by DNA Pols. Finally, we reported the first example of amplifying alkylated DNA, accomplished by combining an engineered polymerase and synthetic triphosphate for which incorporation is templated by a DNA adduct. The presence of the synthetic nucleoside in amplicons could serve as a marker for the presence and location of DNA damage at low levels in DNA strands. Adduct-directed synthetic nucleosides have opened new concepts to interrogate the levels, locations, and biological influences of DNA alkylation.
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Affiliation(s)
- Michael H. Räz
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
| | - Claudia M. N. Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
| | - Hailey L. Gahlon
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
| | - Shana J. Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, Zürich 8092, Switzerland
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7
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Abstract
In this review, we have summarized the research effort into the development of unnatural base pairs beyond standard Watson-Crick (WC) base pairs for synthetic biology. Prior to introducing our research results, we present investigations by four outstanding groups in the field. Their research results demonstrate the importance of shape complementarity and stacking ability as well as hydrogen-bonding (H-bonding) patterns for unnatural base pairs. On the basis of this research background, we developed unnatural base pairs consisting of imidazo[5',4':4.5]pyrido[2,3-d]pyrimidines and 1,8-naphthyridines, i.e., Im : Na pairs. Since Im bases are recognized as ring-expanded purines and Na bases are recognized as ring-expanded pyrimidines, Im : Na pairs are expected to satisfy the criteria of shape complementarity and enhanced stacking ability. In addition, these pairs have four non-canonical H-bonds. Because of these preferable properties, ImNN : NaOO, one of the Im : Na pairs, is recognized as a complementary base pair in not only single nucleotide insertion, but also the PCR.
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8
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Jian Y, Maximowitsch E, Liu D, Adhikari S, Li L, Domratcheva T. Indications of 5' to 3' Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog. Chemistry 2017; 23:7526-7537. [PMID: 28370554 DOI: 10.1002/chem.201700045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 12/12/2022]
Abstract
Pyrimidine dimers are the most common DNA lesions generated under UV radiation. To reveal the molecular mechanisms behind their formation, it is of significance to reveal the roles of each pyrimidine residue. We thus replaced the 5'-pyrimidine residue with a photochemically inert xylene moiety (X). The electron-rich X can be readily oxidized but not reduced, defining the direction of interbase electron transfer (ET). Irradiation of the XpT dinucleotide under 254 nm UV light generates two major photoproducts: a pyrimidine (6-4) pyrimidone analog (6-4PP) and an analog of the so-called spore photoproduct (SP). Both products are formed by reaction at C4=O of the photo-excited 3'-thymidine (T), which indicates that excitation of a single "driver" residue is sufficient to trigger pyrimidine dimerization. Our quantum-chemical calculations demonstrated that photo-excited 3'-T accepts an electron from 5'-X. The resulting charge-separated radical pair lowers its energy upon formation of interbase covalent bonds, eventually yielding 6-4PP and SP.
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Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,School of Chemistry & Chemical Engineering, Shaanxi Normal University (SNNU), No. 620, West Chang'an Avenue, Xi'an, Shaanxi, 710119, P. R. China
| | - Egle Maximowitsch
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Degang Liu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Surya Adhikari
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
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9
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10
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Barbosa AS, da Silva FF, Rebelo A, Hoffmann SV, Bettega MHF, Limão-Vieira P. Valence and Rydberg Excitations of 2,4- and 2,6-Difluorotoluene as Studied by Vacuum Ultraviolet Synchrotron Radiation and ab Initio Calculations. J Phys Chem A 2016; 120:8998-9007. [DOI: 10.1021/acs.jpca.6b07815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Souza Barbosa
- Departamento
de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
- Laboratório
de Colisões Atómicas e Moleculares, CEFITEC, Departamento
de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - F. Ferreira da Silva
- Laboratório
de Colisões Atómicas e Moleculares, CEFITEC, Departamento
de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - A. Rebelo
- Laboratório
de Colisões Atómicas e Moleculares, CEFITEC, Departamento
de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - S. V. Hoffmann
- ISA,
Department of Physics and Astronomy, Aarhus University, Ny Munkegade
120, DK-8000, Aarhus
C, Denmark
| | - M. H. F. Bettega
- Departamento
de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-990 Curitiba, Paraná, Brazil
| | - P. Limão-Vieira
- Laboratório
de Colisões Atómicas e Moleculares, CEFITEC, Departamento
de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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11
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Probst M, Aeschimann W, Chau TTH, Langenegger SM, Stocker A, Häner R. Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease. Nucleic Acids Res 2016; 44:7079-89. [PMID: 27422870 PMCID: PMC5009758 DOI: 10.1093/nar/gkw644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/13/2023] Open
Abstract
The use of the DNA duplex as a supramolecular scaffold is an established approach for the assembly of chromophore aggregates. In the absence of detailed structural insight, the characterization of thus assembled oligochromophores is, today, largely based on solution-phase spectroscopy. Here, we describe the crystal structures of three DNA-organized chromophore aggregates. DNA hybrids containing non-nucleosidic pyrene and phenanthrene building blocks were co-crystallized with the recently described binding domain of the restriction enzyme BpuJI. Crystal structures of these complexes were determined at 2.7, 1.9 and 1.6 Å resolutions. The structures reveal aromatic stacking interactions between pyrene and/or phenanthrene units within the framework of the B-DNA duplex. In hybrids containing a single modification in each DNA strand near the end of the duplex, the two polyaromatic hydrocarbons are engaged in a face-to-face stacking orientation. Due to crystal packing and steric effects, the terminal GC base pair is disrupted in all three crystal structures, which results in a non-perfect stacking arrangement of the aromatic chromophores in two of the structures. In a hybrid containing a total of three pyrenes, crystal lattice induced end-to-end stacking of individual DNA duplexes leads to the formation of an extended aromatic π-stack containing four co-axially arranged pyrenes. The aromatic planes of the stacked pyrenes are oriented in a parallel way. The study demonstrates the value of co-crystallization of chemically modified DNA with the recombinant binding domain of the restriction enzyme BpuJI for obtaining detailed structural insight into DNA-assembled oligochromophores.
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Affiliation(s)
- Markus Probst
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Walter Aeschimann
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Thi T H Chau
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Achim Stocker
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland
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12
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Chawla M, Credendino R, Chermak E, Oliva R, Cavallo L. Theoretical Characterization of the H-Bonding and Stacking Potential of Two Nonstandard Nucleobases Expanding the Genetic Alphabet. J Phys Chem B 2016; 120:2216-24. [DOI: 10.1021/acs.jpcb.6b00125] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mohit Chawla
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raffaele Credendino
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Edrisse Chermak
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department
of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143 Naples, Italy
| | - Luigi Cavallo
- Physical
Sciences and Engineering Division (PSE), Kaust Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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13
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Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics. Methods Enzymol 2015; 566:89-110. [PMID: 26791977 DOI: 10.1016/bs.mie.2015.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proton assignment of nuclear magnetic resonance (NMR) spectra of homopyrimidine/homopurine tract oligonucleotides becomes extremely challenging with increasing helical length due to severe cross-peak overlap. As an alternative to the more standard practice of (15)N and (13)C labeling of oligonucleotides, here, we describe a method for assignment of highly redundant DNA sequences that uses single-site substitution of the thymine isostere 2,4-difluoro-5-methylbenzene (dF). The impact of this approach in facilitating the assignment of intractable spectra and analyzing oligonucleotide structure and dynamics is demonstrated using A-tract and TATA box DNA and two polypurine tract-containing RNA:DNA hybrids derived from HIV-1 and the Saccharomyces cerevisiae long-terminal repeat-containing retrotransposon Ty3. Only resonances proximal to the site of dF substitution exhibit sizable chemical shift changes, providing spectral dispersion while still allowing chemical shift mapping of resonances from unaffected residues distal to the site of modification directly back to the unmodified sequence. It is further illustrated that dF incorporation can subtly alter the conformation and dynamics of homopyrimidine/homopurine tract oligonucleotides, and how these NMR observations can be correlated, in the cases of the TATA box DNA, with modulation in the TATA box-binding protein interaction using an orthogonal gel assay.
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14
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Tarashima N, Komatsu Y, Furukawa K, Minakawa N. Faithful PCR Amplification of an Unnatural Base-Pair Analogue with Four Hydrogen Bonds. Chemistry 2015; 21:10688-95. [DOI: 10.1002/chem.201501484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 12/31/2022]
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15
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2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
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16
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Tanaka Y, Kondo J, Sychrovský V, Šebera J, Dairaku T, Saneyoshi H, Urata H, Torigoe H, Ono A. Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs. Chem Commun (Camb) 2015; 51:17343-60. [DOI: 10.1039/c5cc02693h] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this feature article, recent progress and future perspectives of metal-mediated base-pairs such as T–Hg(ii)–T and C–Ag(i)–C are presented.
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Affiliation(s)
- Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences
- Tokushima Bunri University
- Tokushima
- Japan
- Graduate School of Pharmaceutical Sciences
| | - Jiro Kondo
- Department of Materials and Life Sciences
- Faculty of Science and Technology
- Sophia University
- Chiyoda-ku
- Japan
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6
- Czech Republic
- Institute of Physics
| | - Takenori Dairaku
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai
- Japan
| | - Hisao Saneyoshi
- Department of Material & Life Chemistry
- Kanagawa University
- Yokohama
- Japan
| | - Hidehito Urata
- Osaka University of Pharmaceutical Sciences
- Takatsuki
- Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry
- Faculty of Science
- Tokyo University of Science
- Shinjuku-ku
- Japan
| | - Akira Ono
- Department of Material & Life Chemistry
- Kanagawa University
- Yokohama
- Japan
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17
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Jissy AK, Konar S, Datta A. Molecular Switching Behavior in Isosteric DNA Base Pairs. Chemphyschem 2013; 14:1219-26. [DOI: 10.1002/cphc.201201083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Indexed: 12/22/2022]
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18
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Liu D, Li L. Examining the base stacking interaction in a dinucleotide context via reversible cyclobutane dimer analogue formation under UV irradiation. RSC Adv 2013; 3. [PMID: 24223299 DOI: 10.1039/c3ra41702f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Substituted tolyl groups are considered as close isosteres of the thymine (T) residue. They can be recognized by DNA polymerases as if they were thymine. Although these toluene derivatives are relatively inert toward radical additions, our recent finding suggests that the dinucleotide analogue TpTo (To = 2'-deoxy-1-(3-tolyl)-β-D-ribofuranose) supports an ortho photocycloaddition reaction upon UV irradiation, producing two cyclobutane pyrimidine dimer (CPD) analogues 2 and 3. Our report here further shows that formation of these CPD species is reversible under UVC irradiation, resembling the photochemical property of the CPD species formed between two Ts. Analyzing the stability of these CPD analogues suggests that one (2) is more stable than the other (3). The TpTo conformer responsible for 2 formation is also more stable than that responsible for 3 formation, as indicated by the Gibbs free energy change calculated from the constructed Bordwell thermodynamic cycle. These different stabilities are not due to the varying photochemical properties, as proved by quantum yields determined from the corresponding photoreactions. Instead, they are ascribed to the different stacking interaction between the T and the To rings both in the TpTo dinucleotide as well as in the formed CPD analogues. Factors contributing to the ring stacking interactions are also discussed. Our proof-of-concept approach suggests that a carefully designed Bordwell cycle coupled with reversible CPD formations under UV irradiation can be very useful in studying DNA base interactions.
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Affiliation(s)
- Degang Liu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202
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19
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Hirao I, Kimoto M, Yamashige R. Natural versus artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies. Acc Chem Res 2012; 45:2055-65. [PMID: 22263525 DOI: 10.1021/ar200257x] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Since life began on Earth, the four types of bases (A, G, C, and T(U)) that form two sets of base pairs have remained unchanged as the components of nucleic acids that replicate and transfer genetic information. Throughout evolution, except for the U to T modification, the four base structures have not changed. This constancy within the genetic code raises the question of how these complicated nucleotides were generated from the molecules in a primordial soup on the early Earth. At some prebiotic stage, the complementarity of base pairs might have accelerated the generation and accumulation of nucleotides or oligonucleotides. We have no clues whether one pair of nucleobases initially appeared on the early Earth during this process or a set of two base pairs appeared simultaneously. Recently, researchers have developed new artificial pairs of nucleobases (unnatural base pairs) that function alongside the natural base pairs. Some unnatural base pairs in duplex DNA can be efficiently and faithfully amplified in a polymerase chain reaction (PCR) using thermostable DNA polymerases. The addition of unnatural base pair systems could expand the genetic alphabet of DNA, thus providing a new mechanism for the generation novel biopolymers by the site-specific incorporation of functional components into nucleic acids and proteins. Furthermore, the process of unnatural base pair development might provide clues to the origin of the natural base pairs in a primordial soup on the early Earth. In this Account, we describe the development of three representative types of unnatural base pairs that function as a third pair of nucleobases in PCR and reconsider the origin of the natural nucleic acids. As researchers developing unnatural base pairs, they use repeated "proof of concept" experiments. As researchers design new base pairs, they improve the structures that function in PCR and eliminate those that do not. We expect that this process is similar to the one functioning in the chemical evolution and selection of the natural nucleobases. Interestingly, the initial structures designed by each research group were quite similar to those of the latest successful unnatural base pairs. In this regard, it is tempting to form a hypothesis that the base pairs on the primordial Earth, in which the natural purine bases, A and G, and pyrimidine bases, C and T(U), originated from structurally similar compounds, such as hypoxanthine for a purine base predecessor. Subsequently, the initial base pair evolved to the present two sets of base pairs via a keto-enol tautomerization of the initial compounds.
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Affiliation(s)
- Ichiro Hirao
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Michiko Kimoto
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Rie Yamashige
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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20
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Egli M. The steric hypothesis for DNA replication and fluorine hydrogen bonding revisited in light of structural data. Acc Chem Res 2012; 45:1237-46. [PMID: 22524491 DOI: 10.1021/ar200303k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In DNA, bases pair in a molecular interaction that is both highly predictable and exquisitely specific. Therefore researchers have generally believed that the insertion of the matching nucleotide opposite a template base by DNA polymerases (pols) required Watson-Crick (W-C) hydrogen bond formation. However pioneering work by Kool and co-workers using hydrophobic base analogs such as the thymine (T) isostere 2,4-difluorotoluene (F) showed that shape rather than H-bonding served as the primary source of specificity in DNA replication by certain pols. This steric hypothesis for DNA replication has gained popularity, perhaps discouraging further experimental studies to address potential limitations of this new idea. The idea that shape trumps H-bonding in terms of pol selectivity largely hinges on the belief that fluorine is a poor H-bond acceptor. However, the shape complementarity model was embraced in the absence of any detailed structural data for match (F:A) and mismatch pairs (F:G, F:C, F:T) in DNA duplexes or at active sites of pols. Although the F and T nucleosides are roughly isosteric, it is unclear whether F:A and T:A pairs exhibit similar geometries. If the F:A pair is devoid of H-bonding, it will be notably wider than a T:A pair. Because shape and size and H-bonding are intimately related, it may not be possible to separate these two properties. Thus the geometries of an isolated F:A pair in water may differ considerably from an F:A pair embedded in a stretch of duplex DNA, at the tight active site of an A-family replicative pol, or within the spacious active site of a Y-family translesion pol. The shape complementarity model may have more significance for pol accuracy than efficiency: this model appears to be most relevant for replicative pols that use specific residues to probe the identity of the nascent base pair from the minor groove side. However, researchers have not fully considered the importance of such interactions that include H-bonds compared with W-C H-bonds in terms of pol fidelity and the shape complementarity model. This Account revisits the steric hypothesis for DNA replication in light of recent structural data and discusses the role of fluorine as an H-bond acceptor. Over the last 5 years, crystal structures have emerged for nucleic acid duplexes with F paired opposite to natural bases or located at the active sites of DNA pols. These data permit a more nuanced understanding of the role of shape in DNA replication and the capacity of fluorine to form H-bonds. These studies and additional research involving RNA or other fluorine-containing nucleoside analogs within duplexes indicate that fluorine engages in H-bonding in many cases. Although T and F are isosteric at the nucleoside level, replacement of a natural base by F in pairs often changes their shapes and sizes, and dF in DNA behaves differently from rF in RNA. Similarly, the pairing geometries observed for F and T opposite dATP, dGTP, dTTP, or dCTP and their H-bonding patterns at the active site of a replicative pol differ considerably.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
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21
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Liu D, Zhou Y, Pu J, Li L. 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 2012; 18:7823-33. [PMID: 22588824 PMCID: PMC3374913 DOI: 10.1002/chem.201200816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Indexed: 11/07/2022]
Abstract
Substituted toluenyl groups are considered as close isosteres of the thymine residue. They can be recognized by DNA polymerases as if they were thymine. These toluene derivatives are generally inert toward radical additions, including the [2+2] photo-cycloadditions, due to the stable structure of the aromatic ring and are usually used as solvents for radical reactions. Surprisingly, after incorporating toluene into the dinucleotide framework, we found that the UV excited thymine residue readily dimerizes with the toluenyl moiety through a [2+2] photo-addition reaction. Furthermore, the reaction site on the toluenyl moiety is not the C5=C6 bond, as commonly observed in cyclobutane pyrimidine dimers, but the C4=C5 or C3=C4 instead. Such a reaction pattern suggests that in the stacked structure, it is one of these bonds, not the C5=C6, that is close to the thymine C5=C6 bond. A similar structural feature is found in DNA duplex with a thymine replaced by a 2,4-difluorotoluene. Our results argue that although the substituted toluenyl moieties closely mimic the size and shape of the thymine residue, their more hydrophobic nature determines that they stack on DNA bases differently from the natural thymine residue and likely cause local conformational changes in duplex DNA.
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Affiliation(s)
- Degang Liu
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA), Fax: (+1)317-274-4701
| | - Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA), Fax: (+1)317-274-4701
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA), Fax: (+1)317-274-4701
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University–Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA), Fax: (+1)317-274-4701
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202 (USA)
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22
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Funai T, Miyazaki Y, Aotani M, Yamaguchi E, Nakagawa O, Wada SI, Torigoe H, Ono A, Urata H. AgI Ion Mediated Formation of a C-A Mispair by DNA Polymerases. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201109191] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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23
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Funai T, Miyazaki Y, Aotani M, Yamaguchi E, Nakagawa O, Wada SI, Torigoe H, Ono A, Urata H. AgI Ion Mediated Formation of a C-A Mispair by DNA Polymerases. Angew Chem Int Ed Engl 2012; 51:6464-6. [DOI: 10.1002/anie.201109191] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 04/16/2012] [Indexed: 01/13/2023]
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24
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Xia S, Eom SH, Konigsberg WH, Wang J. Structural basis for differential insertion kinetics of dNMPs opposite a difluorotoluene nucleotide residue. Biochemistry 2012; 51:1476-85. [PMID: 22304682 DOI: 10.1021/bi2016487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have recently challenged the widely held view that 2,4-difluorotoluene (dF) is a nonpolar isosteric analogue of the nucleotide dT, incapable of forming hydrogen bonds (HBs). To gain a further understanding for the kinetic preference that favors dAMP insertion opposite a templating dF, a result that mirrors the base selectivity that favors dAMP insertion opposite dT by RB69 DNA polymerase (RB69pol), we determined presteady-state kinetic parameters for incorporation of four dNMPs opposite dF by RB69pol and solved the structures of corresponding ternary complexes. We observed that both the F2 and F4 substituent of dF in these structures serve as HB acceptors forming HBs either directly with dTTP and dGTP or indirectly with dATP and dCTP via ordered water molecules. We have defined the shape and chemical features of each dF/dNTP pair in the RB69pol active site without the corresponding phosphodiester-linkage constraints of dF/dNs when they are embedded in isolated DNA duplexes. These features can explain the kinetic preferences exhibited by the templating dF when the nucleotide incorporation is catalyzed by wild type RB69pol or its mutants. We further show that the shapes of the dNTP/dF nascent base pair differ markedly from the corresponding dNTP/dT in the pol active site and that these differences have a profound effect on their incorporation efficiencies.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, United States
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25
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Khakshoor O, Wheeler SE, Houk KN, Kool ET. Measurement and theory of hydrogen bonding contribution to isosteric DNA base pairs. J Am Chem Soc 2012; 134:3154-63. [PMID: 22300089 DOI: 10.1021/ja210475a] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We address the recent debate surrounding the ability of 2,4-difluorotoluene (F), a low-polarity mimic of thymine (T), to form a hydrogen-bonded complex with adenine in DNA. The hydrogen bonding ability of F has been characterized as small to zero in various experimental studies, and moderate to small in computational studies. However, recent X-ray crystallographic studies of difluorotoluene in DNA/RNA have indicated, based on interatomic distances, possible hydrogen bonding interactions between F and natural bases in nucleic acid duplexes and in a DNA polymerase active site. Since F is widely used to measure electrostatic contributions to pairing and replication, it is important to quantify the impact of this isostere on DNA stability. Here, we studied the pairing stability and selectivity of this compound and a closely related variant, dichlorotoluene deoxyriboside (L), in DNA, using both experimental and computational approaches. We measured the thermodynamics of duplex formation in three sequence contexts and with all possible pairing partners by thermal melting studies using the van't Hoff approach, and for selected cases by isothermal titration calorimetry (ITC). Experimental results showed that internal F-A pairing in DNA is destabilizing by 3.8 kcal/mol (van't Hoff, 37 °C) as compared with T-A pairing. At the end of a duplex, base-base interactions are considerably smaller; however, the net F-A interaction remains repulsive while T-A pairing is attractive. As for selectivity, F is found to be slightly selective for adenine over C, G, T by 0.5 kcal mol, as compared with thymine's selectivity of 2.4 kcal/mol. Interestingly, dichlorotoluene in DNA is slightly less destabilizing and slightly more selective than F, despite the lack of strongly electronegative fluorine atoms. Experimental data were complemented by computational results, evaluated at the M06-2X/6-31+G(d) and MP2/cc-pVTZ levels of theory. These computations suggest that the pairing energy of F to A is ~28% of that of T-A, and most of this interaction does not arise from the F···HN interaction, but rather from the CH···N interaction. The nucleobase analogue shows no inherent selectivity for adenine over other bases, and L-A pairing energies are slightly weaker than for F-A. Overall, the results are consistent with a small favorable noncovalent interaction of F with A offset by a large desolvation cost for the polar partner. We discuss the findings in light of recent structural studies and of DNA replication experiments involving these analogues.
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Affiliation(s)
- Omid Khakshoor
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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26
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Wierzbinski E, de Leon A, Davis KL, Bezer S, Wolak MA, Kofke MJ, Schlaf R, Achim C, Waldeck DH. Charge transfer through modified peptide nucleic acids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:1971-1981. [PMID: 22217076 DOI: 10.1021/la204445u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We studied the charge transfer properties of bipyridine-modified peptide nucleic acid (PNA) in the absence and presence of Zn(II). Characterization of the PNA in solution showed that Zn(II) interacts with the bipyridine ligands, but the stability of the duplexes was not affected significantly by the binding of Zn(II). The charge transfer properties of these molecules were examined by electrochemistry for self-assembled monolayers of ferrocene-terminated PNAs and by conductive probe atomic force microscopy for cysteine-terminated PNAs. Both electrochemical and single molecular studies showed that the bipyridine modification and Zn(II) binding do not affect significantly the charge transfer of the PNA duplexes.
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Affiliation(s)
- Emil Wierzbinski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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27
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Hirao I, Kimoto M. Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2012; 88:345-67. [PMID: 22850726 PMCID: PMC3422687 DOI: 10.2183/pjab.88.345] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 06/01/2012] [Indexed: 05/30/2023]
Abstract
Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A-T and G-C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating "proof of concept" experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.
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Affiliation(s)
- Ichiro Hirao
- RIKEN Systems and Structural Biology Center (SSBC), Yokohama, Japan.
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28
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Xia S, Konigsberg WH, Wang J. Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex. J Am Chem Soc 2011; 133:10003-5. [PMID: 21667997 DOI: 10.1021/ja2021735] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Results obtained using 2,4-difluorotoluene nucleobase (dF) as a nonpolar thymine isostere by Kool and colleagues challenged the Watson-Crick dogma that hydrogen bonds between complementary bases are an absolute requirement for accurate DNA replication. Here, we report crystal structure of an RB69 DNA polymerase L561A/S565G/Y567A triple mutant ternary complex with a templating dF opposite dTTP at 1.8 Å-resolution. In this structure, direct hydrogen bonds were observed between: (i) dF and the incoming dTTP, (ii) dF and residue G568 of the polymerase, and (iii) dF and ordered water molecules surrounding the nascent base pair. Therefore, this structure provides evidence that a templating dF can form novel hydrogen bonds with the incoming dTTP and with the enzyme that differ from those formed with a templating dT.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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29
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Benitex Y, Baranger AM. Control of the stability of a protein-RNA complex by the position of fluorine in a base analogue. J Am Chem Soc 2011; 133:3687-9. [PMID: 21361282 DOI: 10.1021/ja102601h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The effects of modifying the electronic characteristics of nonpolar base analogues substituted at positions involved in stacking interactions between SL2 RNA and the U1A protein are described. A surprisingly large difference in the stability between complexes formed with base analogues that differ only in the position of substitution of a single fluorine atom is observed. The results of high-level ab initio calculations of the interactions between the nonpolar base analogue and the amino acid side chain correlate with the experimentally observed trends in complex stability, which suggests that changes in stacking interactions that result from varying the position and degree of fluorine substitution contribute to the effects of fluorine substitution on the stability of the U1A-SL2 RNA complex.
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Affiliation(s)
- Yulia Benitex
- Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, United States
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30
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Urata H, Yamaguchi E, Funai T, Matsumura Y, Wada SI. Incorporation of thymine nucleotides by DNA polymerases through T-Hg(II)-T base pairing. Angew Chem Int Ed Engl 2011; 49:6516-9. [PMID: 20602391 DOI: 10.1002/anie.201002142] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hidehito Urata
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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31
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Dallmann A, Dehmel L, Peters T, Mügge C, Griesinger C, Tuma J, Ernsting NP. 2-Aminopurine incorporation perturbs the dynamics and structure of DNA. Angew Chem Int Ed Engl 2010; 49:5989-92. [PMID: 20632340 DOI: 10.1002/anie.201001312] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- André Dallmann
- Humboldt Universität zu Berlin, Institut für Chemie, 12489 Berlin, Germany
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32
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Cravens SL, Navapanich AC, Geierstanger BH, Tahmassebi DC, Dwyer TJ. NMR Solution Structure of a DNA−Actinomycin D Complex Containing a Non-Hydrogen-Bonding Pair in the Binding Site. J Am Chem Soc 2010; 132:17588-98. [DOI: 10.1021/ja107575f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Shannen L. Cravens
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Alyssa C. Navapanich
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Bernhard H. Geierstanger
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Deborah C. Tahmassebi
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Tammy J. Dwyer
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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Urata H, Yamaguchi E, Nakamura Y, Wada SI. Pyrimidine-pyrimidine base pairs stabilized by silver(I) ions. Chem Commun (Camb) 2010; 47:941-3. [PMID: 21076774 DOI: 10.1039/c0cc04091f] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the presence of Ag(I) ions, the C-T and m(5)iC (5-methylisocytosine)-T base pairs showed comparable stability to the C-Ag(I)-C base pair, and the m(5)iC-C base pair was highly stabilized by the synergetic effect of Ag(I) coordination and possible hydrogen bonding.
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Affiliation(s)
- Hidehito Urata
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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Urata H, Yamaguchi E, Funai T, Matsumura Y, Wada SI. Incorporation of Thymine Nucleotides by DNA Polymerases through T-HgII-T Base Pairing. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002142] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Dallmann A, Dehmel L, Peters T, Mügge C, Griesinger C, Tuma J, Ernsting N. Der Einbau von 2-Aminopurin beeinflusst die Dynamik und Struktur von DNA. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001312] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Pallan PS, Egli M. Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography. J Am Chem Soc 2009; 131:12548-9. [PMID: 19685868 DOI: 10.1021/ja905739j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Certain DNA polymerases (pols) were found to efficiently insert A opposite the hydrophobic T isostere 2,4-difluorotoluene (F) and vice versa, resulting in the widely held belief that some pols rely on shape rather than H-bonding for accurate replication. Using X-ray crystallography we have analyzed the geometry of F:A pairs in duplex DNA and observed a distance between fluorine and the exocyclic amino group of A that is consistent with a H-bond, thus challenging the assumption that the F analogue is unable to engage in H-bonding as well as the steric hypothesis of DNA replication. Therefore, shape and H-bonding are inherently related, and steric constraints at a pol active site, or conferred by stacking or the DNA backbone conformation, may enable H-bonding by F.
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Affiliation(s)
- Pradeep S Pallan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
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37
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Duduială CI, Wattis JAD, Dryden IL, Laughton CA. Nonlinear breathing modes at a defect site in DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:061906. [PMID: 20365189 DOI: 10.1103/physreve.80.061906] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 09/09/2009] [Indexed: 05/26/2023]
Abstract
Molecular-dynamics simulations of a normal DNA duplex show that breathing events typically occur on the microsecond time scale. This paper analyzes a 12 base pairs DNA duplex containing the "rogue" base difluorotoluene (F) in place of a thymine base (T), for which the breathing events occur on the nanosecond time scale. Starting from a nonlinear Klein-Gordon lattice model and adding noise and damping, we obtain a mesoscopic model of the DNA duplex close to that observed in experiments and all-atom molecular dynamics simulations. The mesoscopic model is calibrated to data from the all-atom molecular dynamics package AMBER for a variety of twist angles of the DNA duplex. Defects are considered in the interchain interactions as well as in the along-chain interactions. This paper also discusses the role of the fluctuation-dissipation relations in the derivation of reduced (mesoscopic) models, the differences between the potential of mean force and the potential energies used in Klein-Gordon lattices, and how breathing can be viewed as competition between the along-chain elastic energy and the interchain binding energy.
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Affiliation(s)
- Ciprian-Ionuţ Duduială
- School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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38
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Affiliation(s)
- Michal Hocek
- Department of Chemistry, WestChem, University of Glasgow, Glasgow G12 8QQ, United Kingdom, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, CZ-16610 Prague 6, Czech Republic
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39
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Lee I, Berdis AJ. Non-natural nucleotides as probes for the mechanism and fidelity of DNA polymerases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1064-80. [PMID: 19733263 DOI: 10.1016/j.bbapap.2009.08.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Revised: 08/17/2009] [Accepted: 08/19/2009] [Indexed: 11/25/2022]
Abstract
DNA is a remarkable macromolecule that functions primarily as the carrier of the genetic information of organisms ranging from viruses to bacteria to eukaryotes. The ability of DNA polymerases to efficiently and accurately replicate genetic material represents one of the most fundamental yet complex biological processes found in nature. The central dogma of DNA polymerization is that the efficiency and fidelity of this biological process is dependent upon proper hydrogen-bonding interactions between an incoming nucleotide and its templating partner. However, the foundation of this dogma has been recently challenged by the demonstration that DNA polymerases can effectively and, in some cases, selectively incorporate non-natural nucleotides lacking classic hydrogen-bonding capabilities into DNA. In this review, we describe the results of several laboratories that have employed a variety of non-natural nucleotide analogs to decipher the molecular mechanism of DNA polymerization. The use of various non-natural nucleotides has lead to the development of several different models that can explain how efficient DNA synthesis can occur in the absence of hydrogen-bonding interactions. These models include the influence of steric fit and shape complementarity, hydrophobicity and solvation energies, base-stacking capabilities, and negative selection as alternatives to rules invoking simple recognition of hydrogen-bonding patterns. Discussions are also provided regarding how the kinetics of primer extension and exonuclease proofreading activities associated with high-fidelity DNA polymerases are influenced by the absence of hydrogen-bonding functional groups exhibited by non-natural nucleotides.
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Affiliation(s)
- Irene Lee
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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Zhang H, Beckman J, Wang J, Konigsberg W. RB69 DNA polymerase mutants with expanded nascent base-pair-binding pockets are highly efficient but have reduced base selectivity. Biochemistry 2009; 48:6940-50. [PMID: 19522539 DOI: 10.1021/bi900422b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have investigated the effect of systematically enlarging the nascent base-pair-binding pocket (NBP) of a replicative DNA polymerase from bacteriophage RB69 (RB69 pol) on the incorporation efficiency (k(pol)/K(d,app)) for both correct and incorrect dNMPs. Accordingly, we replaced residues L561, Y567, and S565 in the NBP with Ala, Ala, and Gly, respectively. We combined L561A and Y567A to give a double mutant and then introduced the S565G mutation to give a triple mutant. The efficiency of incorrect dNMP insertion increased markedly relative to the wild type with the single mutants and increased further as the number of substitutions in the NBP increased. The difference in incorporation efficiency for mispairs between the mutants and the wild-type RB69 pol was due mainly to k(pol). Unexpectedly, enlarging the NBP had a minimal effect on the incorporation efficiency of correct dNMPs. Our kinetic data suggest that replicative DNA pols exert base discrimination via "negative selection" against mispairs by using residues in the NBP, particularly the three residues analyzed in this study, to allow rapid incorporation of only correct base pairs. This proposal differs from how geometry and "tightness of fit" of the NBP is often invoked to account for rapid incorporation of correct base pairs, namely, that a tighter fit within the NBP leads to an increase in insertion rates [Kool, E. T. (2002) Annu. Rev. Biochem. 71, 191-219]. We related our findings to that of a model translesion DNA pol, Sulfolobus solfataricus Dpo4. We concur with the main conclusion of a previous study [Mizukami, S., et al. (2006) Biochemistry 45, 2772-2778], namely, that lesion bypass pols exhibit low incorporation efficiencies for correct dNMPs (leading to relative promiscuity) not because of a more open NBP but because of a loose fit of substrates bound in the catalytic centers. This is a property not shared by RB69 pol and its mutants.
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Affiliation(s)
- Hong Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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41
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Turner KB, Yi-Brunozzi HY, Brinson RG, Marino JP, Fabris D, Le Grice SFJ. SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids. RNA (NEW YORK, N.Y.) 2009; 15:1605-1613. [PMID: 19535461 PMCID: PMC2714758 DOI: 10.1261/rna.1615409] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 04/29/2009] [Indexed: 05/27/2023]
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) has gained popularity as a facile method of examining RNA structure both in vitro and in vivo, exploiting accessibility of the ribose 2'-OH to acylation by N-methylisatoic anhydride (NMIA) in unpaired or flexible configurations. Subsequent primer extension terminates at the site of chemical modification, and these products are fractionated by high-resolution gel electrophoresis. When applying SHAPE to investigate structural features associated with the wild-type and analog-substituted polypurine tract (PPT)-containing RNA/DNA hybrids, their size (20-25 base pairs) rendered primer extension impractical. As an alternative method of detection, we reasoned that chemical modification could be combined with tandem mass spectrometry, relying on the mass increment of RNA fragments containing the NMIA adduct (M(r) = 133 Da). Using this approach, we demonstrate both specific modification of the HIV-1 PPT RNA primer and variations in its acylation pattern induced by replacing template nucleotides with a non-hydrogen-bonding thymine isostere. Our selective 2'-hydroxyl acylation analyzed by mass spectrometry strategy (SHAMS) should find utility when examining the structure of small RNA fragments or RNA/DNA hybrids where primer extension cannot be performed.
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Affiliation(s)
- Kevin B Turner
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA
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42
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Hwang GT, Hari Y, Romesberg FE. The effects of unnatural base pairs and mispairs on DNA duplex stability and solvation. Nucleic Acids Res 2009; 37:4757-63. [PMID: 19515938 PMCID: PMC2724283 DOI: 10.1093/nar/gkp467] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In an effort to develop unnatural DNA base pairs we examined six pyridine-based nucleotides, d3MPy, d4MPy, d5MPy, d34DMPy, d35DMPy and d45DMPy. Each bears a pyridyl nucleobase scaffold but they are differentiated by methyl substitution, and were designed to vary both inter- and intra-strand packing within duplex DNA. The effects of the unnatural base pairs on duplex stability demonstrate that the pyridine scaffold may be optimized for stable and selective pairing, and identify one self pair, the pair formed between two d34DMPy nucleotides, which is virtually as stable as a dA:dT base pair in the same sequence context. In addition, we found that the incorporation of either the d34DMPy self pair or a single d34DMPy paired opposite a natural dA significantly increases oligonucleotide hybridization fidelity at other positions within the duplex. Hypersensitization of the duplex to mispairing appears to result from global and interdependent solvation effects mediated by the unnatural nucleotide(s) and the mispair. The results have important implications for our efforts to develop unnatural base pairs and suggest that the unnatural nucleotides might be developed as novel biotechnological tools, diagnostics, or therapeutics for applications where hybridization stringency is important.
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Affiliation(s)
- Gil Tae Hwang
- Department of Chemistry, Kyungpook National University, Daegu 702-701, Korea
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Yi-Brunozzi HY, Brinson RG, Brabazon DM, Lener D, Le Grice SFJ, Marino JP. High-resolution NMR analysis of the conformations of native and base analog substituted retroviral and LTR-retrotransposon PPT primers. ACTA ACUST UNITED AC 2008; 15:254-62. [PMID: 18355725 DOI: 10.1016/j.chembiol.2008.01.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 01/24/2008] [Accepted: 01/30/2008] [Indexed: 11/17/2022]
Abstract
A purine-rich region of the plus-strand RNA genome of retroviruses and long terminal repeat (LTR)-containing retrotransposons, known as the polypurine tract (PPT), is resistant to hydrolysis by the RNase H domain of reverse transcriptase (RT) and ultimately serves as a primer for plus-strand DNA synthesis. The mechanisms underlying PPT resistance and selective processing remain largely unknown. Here, two RNA/DNA hybrids derived from the PPTs of HIV-1 and Ty3 were probed using high-resolution NMR for preexisting structural distortions in the absence of RT. The PPTs were selectively modified through base-pair changes or by incorporation of the thymine isostere, 2,4-difluoro-5-methylbenzene (dF), into the DNA strand. Although both wild-type (WT) and mutated hybrids adopted global A-form-like helical geometries, observed structural perturbations in the base-pair and dF-modified hybrids suggested that the PPT hybrids may function as structurally coupled domains.
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Affiliation(s)
- Hye Young Yi-Brunozzi
- HIV Drug Resistance Program, NCI-Frederick National Institutes of Health, Frederick, MD 21702, USA
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Johar Z, Zahn A, Leumann CJ, Jaun B. Solution structure of a DNA duplex containing a biphenyl pair. Chemistry 2008; 14:1080-6. [PMID: 18038386 DOI: 10.1002/chem.200701304] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydrogen-bonding and stacking interactions between nucleobases are considered to be the major noncovalent interactions that stabilize the DNA and RNA double helices. In recent work we found that one or multiple biphenyl pairs, devoid of any potential for hydrogen bond formation, can be introduced into a DNA double helix without loss of duplex stability. We hypothesized that interstrand stacking interactions of the biphenyl residues maintain duplex stability. Here we present an NMR structure of the decamer duplex d(GTGACXGCAG) d(CTGCYGTCAC) that contains one such X/Y biaryl pair. X represents a 3'',5''-dinitrobiphenyl- and Y a 3'',4''-dimethoxybiphenyl C-nucleoside unit. The experimentally determined solution structure shows a B-DNA duplex with a slight kink at the site of modification. The biphenyl groups are intercalated side by side as a pair between the natural base pairs and are stacked head to tail in van der Waals contact with each other. The first phenyl rings of the biphenyl units each show tight intrastrand stacking to their natural base neighbors on the 3'-side, thus strongly favoring one of two possible interstrand intercalation structures. In order to accommodate the biphenyl units in the duplex the helical pitch is widened while the helical twist at the site of modification is reduced. Interestingly, the biphenyl rings are not static in the duplex but are in dynamic motion even at 294 K.
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Affiliation(s)
- Zeena Johar
- Laboratory of Organic Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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45
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Pfaff DA, Clarke KM, Parr TA, Cole JM, Geierstanger BH, Tahmassebi DC, Dwyer TJ. Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding? J Am Chem Soc 2008; 130:4869-78. [PMID: 18341343 DOI: 10.1021/ja7103608] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.
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Affiliation(s)
- Danielle A Pfaff
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, USA
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46
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Zahn A, Leumann C. Recognition Properties of Donor- and Acceptor-Modified Biphenyl-DNA. Chemistry 2008; 14:1087-94. [DOI: 10.1002/chem.200701345] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Irimia A, Eoff RL, Pallan PS, Guengerich FP, Egli M. Structure and activity of Y-class DNA polymerase DPO4 from Sulfolobus solfataricus with templates containing the hydrophobic thymine analog 2,4-difluorotoluene. J Biol Chem 2007; 282:36421-33. [PMID: 17951245 DOI: 10.1074/jbc.m707267200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 2,4-difluorotoluene (DFT) analog of thymine has been used extensively to probe the relative importance of shape and hydrogen bonding for correct nucleotide insertion by DNA polymerases. As far as high fidelity (A-class) polymerases are concerned, shape is considered by some as key to incorporation of A(T) opposite T(A) and G(C) opposite C(G). We have carried out a detailed kinetic analysis of in vitro primer extension opposite DFT-containing templates by the trans-lesion (Y-class) DNA polymerase Dpo4 from Sulfolobus solfataricus. Although full-length product formation was observed, steady-state kinetic data show that dATP insertion opposite DFT is greatly inhibited relative to insertion opposite T (approximately 5,000-fold). No products were observed in the pre-steady-state. Furthermore, it is noteworthy that Dpo4 strongly prefers dATP opposite DFT over dGTP (approximately 200-fold) and that the polymerase is able to extend an A:DFT but not a G:DFT pair. We present crystal structures of Dpo4 in complex with DNA duplexes containing the DFT analog, the first for any DNA polymerase. In the structures, template-DFT is either positioned opposite primer-A or -G at the -1 site or is unopposed by a primer base and followed by a dGTP:A mismatch pair at the active site, representative of a -1 frameshift. The three structures provide insight into the discrimination by Dpo4 between dATP and dGTP opposite DFT and its inability to extend beyond a G:DFT pair. Although hydrogen bonding is clearly important for error-free replication by this Y-class DNA polymerase, our work demonstrates that Dpo4 also relies on shape and electrostatics to distinguish between correct and incorrect incoming nucleotide.
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Affiliation(s)
- Adriana Irimia
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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Li F, Pallan PS, Maier MA, Rajeev KG, Mathieu SL, Kreutz C, Fan Y, Sanghvi J, Micura R, Rozners E, Manoharan M, Egli M. Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme. Nucleic Acids Res 2007; 35:6424-38. [PMID: 17881374 PMCID: PMC2095806 DOI: 10.1093/nar/gkm664] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Short interfering RNA (siRNA) duplexes are currently being evaluated as antisense agents for gene silencing. Chemical modification of siRNAs is widely expected to be required for therapeutic applications in order to improve delivery, biostability and pharmacokinetic properties. Beyond potential improvements in the efficacy of oligoribonucleotides, chemical modification may also provide insight into the mechanism of mRNA downregulation mediated by the RNA–protein effector complexes (RNA-induced silencing complex or RISC). We have studied the in vitro activity in HeLa cells of siRNA duplexes against firefly luciferase with substitutions in the guide strand of U for the apolar ribo-2,4-difluorotoluyl nucleotide (rF) [Xia, J. et al. (2006) ACS Chem. Biol., 1, 176–183] as well as of C for rF. Whereas an internal rF:A pair adjacent to the Ago2 (‘slicer’ enzyme) cleavage site did not affect silencing relative to the native siRNA duplex, the rF:G pair and other mismatches such as A:G or A:A were not tolerated. The crystal structure at atomic resolution determined for an RNA dodecamer duplex with rF opposite G manifests only minor deviations between the geometries of rF:G and the native U:G wobble pair. This is in contrast to the previously found, significant deviations between the geometries of rF:A and U:A pairs. Comparison between the structures of the RNA duplex containing rF:G and a new structure of an RNA with A:G mismatches with the structures of standard Watson–Crick pairs in canonical duplex RNA leads to the conclusion that local widening of the duplex formed by the siRNA guide strand and the targeted region of mRNA is the most likely reason for the intolerance of human Ago2 (hAgo2), the RISC endonuclease, toward internal mismatch pairs involving native or chemically modified RNA. Contrary to the influence of shape, the thermodynamic stabilities of siRNA duplexes with single rF:A, A:A, G:A or C:A (instead of U:A) or rF:G pairs (instead of C:G) show no obvious correlation with their activities. However, incorporation of three rF:A pairs into an siRNA duplex leads to loss of activity. Our structural and stability data also shed light on the role of organic fluorine as a hydrogen bond acceptor. Accordingly, UV melting (TM) data, osmotic stress measurements, X-ray crystallography at atomic resolution and the results of semi-empirical calculations are all consistent with the existence of weak hydrogen bonds between fluorine and the H-N1(G) amino group in rF:G pairs of the investigated RNA dodecamers.
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Affiliation(s)
- Feng Li
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Pradeep S. Pallan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Martin A. Maier
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Kallanthottathil G. Rajeev
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Steven L. Mathieu
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Yupeng Fan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Jayodita Sanghvi
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Ronald Micura
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Eriks Rozners
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Muthiah Manoharan
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, Department of Drug Discovery, Alnylam Pharmaceuticals, Inc., 300 Third Street, Cambridge, MA 02142, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA and Institute of Organic Chemistry, Center for Molecular Biosciences (CMBI), Leopold-Franzens University, 6020 Innsbruck, Austria
- *To whom correspondence should be addressed. +1 615 343 8070+1 615 322 7122
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Matsuda S, Fillo JD, Henry AA, Rai P, Wilkens SJ, Dwyer TJ, Geierstanger BH, Wemmer DE, Schultz PG, Spraggon G, Romesberg FE. Efforts toward expansion of the genetic alphabet: structure and replication of unnatural base pairs. J Am Chem Soc 2007; 129:10466-73. [PMID: 17685517 PMCID: PMC2536688 DOI: 10.1021/ja072276d] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Expansion of the genetic alphabet has been a long-time goal of chemical biology. A third DNA base pair that is stable and replicable would have a great number of practical applications and would also lay the foundation for a semisynthetic organism. We have reported that DNA base pairs formed between deoxyribonucleotides with large aromatic, predominantly hydrophobic nucleobase analogues, such as propynylisocarbostyril (dPICS), are stable and efficiently synthesized by DNA polymerases. However, once incorporated into the primer, these analogues inhibit continued primer elongation. More recently, we have found that DNA base pairs formed between nucleobase analogues that have minimal aromatic surface area in addition to little or no hydrogen-bonding potential, such as 3-fluorobenzene (d3FB), are synthesized and extended by DNA polymerases with greatly increased efficiency. Here we show that the rate of synthesis and extension of the self-pair formed between two d3FB analogues is sufficient for in vitro DNA replication. To better understand the origins of efficient replication, we examined the structure of DNA duplexes containing either the d3FB or dPICS self-pairs. We find that the large aromatic rings of dPICS pair in an intercalative manner within duplex DNA, while the d3FB nucleobases interact in an edge-on manner, much closer in structure to natural base pairs. We also synthesized duplexes containing the 5-methyl-substituted derivatives of d3FB (d5Me3FB) paired opposite d3FB or the unsubstituted analogue (dBEN). In all, the data suggest that the structure, electrostatics, and dynamics can all contribute to the extension of unnatural primer termini. The results also help explain the replication properties of many previously examined unnatural base pairs and should help design unnatural base pairs that are better replicated.
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Affiliation(s)
- Shigeo Matsuda
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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Lee HR, Helquist SA, Kool ET, Johnson KA. Base pair hydrogen bonds are essential for proofreading selectivity by the human mitochondrial DNA polymerase. J Biol Chem 2007; 283:14411-6. [PMID: 17650503 PMCID: PMC2386942 DOI: 10.1074/jbc.m705006200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have characterized the role of Watson-Crick hydrogen bonding in the 3'-terminal base pair on the 3'-5' exonuclease activity of the human mitochondrial DNA polymerase. Nonpolar nucleoside analogs of thymidine (dF) and deoxyadenosine (dQ) were used to eliminate hydrogen bonds while maintaining base pair size and shape. Exonuclease reactions were examined using pre-steady state kinetic methods. The time dependence of removal of natural nucleotides from the primer terminus paired opposite the nonpolar analogs dF and dQ were best fit to a double exponential function. The double exponential kinetics as well as the rates of excision (3-6 s(-1) fast phase, 0.16-0.3 s(-1) slow phase) are comparable with those observed during mismatch removal of natural nucleotides even when the analog was involved in a sterically correct base pair. Additionally, incorporation of the next correct base beyond a nonpolar analog was slow (0.04-0.22 s(-1)), so that more than 95% of terminal base pairs were removed rather than extended. The polymerase responds to all 3'-terminal base pairs containing a nonpolar analog as if it were a mismatch regardless of the identity of the paired base, and kinetic partitioning between polymerase and exonuclease sites failed to discriminate between correct and incorrect base pairs. Thus, sterics alone are insufficient, whereas hydrogen bond formation is essential for proper proofreading selectivity by the mitochondrial polymerase. The enzyme may use the alignment and prevention of fraying provided by proper hydrogen bonding and minor groove hydrogen bonding interactions as critical criteria for correct base pair recognition.
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Affiliation(s)
- Harold R Lee
- Department of Chemistry and Biochemistry, Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
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