1
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Berdis A. Nucleobase-modified nucleosides and nucleotides: Applications in biochemistry, synthetic biology, and drug discovery. Front Chem 2022; 10:1051525. [PMID: 36531317 PMCID: PMC9748101 DOI: 10.3389/fchem.2022.1051525] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
. DNA is often referred to as the "molecule of life" since it contains the genetic blueprint for all forms of life on this planet. The core building blocks composing DNA are deoxynucleotides. While the deoxyribose sugar and phosphate group are ubiquitous, it is the composition and spatial arrangement of the four natural nucleobases, adenine (A), cytosine (C), guanine (G), and thymine (T), that provide diversity in the coding information present in DNA. The ability of DNA to function as the genetic blueprint has historically been attributed to the formation of proper hydrogen bonding interactions made between complementary nucleobases. However, recent chemical and biochemical studies using nucleobase-modified nucleotides that contain "non-hydrogen bonding" functional groups have challenged many of the dogmatic views for the necessity of hydrogen-bonding interactions for DNA stability and function. Based on years of exciting research, this area has expanded tremendously and is thus too expansive to provide a comprehensive review on the topic. As such, this review article provides an opinion highlighting how nucleobase-modified nucleotides are being applied in diverse biomedical fields, focusing on three exciting areas of research. The first section addresses how these analogs are used as mechanistic probes for DNA polymerase activity and fidelity during replication. This section outlines the synthetic logic and medicinal chemistry approaches used to replace hydrogen-bonding functional groups to examine the contributions of shape/size, nucleobase hydrophobicity, and pi-electron interactions. The second section extends these mechanistic studies to provide insight into how nucleobase-modified nucleosides are used in synthetic biology. One example is through expansion of the genetic code in which changing the composition of DNA makes it possible to site-specifically incorporate unnatural amino acids bearing unique functional groups into enzymes and receptors. The final section describes results of pre-clinical studies using nucleobase-modified nucleosides as potential therapeutic agents against diseases such as cancer.
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Affiliation(s)
- Anthony Berdis
- Department of Chemistry, Cleveland State University, Cleveland, OH, United States
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2
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Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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3
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Gomez Fernandez MA, Lefebvre C, Sudau A, Genix P, Vors JP, Abe M, Hoffmann N. Studies on The Application of The Paternò-Büchi Reaction to The Synthesis of Novel Fluorinated Scaffolds. Chemistry 2021; 27:15722-15729. [PMID: 34523761 DOI: 10.1002/chem.202102621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 11/08/2022]
Abstract
In the context of new scaffolds obtained by photochemical reactions, Paternò-Büchi reactions between heteroaromatic, trifluoromethylphenyl ketone and electron rich alkenes to give oxetanes are described. A comprehensive study has then been carried out on the reaction of aromatic ketones with fluorinated alkenes. Depending on the substitution pattern at the oxetane ring, a metathesis reaction is described as a minor side process to give mono fluorinated alkenes. Overall, this last reaction corresponds to a photo-Wittig reaction and yield amid isosteres. In order to explain the uncommon regioselectivity of the Paternò-Büchi reaction with these alkenes, electrostatic-potential derived charges (ESP) have been determined. In a second computational study, the relative stabilities of the typical 1,4-diradical intermediates of the Paternò-Büchi reaction have been determined. The results well explain the regioselectivity. Further transformations of the oxetanes or previous functionalization of the fluoroalkenes open perspectives for oxetanes as core structures for biologically active compounds.
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Affiliation(s)
- Mario Andrés Gomez Fernandez
- ICMR, Equipe de Photochimie, CNRS, Université de Reims Champagne-Ardenne, 1 UFR Sciences, B.P. 1039, 51687, Reims, France
| | - Corentin Lefebvre
- ICMR, Equipe de Photochimie, CNRS, Université de Reims Champagne-Ardenne, 1 UFR Sciences, B.P. 1039, 51687, Reims, France
| | - Alexander Sudau
- Research & Development, Crop Science, Lab 2, Bayer AG, 2 Alfred-Nobel-Str., 40789, Monheim, Germany
| | - Pierre Genix
- Crop Science Division, Disease Control Chemistry 2, Bayer S.A.S., Building La Dargoire D1 366, 69263, Lyon, France
| | - Jean-Pierre Vors
- Crop Science Division, Disease Control Chemistry 2, Bayer S.A.S., Building La Dargoire D1 366, 69263, Lyon, France
| | - Manabu Abe
- Department of Chemistry, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.,Hiroshima Research Center for Photo-Drug-Delivery Systems (Hi-P-DDS), 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Norbert Hoffmann
- ICMR, Equipe de Photochimie, CNRS, Université de Reims Champagne-Ardenne, 1 UFR Sciences, B.P. 1039, 51687, Reims, France
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4
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De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules. Life (Basel) 2020; 10:life10120346. [PMID: 33322642 PMCID: PMC7764398 DOI: 10.3390/life10120346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 01/30/2023] Open
Abstract
Modern terran life uses several essential biopolymers like nucleic acids, proteins and polysaccharides. The nucleic acids, DNA and RNA are arguably life’s most important, acting as the stores and translators of genetic information contained in their base sequences, which ultimately manifest themselves in the amino acid sequences of proteins. But just what is it about their structures; an aromatic heterocyclic base appended to a (five-atom ring) sugar-phosphate backbone that enables them to carry out these functions with such high fidelity? In the past three decades, leading chemists have created in their laboratories synthetic analogues of nucleic acids which differ from their natural counterparts in three key areas as follows: (a) replacement of the phosphate moiety with an uncharged analogue, (b) replacement of the pentose sugars ribose and deoxyribose with alternative acyclic, pentose and hexose derivatives and, finally, (c) replacement of the two heterocyclic base pairs adenine/thymine and guanine/cytosine with non-standard analogues that obey the Watson–Crick pairing rules. This manuscript will examine in detail the physical and chemical properties of these synthetic nucleic acid analogues, in particular on their abilities to serve as conveyors of genetic information. If life exists elsewhere in the universe, will it also use DNA and RNA?
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5
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Kimoto M, Soh SHG, Tan HP, Okamoto I, Hirao I. Cognate base-pair selectivity of hydrophobic unnatural bases in DNA ligation by T4 DNA ligase. Biopolymers 2020; 112:e23407. [PMID: 33156531 PMCID: PMC7900958 DOI: 10.1002/bip.23407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/28/2022]
Abstract
We present cognate base pair selectivity in template-dependent ligation by T4 DNA ligase using a hydrophobic unnatural base pair (UBP), Ds-Pa. T4 DNA ligase efficiently recognizes the Ds-Pa pairing at the conjugation position, and Ds excludes the noncognate pairings with the natural bases. Our results indicate that the hydrophobic base pairing is allowed in enzymatic ligation with higher cognate base-pair selectivity, relative to the hydrogen-bond interactions between pairing bases. The efficient ligation using Ds-Pa can be employed in recombinant DNA technology using genetic alphabet expansion, toward the creation of semi-synthetic organisms containing UBPs.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Si Hui Gabriella Soh
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore.,Raffles Institution, Singapore, Singapore
| | - Hui Pen Tan
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Itaru Okamoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore, Singapore
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6
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Rosenberg RE, Chapman BK, Ferrill RN, Jung ES, Samaan CA. Approximating the Strength of the Intramolecular Hydrogen Bond in 2-Fluorophenol and Related Compounds: A New Application of a Classic Technique. J Phys Chem A 2020; 124:3851-3858. [PMID: 32312049 DOI: 10.1021/acs.jpca.0c01641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of hydrogen bonds involving fluorine. While established techniques can determine these strengths for intermolecular complexes, there is no analogous scheme for intramolecular hydrogen bonds. This work uses 1H nuclear magnetic resonance spectroscopy to measure the strength of intramolecular hydrogen bonds in ortho-substituted phenols. Titration of each phenol with DMSO in CCl4 yields a free energy of binding (ΔG). Subtraction of this value from the ΔG of binding of the standard, 4-fluorophenol, is shown to give the difference in ΔG for the cis and trans isomers of the ortho-substituted phenols. This difference is conventionally taken to be approximately equal to the ΔG of the intramolecular hydrogen bond. These data complement theoretical methods, which yield slightly larger ΔGs. Both theory and experiment point to a weak intramolecular hydrogen bond in 2-fluorophenol. The other 2-X-phenols have stronger hydrogen bonds, following the order F < Cl ≈ Br < OCH3. The methodology developed here can be readily applied to other systems with intramolecular hydrogen bonds.
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Affiliation(s)
- Robert E Rosenberg
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Bradley K Chapman
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Rachel N Ferrill
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Eiu Suk Jung
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Chris A Samaan
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
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7
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Johnson A, Karimi A, Luedtke NW. Enzymatic Incorporation of a Coumarin–Guanine Base Pair. Angew Chem Int Ed Engl 2019; 58:16839-16843. [DOI: 10.1002/anie.201910059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Aaron Johnson
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Ashkan Karimi
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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8
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Johnson A, Karimi A, Luedtke NW. Enzymatic Incorporation of a Coumarin–Guanine Base Pair. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Aaron Johnson
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Ashkan Karimi
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
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9
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Bello D, Rubanu MG, Bandaranayaka N, Götze JP, Bühl M, O'Hagan D. Acetyl Coenzyme A Analogues as Rationally Designed Inhibitors of Citrate Synthase. Chembiochem 2019; 20:1174-1182. [PMID: 30605257 DOI: 10.1002/cbic.201800700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Indexed: 12/14/2022]
Abstract
In this study, we probed the inhibition of pig heart citrate synthase (E.C. 4.1.3.7) by synthesising seven analogues either designed to mimic the proposed enolate intermediate in this enzyme reaction or developed from historical inhibitors. The most potent inhibitor was fluorovinyl thioether 9 (Ki =4.3 μm), in which a fluorine replaces the oxygen atom of the enolate. A comparison of the potency of 9 with that of its non-fluorinated vinyl thioether analogue 10 (Ki =68.3 μm) revealed a clear "fluorine effect" favouring 9 by an order of magnitude. The dethia analogues of 9 and 10 proved to be poor inhibitors. A methyl sulfoxide analogue was a moderate inhibitor (Ki =11.1 μm), thus suggesting hydrogen bonding interactions in the enolate site. Finally, E and Z propenoate thioether isomers were explored as conformationally constrained carboxylates, but these were not inhibitors. All compounds were prepared by the synthesis of the appropriate pantetheinyl diol and then assembly of the coenzyme A structure according to a three-enzyme biotransformation protocol. A quantum mechanical study, modelling both inhibitors 9 and 10 into the active site indicated short CF⋅⋅⋅H contacts of ≈2.0 Å, consistent with fluorine making two stabilising hydrogen bonds, and mimicking an enolate rather than an enol intermediate. Computation also indicated that binding of 9 to citrate synthase increases the basicity of a key aspartic acid carboxylate, which becomes protonated.
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Affiliation(s)
- Davide Bello
- University of St Andrews, School of Chemistry, North Haugh, St. Andrews, KY16 9ST, UK
| | - Maria Grazia Rubanu
- University of St Andrews, School of Chemistry, North Haugh, St. Andrews, KY16 9ST, UK
| | | | - Jan P Götze
- University of St Andrews, School of Chemistry, North Haugh, St. Andrews, KY16 9ST, UK.,Present address: Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14495, Berlin, Germany
| | - Michael Bühl
- University of St Andrews, School of Chemistry, North Haugh, St. Andrews, KY16 9ST, UK
| | - David O'Hagan
- University of St Andrews, School of Chemistry, North Haugh, St. Andrews, KY16 9ST, UK
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10
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Räz MH, Sturla SJ, Gahlon HL. Hydrogen-Bonding Interactions at the DNA Terminus Promote Extension from Methylguanine Lesions by Human Extender DNA Polymerase ζ. Biochemistry 2018; 57:5978-5988. [PMID: 30222325 DOI: 10.1021/acs.biochem.8b00861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chemically induced DNA lesions can become DNA replication substrates that are bypassed by low-fidelity DNA polymerases. Following nucleotide misinsertion opposite a DNA lesion, the extension step can contribute to preserving such errors and lead to genomic instability and cancer. DNA polymerase ζ, a B-family polymerase, is proficient as an extender polymerase that catalyzes elongation; however, the chemical factors that impact its DNA replication are not understood. This study addresses the question of how DNA polymerase ζ achieves extension by examining the ability of recombinant human DNA polymerase ζ to extend from a series of methylated guanine lesions. The influence of H-bonding was examined by placing structurally altered nucleoside analogues and canonical bases opposite G, O6-MeG, N1-MeG, and N2-MeG. We determined that terminal base pairs with the highest proclivity for H-bonding were most efficiently extended in both primer extension assays and steady-state kinetic analysis. In contrast, when no H-bonding was possible at the DNA terminus, the least efficient steady-state kinetics were observed. To evaluate H-bonding protein minor groove interactions that may underlie this phenomenon, we performed computational modeling with Escherichia coli DNA polymerase II, a homologue for DNA polymerase ζ. The modeling data together with the primer extension assays demonstrate the importance of having a carbonyl group on the primer strand that can interact with a lysine residue found to be conserved in many B-family polymerases, including human Pol ζ. These data provide a model whereby interbase H-bonding interactions at the DNA terminus promote lesion bypass and extension by human DNA polymerase ζ.
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Affiliation(s)
- Michael H Räz
- 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
| | - Hailey L Gahlon
- Department of Health Sciences and Technology , ETH Zürich , Schmelzbergstrasse 9 , Zürich 8092 , Switzerland
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11
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Raper AT, Reed AJ, Suo Z. Kinetic Mechanism of DNA Polymerases: Contributions of Conformational Dynamics and a Third Divalent Metal Ion. Chem Rev 2018; 118:6000-6025. [DOI: 10.1021/acs.chemrev.7b00685] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Austin T. Raper
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andrew J. Reed
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
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12
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Rosenberg RE. The Strength of Hydrogen Bonds between Fluoro-Organics and Alcohols, a Theoretical Study. J Phys Chem A 2018; 122:4521-4529. [DOI: 10.1021/acs.jpca.8b01148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Robert E. Rosenberg
- Department of Chemistry, Transylvania University, 300 North Broadway, Lexington, Kentucky 40508, United States
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13
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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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14
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Gowda ASP, Lee M, Spratt TE. N 2
-Substituted 2′-Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- A. S. Prakasha Gowda
- Department of Biochemistry and Molecular Biology; Pennsylvania State University; 500 University Dr. Hershey PA 17033 USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla NY 10595 USA
| | - Thomas E. Spratt
- Department of Biochemistry and Molecular Biology; Pennsylvania State University; 500 University Dr. Hershey PA 17033 USA
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15
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Gowda ASP, Lee M, Spratt TE. N 2 -Substituted 2'-Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ. Angew Chem Int Ed Engl 2017; 56:2628-2631. [PMID: 28140505 DOI: 10.1002/anie.201611607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/12/2017] [Indexed: 11/09/2022]
Abstract
N2 -Alkyl-2'-deoxyguanosine triphosphate (N2 -alkyl-dGTP) derivatives with methyl, butyl, benzyl, or 4-ethynylbenzyl substituents were prepared and tested as substrates for human DNA polymerases. N2 -Benzyl-dGTP was equal to dGTP as a substrate for DNA polymerase κ (pol κ), but was a poor substrate for pols β, δ, η, ι, or ν. In vivo reactivity was evaluated through incubation of N2 -4-ethynylbenzyl-dG with wild-type and pol κ deficient mouse embryonic fibroblasts. CuAAC reaction with 5(6)-FAM-azide demonstrated that only cells containing pol κ were able to incorporate N2 -4-ethynylbenzyl-dG into the nucleus. This is the first instance of a Y-family-polymerase-specific dNTP, and this method could be used to probe the activity of pol κ in vivo.
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Affiliation(s)
- A S Prakasha Gowda
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 500 University Dr., Hershey, PA, 17033, USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA
| | - Thomas E Spratt
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 500 University Dr., Hershey, PA, 17033, USA
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16
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17
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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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18
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Affiliation(s)
- Robert E. Rosenberg
- Department of Chemistry, Transylvania University, 300 North Broadway, Lexington, Kentucky 40508, United States
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19
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Welter M, Verga D, Marx A. Sequence-Specific Incorporation of Enzyme-Nucleotide Chimera by DNA Polymerases. Angew Chem Int Ed Engl 2016; 55:10131-5. [PMID: 27392211 DOI: 10.1002/anie.201604641] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 02/06/2023]
Abstract
DNA polymerases select the right nucleotide for the growing polynucleotide chain based on the shape and geometry of the nascent nucleotide pairs and thereby ensure high DNA replication selectivity. High-fidelity DNA polymerases are believed to possess tight active sites that allow little deviation from the canonical structures. However, DNA polymerases are known to use nucleotides with small modifications as substrates, which is key for numerous core biotechnology applications. We show that even high-fidelity DNA polymerases are capable of efficiently using nucleotide chimera modified with a large protein like horseradish peroxidase as substrates for template-dependent DNA synthesis, despite this "cargo" being more than 100-fold larger than the natural substrates. We exploited this capability for the development of systems that enable naked-eye detection of DNA and RNA at single nucleotide resolution.
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Affiliation(s)
- Moritz Welter
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Daniela Verga
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.
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Welter M, Verga D, Marx A. Sequenz-spezifischer Einbau von Enzym-Nukleotid-Chimären durch DNA-Polymerasen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Moritz Welter
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Daniela Verga
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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21
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Rozov A, Demeshkina N, Westhof E, Yusupov M, Yusupova G. New Structural Insights into Translational Miscoding. Trends Biochem Sci 2016; 41:798-814. [PMID: 27372401 DOI: 10.1016/j.tibs.2016.06.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/23/2016] [Accepted: 06/02/2016] [Indexed: 01/16/2023]
Abstract
The fidelity of translation depends strongly on the selection of the correct aminoacyl-tRNA that is complementary to the mRNA codon present in the ribosomal decoding center. The ribosome occasionally makes mistakes by selecting the wrong substrate from the pool of aminoacyl-tRNAs. Here, we summarize recent structural advances that may help to clarify the origin of missense errors that occur during decoding. These developments suggest that discrimination between tRNAs is based primarily on steric complementarity and shape acceptance rather than on the number of hydrogen bonds between the molding of the decoding center and the codon-anticodon duplex. They strengthen the hypothesis that spatial mimicry, due either to base tautomerism or ionization, drives infidelity in ribosomal translation.
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Affiliation(s)
- Alexey Rozov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France
| | - Natalia Demeshkina
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France
| | - Eric Westhof
- Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS UPR9002/University of Strasbourg, Strasbourg, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, CNRS, UMR7104/INSERM, U964/University of Strasbourg, Strasbourg, France.
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22
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Rozov A, Westhof E, Yusupov M, Yusupova G. The ribosome prohibits the G•U wobble geometry at the first position of the codon-anticodon helix. Nucleic Acids Res 2016; 44:6434-41. [PMID: 27174928 PMCID: PMC5291260 DOI: 10.1093/nar/gkw431] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/06/2016] [Indexed: 01/05/2023] Open
Abstract
Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a G•U base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical G•C pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.
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Affiliation(s)
- Alexey Rozov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS, UMR7104/University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Eric Westhof
- Architecture & Reactivity of RNA, University of Strasbourg, Institute of Molecular and Cellular Biology of the CNRS, UPR9002, 15 rue R. Descartes, 67084 Strasbourg, France
| | - Marat Yusupov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS, UMR7104/University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Gulnara Yusupova
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, INSERM, U964; CNRS, UMR7104/University of Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
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23
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Abstract
All biological information, since the last common ancestor of all life on Earth, has been encoded by a genetic alphabet consisting of only four nucleotides that form two base pairs. Long-standing efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on alternative hydrogen bonding, and two based on hydrophobic and packing forces. All three of these UBPs are replicated and transcribed with remarkable efficiency and fidelity, and the latter two thus demonstrate that hydrogen bonding is not unique in its ability to underlie the storage and retrieval of genetic information. This Review highlights these recent developments as well as the applications enabled by the UBPs, including the expansion of the evolution process to include new functionality and the creation of semi-synthetic life that stores increased information.
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Affiliation(s)
- Denis A Malyshev
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA).
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25
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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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26
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Plöger TA, von Kiedrowski G. A self-replicating peptide nucleic acid. Org Biomol Chem 2015; 12:6908-14. [PMID: 25065957 DOI: 10.1039/c4ob01168f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While the non-enzymatic ligation and template-directed synthesis of peptide nucleic acids (PNA) have been reported since 1995, a case of self-replication of PNA has not been achieved yet. Here, we present evidence for autocatalytic feedback in a template directed synthesis of a self-complementary hexa-PNA from two trimeric building blocks. The course of the reaction was monitored in the presence of increasing initial concentrations of the product by RP-HPLC. Kinetic modeling with the SimFit program revealed parabolic growth characteristics. The observed template effect, as well as the rate of ligation, was significantly influenced by nucleophilic catalysts, pH value, and uncharged co-solvents. Systematic optimization of the reaction conditions allowed us to increase the autocatalytic efficiency of the system by two orders of magnitude. Our findings contribute to the hypothesis that PNA may have served as a primordial genetic molecule and was involved in a potential precursor of a RNA world.
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Affiliation(s)
- Tobias A Plöger
- Ruhr-Universität Bochum, Chair of Organic Chemistry I - Bioorganic Chemistry, 44780 Bochum, Germany.
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27
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Guo M, Zheng Y, Terell JL, Ad M, Opoku-Temeng C, Bentley WE, Sintim HO. Geminal dihalogen isosteric replacement in hydrated AI-2 affords potent quorum sensing modulators. Chem Commun (Camb) 2015; 51:2617-20. [DOI: 10.1039/c4cc09361e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Geminal dibromo moiety can replace hydrated carbonyl groups in AI-2, a quorum sensing autoinducer, without diminution of activity. This group can form halogen bond with active site electron donor.
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Affiliation(s)
- Min Guo
- Department of Chemistry and Biochemistry
- University of Maryland College Park
- USA
| | - Yue Zheng
- Department of Chemistry and Biochemistry
- University of Maryland College Park
- USA
| | - Jessica L. Terell
- Fischell Department of Bioengineering
- University of Maryland
- College Park
- USA
| | - Michal Ad
- Department of Chemistry and Biochemistry
- University of Maryland College Park
- USA
| | | | - William E. Bentley
- Fischell Department of Bioengineering
- University of Maryland
- College Park
- USA
| | - Herman O. Sintim
- Department of Chemistry and Biochemistry
- University of Maryland College Park
- USA
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28
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Bello D, Cormanich RA, O'Hagan D. Fluorovinyl Thioethers as Putative Steric and Electronic Thioester Enolate Mimetics: Chemoselective HF Addition to Acetylene Thioethers. Aust J Chem 2015. [DOI: 10.1071/ch14298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Fluorovinyl thioethers are presented as a putative biomimetic surrogate for the enol/ate of a thioester. A method is explored for the preparation of fluorovinyl thioethers by treatment of acetylene thioethers with pyridinium (poly)-hydrogen fluoride. Titration with pyridine is important for the selectivity of the reaction. Without titration the corresponding gem-difluoroethyl thioethers are generated. With titration the hydrofluorination reaction can be stopped at an intermediate stage to recover the fluorovinyl thioether, which is a relatively stable functionality to purification and manipulation. Preliminary density functional theory calculations indicate that the fluorovinyl thioether motif shares a comparable steric and electronic profile to a thioester enol. A fluorovinyl thioether representing the terminus of the pantothenoyl chain of acetyl-CoA is prepared as a relevant biomimetic example.
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29
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Tsai MD. How DNA polymerases catalyze DNA replication, repair, and mutation. Biochemistry 2014; 53:2749-51. [PMID: 24716436 DOI: 10.1021/bi500417m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica , Nankang, Taipei 115, Taiwan , and Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
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30
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Abstract
![]()
This review will summarize our structural
and kinetic studies of
RB69 DNA polymerase (RB69pol) as well as selected variants of the
wild-type enzyme that were undertaken to obtain a deeper understanding
of the exquisitely high fidelity of B family replicative DNA polymerases.
We discuss how the structures of the various RB69pol ternary complexes
can be used to rationalize the results obtained from pre-steady-state
kinetic assays. Our main findings can be summarized as follows. (i)
Interbase hydrogen bond interactions can increase catalytic efficiency
by 5000-fold; meanwhile, base selectivity is not solely determined
by the number of hydrogen bonds between the incoming dNTP and the
templating base. (ii) Minor-groove hydrogen bond interactions at positions n – 1 and n – 2 of the primer
strand and position n – 1 of the template
strand in RB69pol ternary complexes are essential for efficient primer
extension and base selectivity. (iii) Partial charge interactions
among the incoming dNTP, the penultimate base pair, and the hydration
shell surrounding the incoming dNTP modulate nucleotide insertion
efficiency and base selectivity. (iv) Steric clashes between mismatched
incoming dNTPs and templating bases with amino acid side chains in
the nascent base pair binding pocket (NBP) as well as weak interactions
and large gaps between the incoming dNTPs and the templating base
are some of the reasons that incorrect dNTPs are incorporated so inefficiently
by wild-type RB69pol. In addition, we developed a tC°–tCnitro Förster resonance energy transfer assay to monitor
partitioning of the primer terminus between the polymerase and exonuclease
subdomains.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8024, United States
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31
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Westhof E, Yusupov M, Yusupova G. Recognition of Watson-Crick base pairs: constraints and limits due to geometric selection and tautomerism. F1000PRIME REPORTS 2014; 6:19. [PMID: 24765524 PMCID: PMC3974571 DOI: 10.12703/p6-19] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The natural bases of nucleic acids have a strong preference for one tautomer form, guaranteeing fidelity in their hydrogen bonding potential. However, base pairs observed in recent crystal structures of polymerases and ribosomes are best explained by an alternative base tautomer, leading to the formation of base pairs with Watson-Crick-like geometries. These observations set limits to geometric selection in molecular recognition of complementary Watson-Crick pairs for fidelity in replication and translation processes.
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Affiliation(s)
- Eric Westhof
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de Biologie Moléculaire et CellulaireCNRS, 15 rue René Descartes, F-67084 Strasbourg CedexFrance
| | - Marat Yusupov
- Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et CellulaireCNRS, INSERM, Université de Strasbourg, F-67400 IllkirchFrance
| | - Gulnara Yusupova
- Département de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et CellulaireCNRS, INSERM, Université de Strasbourg, F-67400 IllkirchFrance
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32
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Zhou J, Watt S, Wang J, Nakayama S, Sayre DA, Lam YF, Lee VT, Sintim HO. Potent suppression of c-di-GMP synthesis via I-site allosteric inhibition of diguanylate cyclases with 2'-F-c-di-GMP. Bioorg Med Chem 2013; 21:4396-404. [PMID: 23685177 DOI: 10.1016/j.bmc.2013.04.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/10/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a central regulator of bacterial behavior. Various studies have implicated c-di-GMP in biofilm formation and virulence factor production in multitudes of bacteria. Hence it is expected that the disruption of c-di-GMP signaling could provide an effective means to disrupt biofilm and/or virulence factor formation in several bacteria of clinical relevance. C-di-GMP achieves the regulation of bacterial phenotype via binding to several effector molecules including transcription factors, enzymes and riboswitches. Crystal structure analyses of c-di-GMP effector molecules, in complex with the ligand, reveal that various classes of c-di-GMP receptors recognize this dinucleotide using different sets of recognition elements. Therefore, it is plausible that different analogues of c-di-GMP could be used to selectively modulate a specific class of c-di-GMP binding receptors, and hence modulate the bacterial phenotype. Thus far only a detailed study of the differential binding of c-di-GMP analogues to riboswitches, but not proteins, has been reported. In this report, we prepared various 2'-modified analogues of c-di-GMP and studied both polymorphisms of these analogues using DOSY NMR and the binding to several effector proteins, such as PilZ-containing proteins, diguanylate cyclases (DGC) containing I-sites, and phoshphodiesterases (PDE). 2'-Modification of c-di-GMP did not adversely affect the propensity to form higher aggregates, such as octameric forms, in the presence of potassium salts. Interestingly, we find that the selective binding to different classes of c-di-GMP binding proteins could be achieved with the 2'-modified analogues and that 2'-F analogue of c-di-GMP binds to the I-site of DGCs better (four times) than the native dinucleotide, c-di-GMP, whereas c-di-GMP binds to PDEs better (10 times) than 2'-F-c-di-GMP. 2'-F-c-di-GMP potently inhibits c-di-GMP synthesis by DGCs and hence raises the potential that cell permeable analogues of 2'-F-c-di-GMP could be used to disrupt c-di-GMP signaling in bacteria.
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Affiliation(s)
- Jie Zhou
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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Luo Y, Zhou J, Wang J, Dayie TK, Sintim HO. Selective binding of 2'-F-c-di-GMP to Ct-E88 and Cb-E43, new class I riboswitches from Clostridium tetani and Clostridium botulinum respectively. MOLECULAR BIOSYSTEMS 2013; 9:1535-9. [PMID: 23559271 DOI: 10.1039/c3mb25560c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
C-di-GMP is a second messenger in bacteria and partly regulates bacterial physiology by binding to class I and II riboswitches. Four class I c-di-GMP riboswitch aptamer candidates, Ct-E88, Cb-17B, Cb-E43 and Cd-630 RNAs, selected from a GEMM RNA sequence motif in the Rfam database, were expressed and experimentally verified to bind to c-di-GMP. The two newly characterized c-di-GMP riboswitches, Ct-E88 and Cb-E43, bound c-di-GMP with nanomolar Kd whereas the affinities of Cb-17B and Cd-630 for c-di-GMP were at least a 100-fold weaker. Interestingly, whereas the three riboswitches (Vc2, Et-E88 and Cb-E43) bound c-di-GMP with similar Kd values, 2'-modified analogs of c-di-GMP differentially bound to these three class I aptamers. For example, 2'-F-c-di-GMP bound Vc2 with a Kd value of 102 nM whereas the Kd value of 2'-F-c-di-GMP-Ct-E88 is 43 μM (422× higher than that for Vc2 RNA), revealing that there are differences in the binding sites of functional class I c-di-GMP riboswitches.
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Affiliation(s)
- Yiling Luo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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34
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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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35
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Bartolomé C, Villafañe F, Martín-Alvarez JM, Martínez-Ilarduya JM, Espinet P. [Pd(Fmes)2(tmeda)]: A Case of Intermittent CH⋅⋅⋅FC Hydrogen-Bond Interaction in Solution. Chemistry 2013; 19:3702-9. [DOI: 10.1002/chem.201203512] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Indexed: 11/08/2022]
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36
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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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37
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Xia S, Wang J, Konigsberg WH. DNA mismatch synthesis complexes provide insights into base selectivity of a B family DNA polymerase. J Am Chem Soc 2012; 135:193-202. [PMID: 23214497 DOI: 10.1021/ja3079048] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Current hypotheses that attempt to rationalize the high degree of base selectivity exhibited by replicative DNA polymerases (pols) concur that ternary complexes formed with incorrect dNTPs are destabilized. Knowing what accounts for this destabilization is likely to be the key to understanding base discrimination. To address this issue, we have determined crystal structures of ternary complexes with all 12 mismatches using an engineered RB69 pol quadruple mutant (qm, L415A/L561A/S565G/Y567A) that enabled us to capture nascent mispaired dNTPs. These structures show that mismatches in the nascent base-pair binding pocket (NBP) of the qm pol differ markedly from mismatches embedded in binary pol-DNA complexes. Surprisingly, only 3 of 12 mismatches clash with the NBP when they are modeled into the wild-type (wt) pol. The remaining can fit into a wt pol ternary complex but deviate from normal Watson-Crick base-pairs. Repositioning of the templating nucleotide residue and the enlarged NBP in qm ternary complex play important roles in accommodating incorrect incoming dNTPs. From these structures, we propose additional reasons as to why incorrect dNTPs are incorporated so inefficiently by wt RB69 pol: (i) steric clashes with side chains in the NBP after Fingers closing; (ii) weak interactions or large gaps between the incoming dNTP and the templating base; and (iii) burying a protonated base in the hydrophobic environment of the NBP. All of these possibilities would be expected to destabilize the closed ternary complex so that incorporation of incorrect dNTP would be a rare event.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
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38
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Affiliation(s)
- Robert E. Rosenberg
- Department of Chemistry, Transylvania University, 300 North Broadway, Lexington, Kentucky
40508, United States
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39
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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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40
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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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41
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Xia S, Christian TD, Wang J, Konigsberg WH. Probing minor groove hydrogen bonding interactions between RB69 DNA polymerase and DNA. Biochemistry 2012; 51:4343-53. [PMID: 22571765 DOI: 10.1021/bi300416z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Minor groove hydrogen bonding (HB) interactions between DNA polymerases (pols) and N3 of purines or O2 of pyrimidines have been proposed to be essential for DNA synthesis from results obtained using various nucleoside analogues lacking the N3 or O2 contacts that interfered with primer extension. Because there has been no direct structural evidence to support this proposal, we decided to evaluate the contribution of minor groove HB interactions with family B pols. We have used RB69 DNA pol and 3-deaza-2'-deoxyadenosine (3DA), an analogue of 2-deoxyadenosine, which has the same HB pattern opposite T but with N3 replaced with a carbon atom. We then determined pre-steady-state kinetic parameters for the insertion of dAMP opposite dT using primer/templates (P/T)-containing 3DA. We also determined three structures of ternary complexes with 3DA at various positions in the duplex DNA substrate. We found that the incorporation efficiency of dAMP opposite dT decreased 10(2)-10(3)-fold even when only one minor groove HB interaction was missing. Our structures show that the HB pattern and base pair geometry of 3DA/dT is exactly the same as those of dA/dT, which makes 3DA an optimal analogue for probing minor groove HB interactions between a DNA polymerase and a nucleobase. In addition, our structures provide a rationale for the observed 10(2)-10(3)-fold decrease in the rate of nucleotide incorporation. The minor groove HB interactions between position n - 2 of the primer strand and RB69pol fix the rotomer conformations of the K706 and D621 side chains, as well as the position of metal ion A and its coordinating ligands, so that they are in the optinal orientation for DNA synthesis.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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42
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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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43
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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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44
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Piotrowska DG, Balzarini J, Głowacka IE. Design, synthesis, antiviral and cytostatic evaluation of novel isoxazolidine nucleotide analogues with a 1,2,3-triazole linker. Eur J Med Chem 2011; 47:501-9. [PMID: 22137458 PMCID: PMC7125624 DOI: 10.1016/j.ejmech.2011.11.021] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 11/10/2011] [Accepted: 11/10/2011] [Indexed: 12/01/2022]
Abstract
Azidation (TMSN(3), SnCl(4)) of a 9:1 mixture of trans- and cis-5-acetoxy-2-methylisoxazolidin-3-yl-3-phosphonates at the anomeric carbon atom led to the formation of the equimolar mixture of cis- and trans-5-azido-2-methylisoxazolidin-3-yl-3-phosphonates, which were efficiently separated. The 1,3-dipolar cycloaddition of pure trans- and cis-5-azidoisoxazolidin-3-yl-3-phosphonates with selected alkynes gave the respective nucleoside mimetics containing a 1,2,3-triazole linker. The (1,2,3-triazolyl)isoxazolidine phosphonates obtained herein were evaluated in vitro for activity against a variety of DNA and RNA viruses. None of the compounds were endowed with antiviral activity at subtoxic concentrations. Compounds 15f-j and 16f-j were cytostatic in the higher micromolar range.
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Affiliation(s)
- Dorota G Piotrowska
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Łódź, 90-151 Łódź, Muszyńskiego 1, Poland.
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45
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Plöger TA, von Kiedrowski G. Improved Large-Scale Liquid-Phase Synthesis and High-Temperature NMR Characterization of Short (F-)PNAs. Helv Chim Acta 2011. [DOI: 10.1002/hlca.201100243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Ulrich S, Kool ET. Importance of steric effects on the efficiency and fidelity of transcription by T7 RNA polymerase. Biochemistry 2011; 50:10343-9. [PMID: 22044042 DOI: 10.1021/bi2011465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA-dependent RNA polymerases such as T7 RNA polymerase (T7 RNAP) perform the transcription of DNA into mRNA with high efficiency and high fidelity. Although structural studies have provided a detailed account of the molecular basis of transcription, the relative importance of factors like hydrogen bonds and steric effects remains poorly understood. We report herein the first study aimed at systematically probing the importance of steric and electrostatic effects on the efficiency and fidelity of DNA transcription by T7 RNAP. We used synthetic nonpolar analogues of thymine with sizes varying in subangstrom increments to probe the steric requirements of T7 RNAP during the elongation mode of transcription. Enzymatic assays with internal radiolabeling were performed to compare the efficiency of transcription of modified DNA templates with a natural template containing thymine as a reference. Furthermore, we analyzed effects on the fidelity by measuring the composition of RNA transcripts by enzymatic digestion followed by two-dimensional thin layer chromatography separation. Our results demonstrate that hydrogen bonds play an important role in the efficiency of transcription but, interestingly, do not appear to be required for faithful transcription. Steric effects (size and shape variations) are found to be significant both in insertion of a new RNA base and in extension beyond it.
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Affiliation(s)
- Sébastien Ulrich
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
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47
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Kimoto M, Cox RS, Hirao I. Unnatural base pair systems for sensing and diagnostic applications. Expert Rev Mol Diagn 2011; 11:321-31. [PMID: 21463241 DOI: 10.1586/erm.11.5] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Expansion of the genetic alphabet by an unnatural base pair system provides a platform for the site-specific, enzymatic incorporation of extra, functional components into nucleic acids. Recently, several unnatural base pairs that exhibit high fidelity and efficiency in PCR have been developed. Functional groups of interest, such as fluorescent dyes, can be linked to the unnatural bases, and the modified base substrates are site-specifically incorporated into nucleic acids by polymerases. Furthermore, unique unnatural base pairs between fluorophore and quencher base analogs have been developed for imaging PCR amplification and as molecular beacons. Here, we describe the recent progress in the development of unnatural base pairs that function in PCR amplification and their applications as sensing and diagnostic tools.
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Affiliation(s)
- Michiko Kimoto
- RIKEN Systems and Structural Biology Center (SSBC), Yokohama, Japan
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48
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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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49
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Megger DA, Fonseca Guerra C, Hoffmann J, Brutschy B, Bickelhaupt FM, Müller J. Contiguous Metal‐Mediated Base Pairs Comprising Two Ag
I
Ions. Chemistry 2011; 17:6533-44. [DOI: 10.1002/chem.201002944] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/12/2011] [Indexed: 12/28/2022]
Affiliation(s)
- Dominik A. Megger
- Institute for Inorganic and Analytical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Münster (Germany), Fax: (+49) 251‐83‐36007
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands), Fax: (+31) 20‐59‐87629
| | - Jan Hoffmann
- Institut für Physikalische and Theoretische Chemie, Goethe‐Universität Frankfurt, Max‐von‐Laue‐Str. 7, 60438 Frankfurt (Germany)
| | - Bernhard Brutschy
- Institut für Physikalische and Theoretische Chemie, Goethe‐Universität Frankfurt, Max‐von‐Laue‐Str. 7, 60438 Frankfurt (Germany)
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands), Fax: (+31) 20‐59‐87629
| | - Jens Müller
- Institute for Inorganic and Analytical Chemistry, University of Muenster, Corrensstr. 28/30, 48149 Münster (Germany), Fax: (+49) 251‐83‐36007
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50
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Guza R, Kotandeniya D, Murphy K, Dissanayake T, Lin C, Giambasu GM, Lad RR, Wojciechowski F, Amin S, Sturla SJ, Hudson RH, York DM, Jankowiak R, Jones R, Tretyakova NY. Influence of C-5 substituted cytosine and related nucleoside analogs on the formation of benzo[a]pyrene diol epoxide-dG adducts at CG base pairs of DNA. Nucleic Acids Res 2011; 39:3988-4006. [PMID: 21245046 PMCID: PMC3089471 DOI: 10.1093/nar/gkq1341] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 01/13/2023] Open
Abstract
Endogenous 5-methylcytosine ((Me)C) residues are found at all CG dinucleotides of the p53 tumor suppressor gene, including the mutational 'hotspots' for smoking induced lung cancer. (Me)C enhances the reactivity of its base paired guanine towards carcinogenic diolepoxide metabolites of polycyclic aromatic hydrocarbons (PAH) present in cigarette smoke. In the present study, the structural basis for these effects was investigated using a series of unnatural nucleoside analogs and a representative PAH diolepoxide, benzo[a]pyrene diolepoxide (BPDE). Synthetic DNA duplexes derived from a frequently mutated region of the p53 gene (5'-CCCGGCACCC GC[(15)N(3),(13)C(1)-G]TCCGCG-3', + strand) were prepared containing [(15)N(3), (13)C(1)]-guanine opposite unsubstituted cytosine, (Me)C, abasic site, or unnatural nucleobase analogs. Following BPDE treatment and hydrolysis of the modified DNA to 2'-deoxynucleosides, N(2)-BPDE-dG adducts formed at the [(15)N(3), (13)C(1)]-labeled guanine and elsewhere in the sequence were quantified by mass spectrometry. We found that C-5 alkylcytosines and related structural analogs specifically enhance the reactivity of the base paired guanine towards BPDE and modify the diastereomeric composition of N(2)-BPDE-dG adducts. Fluorescence and molecular docking studies revealed that 5-alkylcytosines and unnatural nucleobase analogs with extended aromatic systems facilitate the formation of intercalative BPDE-DNA complexes, placing BPDE in a favorable orientation for nucleophilic attack by the N(2) position of guanine.
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MESH Headings
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/analogs & derivatives
- 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide/chemistry
- Base Pairing
- Chromatography, High Pressure Liquid
- Cytosine/analogs & derivatives
- DNA Adducts/chemistry
- Deoxyguanosine/analogs & derivatives
- Deoxyguanosine/chemistry
- Genes, p53
- Guanine/chemistry
- Isotope Labeling
- Models, Molecular
- Oligodeoxyribonucleotides/chemical synthesis
- Oligodeoxyribonucleotides/chemistry
- Spectrometry, Fluorescence
- Spectrometry, Mass, Electrospray Ionization
- Tandem Mass Spectrometry
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Affiliation(s)
- Rebecca Guza
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Delshanee Kotandeniya
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Kristopher Murphy
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Thakshila Dissanayake
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Chen Lin
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - George Madalin Giambasu
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Rahul R. Lad
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Filip Wojciechowski
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shantu Amin
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shana J. Sturla
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Robert H.E. Hudson
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Ryszard Jankowiak
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Roger Jones
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, Department of Chemistry, Kansas State University, Manhattan, KS 66505, USA, Institute of Food, Nutrition and Health, ETH Zurich, 8092 Zurich, Switzerland, Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, Department of Chemistry, Pennsylvania State University and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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