1
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Huo B, Wang C, Hu X, Wang H, Zhu G, Zhu A, Li L. Peripheral substitution effects on unnatural base pairs: A case of brominated TPT3 to enhance replication fidelity. Bioorg Chem 2023; 140:106827. [PMID: 37683537 DOI: 10.1016/j.bioorg.2023.106827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
The high fidelity poses a central role in developing unnatural base pairs (UBPs), which means the high pairing capacity of unnatural bases with their partners, and low mispairing with all the natural bases. Different strategies have been used to develop higher-fidelity UBPs, including optimizing hydrophobic interaction forces between UBPs. Variant substituent groups are allowed to fine tune the hydrophobic forces of different UBPs' candidates. However, the modifications on the skeleton of TPT3 base are rare and the replication fidelity of TPT3-NaM remains hardly to improve so far. In this paper, we reasoned that modifying and/or expanding the aromatic surface by Bromo-substituents to slightly increase hydrophobicity of TPT3 might offer a way to increase the fidelity of this pair. Based on the hypothesis, we synthesized the bromine substituted TPT3, 2-bromo-TPT3 and 2, 4-dibromo-TPT3 as the new TPT3 analogs. While the enzyme reaction kinetic experiments showed that d2-bromo-TPT3-dNaM pair and d2, 4-dibromo-TPT3TP-dNaM pair had slightly less efficient incorporation and extension rates than that of dTPT3-dNaM pair, the assays did reveal that the mispairing of 2-bromo-TPT3 and 2, 4-dibromo-TPT3 with all the natural bases could dramatically decrease in contrast to TPT3. Their lower mispairing capacity promoted us to run polymerase chain amplification reactions, and a higher fidelity of d2-bromo-TPT3-dNaM pair could be obtained with 99.72 ± 0.01% of the in vitro replication fidelity than that of dTPT3-dNaM pair, 99.52 ± 0.09%. In addition, d2-bromo-TPT3-dNaM can also be effectively copied in E. coli cells, which showed the same replication fidelity as that of dTPT3-dNaM in the specific sequence, but a higher fidelity in the random sequence context.
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Affiliation(s)
- Bianbian Huo
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Chao Wang
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Xiaoqi Hu
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Honglei Wang
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Gongming Zhu
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China
| | - Anlian Zhu
- Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China
| | - Lingjun Li
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, China Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, Henan Normal University, Xinxiang, Henan 453007, China; Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan 453007, China; Pingyuan Laboratory, Henan Normal University, Xinxiang 453007, China.
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2
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Affiliation(s)
- Jean‐François Lutz
- Université de Strasbourg, CNRSInstitut Charles Sadron, UPR22 23 rue du Loess 67034 Strasbourg Cedex 2 France
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3
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Szatylowicz H, Jezuita A, Marek PH, Krygowski TM. Substituent effects on the stability of the four most stable tautomers of adenine and purine. RSC Adv 2019; 9:31343-31356. [PMID: 35527924 PMCID: PMC9072591 DOI: 10.1039/c9ra04615a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/20/2019] [Indexed: 11/21/2022] Open
Abstract
Substituent effects at the C2-, C8- and N-positions of adenine and purine in their four the most stable tautomers are studied by means of B97D3/aug-cc-pvdz computation applying substituents of varying electronic properties: NO2, CN, CHO, Cl, F, H, Me, OMe, OH and NH2. The substituent effect is characterized by the substituent effect stabilization energy (SESE) and substituent Hammett constant σ. For adenine, SESE is obtained with purine as the reference system. Additionally, for both adenine and purine, SESE characteristics are estimated with benzene, imidazole and amino-pyrimidine as reference systems, when possible, taking into account substitution in topologically equivalent positions. The role of a C6-NH2 group in adenine in modifying the substitution effect is observed and discussed. Additionally, the proximity effect for some asymmetric substituents (e.g. CHO, OMe) is recognized and meticulously analyzed.
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Affiliation(s)
- Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology Noakowskiego 3 00-664 Warsaw Poland
| | - Anna Jezuita
- Faculty of Chemistry, Opole University Oleska 48 45-052 Opole Poland
| | - Paulina H Marek
- Faculty of Chemistry, Warsaw University of Technology Noakowskiego 3 00-664 Warsaw Poland .,Faculty of Chemistry, University of Warsaw Pasteura 1 02-093 Warsaw Poland
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4
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Vichier-Guerre S, Dugué L, Pochet S. 2'-Deoxyribonucleoside 5'-triphosphates bearing 4-phenyl and 4-pyrimidinyl imidazoles as DNA polymerase substrates. Org Biomol Chem 2019; 17:290-301. [PMID: 30543241 DOI: 10.1039/c8ob02464b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed a versatile access to a series of 4-substituted imidazole 2'-deoxynucleoside triphosphate bearing functionalized phenyl or pyrimidinyl rings. 4-Iodo-1H-imidazole was enzymatically converted into the corresponding 2'-deoxynucleoside, which was then chemically derived into its 5'-triphosphate, followed by 4-arylation via Suzuki-Miyaura coupling using (hetero)arylboronic acids. Both KF (exo-) and Deep Vent (exo-) DNA polymerases incorporated these modified nucleotides in primer-extension assays, adenine being the preferred pairing partner in the template. The 4-(3-aminophenyl)imidazole derivative (3APh) was the most efficiently inserted opposite A by KF (exo-) with only a 37-fold lower efficiency (Vmax/KM) than that of the correct dTTP. No further extension occurred after the incorporation of a single aryl-imidazole nucleotide. Interestingly, the aryl-imidazole dNTPs were found to undergo successive incorporation by calf thymus terminal deoxynucleotidyl transferase with different tailing efficiencies among this series and with a marked preference for 2APyr polymerization.
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Affiliation(s)
- Sophie Vichier-Guerre
- Unité de Chimie et Biocatalyse, Institut Pasteur, CNRS, UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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5
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Fesenko DO, Guseinov TO, Lapa SA, Kuznetsova VE, Shershov VE, Spitsyn MA, Nasedkina TV, Zasedatelev AS, Chudinov AV. Substrate Properties of New Fluorescently Labeled Deoxycytidine Triphosphates in Enzymatic Synthesis of DNA with Polymerases of Families A and B. Mol Biol 2018. [DOI: 10.1134/s0026893318030044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
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The information available to any organism is encoded in a four
nucleotide, two base pair genetic code. Since its earliest days, the
field of synthetic biology has endeavored to impart organisms with
novel attributes and functions, and perhaps the most fundamental approach
to this goal is the creation of a fifth and sixth nucleotide that
pair to form a third, unnatural base pair (UBP) and thus allow for
the storage and retrieval of increased information. Achieving this
goal, by definition, requires synthetic chemistry to create unnatural
nucleotides and a medicinal chemistry-like approach to guide their
optimization. With this perspective, almost 20 years ago we began
designing unnatural nucleotides with the ultimate goal of developing
UBPs that function in vivo, and thus serve as the
foundation of semi-synthetic organisms (SSOs) capable of storing and
retrieving increased information. From the beginning, our efforts
focused on the development of nucleotides that bear predominantly
hydrophobic nucleobases and thus that pair not based on the complementary
hydrogen bonds that are so prominent among the natural base pairs
but rather via hydrophobic and packing interactions. It was envisioned
that such a pairing mechanism would provide a basal level of selectivity
against pairing with natural nucleotides, which we expected would
be the greatest challenge; however, this choice mandated starting
with analogs that have little or no homology to their natural counterparts
and that, perhaps not surprisingly, performed poorly. Progress toward
their optimization was driven by the construction of structure–activity
relationships, initially from in vitro steady-state
kinetic analysis, then later from pre-steady-state and PCR-based assays,
and ultimately from performance in vivo, with the
results augmented three times with screens that explored combinations
of the unnatural nucleotides that were too numerous to fully characterize
individually. The structure–activity relationship data identified
multiple features required by the UBP, and perhaps most prominent
among them was a substituent ortho to the glycosidic linkage that
is capable of both hydrophobic packing and hydrogen bonding, and nucleobases
that stably stack with flanking natural nucleobases in lieu of the potentially more stabilizing stacking interactions afforded
by cross strand intercalation. Most importantly, after the examination
of hundreds of unnatural nucleotides and thousands of candidate UBPs,
the efforts ultimately resulted in the identification of a family
of UBPs that are well recognized by DNA polymerases when incorporated
into DNA and that have been used to create SSOs that store and retrieve
increased information. In addition to achieving a longstanding goal
of synthetic biology, the results have important implications for
our understanding of both the molecules and forces that can underlie
biological processes, so long considered the purview of molecules
benefiting from eons of evolution, and highlight the promise of applying
the approaches and methodologies of synthetic and medical chemistry
in the pursuit of synthetic biology.
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Affiliation(s)
- Aaron W. Feldman
- Department of Chemistry, The Scripps Research Institute, La
Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La
Jolla, California 92037, United States
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7
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Dorigundla AR, Gurrapu R, Batchu VR. Stereoselective synthesis of peracetylated (−)-gloeosporiol via acid catalysed intramolecular etherification. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2016.12.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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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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10
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Kervio E, Claasen B, Steiner UE, Richert C. The strength of the template effect attracting nucleotides to naked DNA. Nucleic Acids Res 2014; 42:7409-20. [PMID: 24875480 PMCID: PMC4066754 DOI: 10.1093/nar/gku314] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transmission of genetic information relies on Watson–Crick base pairing between nucleoside phosphates and template bases in template–primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template–primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, Kd′s range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.
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Affiliation(s)
- Eric Kervio
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Birgit Claasen
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ulrich E Steiner
- Fachbereich Chemie, Universität Konstanz, 78457 Konstanz, Germany
| | - Clemens Richert
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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11
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Hou D, Greenberg MM. DNA interstrand cross-linking upon irradiation of aryl halide C-nucleotides. J Org Chem 2014; 79:1877-84. [PMID: 24559326 DOI: 10.1021/jo4028227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
γ-Radiolysis kills cells by damaging DNA via radical processes. Many of the radical pathways are O2 dependent, which results in a reduction in the cytotoxicity of ionizing radiation in hypoxic tumor cells. Consequently, there is a need for chemical agents that increase DNA damage by ionizing radiation under O2-deficient conditions. Modified nucleotides that are incorporated in DNA and produce highly reactive σ-radicals are useful as radiosensitizing agents. Aryl halide C-nucleotides (4-6) were incorporated into oligonucleotides by solid-phase synthesis. Duplex DNA containing 4-6 forms interstrand cross-links upon γ-radiolysis under anaerobic conditions or UV irradiation. Deep Vent (exo(-)) DNA polymerase accepted the nucleotide triphosphate of C-nucleotide 6 as a substrate and preferentially incorporated it opposite pyrimidines, but no further extension was detected. Incorporation of 6 in extended products by Deep Vent (exo(-)) during PCR or by Sequenase during copying of single stranded DNA plasmid was undetectable. Aryl halide nucleotide analogues that produce DNA interstrand cross-links under anaerobic conditions upon irradiation are potentially useful as radiosensitizing agents, but further research is needed to identify molecules that are incorporated by DNA polymerases and do not block further polymerization for this approach to be useful in cells.
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Affiliation(s)
- Dianjie Hou
- Department of Chemistry Johns Hopkins University 3400 North Charles Street, Baltimore, Maryland 21218, United States
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12
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Walsh JM, Beuning PJ. Synthetic nucleotides as probes of DNA polymerase specificity. J Nucleic Acids 2012; 2012:530963. [PMID: 22720133 PMCID: PMC3377560 DOI: 10.1155/2012/530963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 03/21/2012] [Indexed: 12/17/2022] Open
Abstract
The genetic code is continuously expanding with new nucleobases designed to suit specific research needs. These synthetic nucleotides are used to study DNA polymerase dynamics and specificity and may even inhibit DNA polymerase activity. The availability of an increasing chemical diversity of nucleotides allows questions of utilization by different DNA polymerases to be addressed. Much of the work in this area deals with the A family DNA polymerases, for example, Escherichia coli DNA polymerase I, which are DNA polymerases involved in replication and whose fidelity is relatively high, but more recent work includes other families of polymerases, including the Y family, whose members are known to be error prone. This paper focuses on the ability of DNA polymerases to utilize nonnatural nucleotides in DNA templates or as the incoming nucleoside triphosphates. Beyond the utility of nonnatural nucleotides as probes of DNA polymerase specificity, such entities can also provide insight into the functions of DNA polymerases when encountering DNA that is damaged by natural agents. Thus, synthetic nucleotides provide insight into how polymerases deal with nonnatural nucleotides as well as into the mutagenic potential of nonnatural nucleotides.
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Affiliation(s)
- Jason M. Walsh
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 102 Hurtig Hall, Boston, MA 02115, USA
| | - Penny J. Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 102 Hurtig Hall, Boston, MA 02115, USA
- Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, MA 02115, USA
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13
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Chapuis H, Kubelka T, Joubert N, Pohl R, Hocek M. Synthesis of 6-Substituted 2(1H)-Pyridon-3-yl C-2′-Deoxyribonucleosides. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101662] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Štambaský J, Kapras V, Štefko M, Kysilka O, Hocek M, Malkov AV, Kočovský P. A Modular Approach to Aryl-C-ribonucleosides via the Allylic Substitution and Ring-Closing Metathesis Sequence. A Stereocontrolled Synthesis of All Four α-/β- and d-/l-C-Nucleoside Stereoisomers. J Org Chem 2011; 76:7781-803. [DOI: 10.1021/jo201110z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jan Štambaský
- Department of Chemistry, WestChem, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Vojtěch Kapras
- Department of Chemistry, WestChem, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Martin Štefko
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, CZ-16610, Prague 6, Czech Republic
| | - Ondřej Kysilka
- Department of Chemistry, WestChem, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, CZ-16610, Prague 6, Czech Republic
| | - Andrei V. Malkov
- Department of Chemistry, WestChem, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Pavel Kočovský
- Department of Chemistry, WestChem, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
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15
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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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16
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Turygin DS, Subat M, Arslanov VV, König B, Kalinina MA. Hydrogen-bond-guided self-assembly of nucleotides on a receptor-array surface. Chemistry 2010; 16:10560-8. [PMID: 20648485 DOI: 10.1002/chem.201000356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The hydrogen-bond-guided self-assembly of 5'-ribonucleotides bearing adenine(A), cytosine (C), uracil (U), or guanine (G) bases from aqueous solution on a lipid-like surface decorated with synthetic bis(Zn(II)-cyclen) (cyclen=1,4,7,10-tetraazacyclodododecane) metal-complex receptor sites is described. The process was studied by using surface plasmon resonance spectroscopy. The data show that the mechanism of nucleotide binding to the 2D template is influenced by the chemistry of the bases and the pH value of the solution. In a neutral solution of pH 7.5, the process is cooperative and selective with respect to Watson-Crick pairs (A-U and C-G), which form stable double planes in accordance with the Chargaff rule. In a more acidic solution at pH 6.0, the interactions between complementary partners become non-cooperative and the surface also stabilizes mismatched and wobble pairs due to the pH-induced changes in the receptor coordination state. The results suggest that hydrogen bonding plays a key role in the self-assembly of complementary nucleotides at the lipid-like interface, and the cooperative character of the process stems from the ideal matching of the orientation and chemistry of all the interacting components with respect to each other in neutral solution.
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Affiliation(s)
- Dmitry S Turygin
- Department of Physical Chemistry of Supramolecular Systems, Frumkin Institute of Physical Chemistry and Electrochemistry RAS, 31 Leninsky Prospect, Moscow 119991, Russia
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Heo JY, Hwang GT. 2-Aminobenzene Derivatives as Unnatural Nucleobases and Their DNA Duplex Stabilities. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.12.3794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Bárta J, Slavětínská L, Klepetářová B, Hocek M. Modular Synthesis of 5-Substituted Furan-2-yl C-2′-Deoxyribonucleosides and Biaryl Covalent Base-Pair Analogues. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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Stefko M, Slavetínská L, Klepetárová B, Hocek M. A general and efficient synthesis of pyridin-2-yl C-ribonucleosides bearing diverse alkyl, aryl, amino, and carbamoyl groups in position 6. J Org Chem 2010; 75:442-9. [PMID: 20000693 DOI: 10.1021/jo902313g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
An efficient and practical methodology of preparation of 6-substituted pyridin-2-yl C-ribonucleosides was developed. A one-pot two-step addition of 2-lithio-6-bromopyridine to TBS-protected ribonolactone followed by acetylation gave 1beta-(6-bromopyridin-2-yl)-1-O-acetyl-2,3,5-tri-O-(tert-butyldimethylsilyl)-D-ribofuranose in high yield. Its reduction with Et(3)SiH and BF(3) x Et(2)O afforded the desired TBS-protected 6-bromopyridine C-ribonucleoside as pure beta-anomer in good overall yield of 63%. This intermediate was then subjected to a series of palladium catalyzed cross-coupling reactions, aminations and aminocarbonylations to give a series of protected 1beta-(6-alkyl-, 6-aryl-, 6-amino-, and 6-carbamoylpyridin-2-yl)-C-ribonucleosides. Deprotection of silylated nucleosides by Et(3)N x 3HF gave a series of title free C-ribonucleosides (12 examples).
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Affiliation(s)
- Martin Stefko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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21
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Kubelka T, Slavětínská L, Klepetářová B, Hocek M. Synthesis of 2,4-Disubstituted Pyrimidin-5-yl C-2′-Deoxyribonucleosides by Sequential Regioselective Reactions of 2,4-Dichloropyrimidine Nucleosides. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000164] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Ding H, Greenberg MM. DNA damage and interstrand cross-link formation upon irradiation of aryl iodide C-nucleotide analogues. J Org Chem 2010; 75:535-44. [PMID: 20067226 PMCID: PMC2813935 DOI: 10.1021/jo902071y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The 5-halopyrimidine nucleotides damage DNA upon UV-irradiation or exposure to gamma-radiolysis via the formation of the 2'-deoxyuridin-5-yl sigma-radical. The bromo and iodo derivatives of these molecules are useful tools for probing DNA structure and as therapeutically useful radiosensitizing agents. A series of aryl iodide C-nucleotides were incorporated into synthetic oligonucleotides and exposed to UV-irradiation and gamma-radiolysis. The strand damage produced upon irradiation of DNA containing these molecules is consistent with the generation of highly reactive sigma-radicals. Direct stand breaks and alkali-labile lesions are formed at the nucleotide analogue and flanking nucleotides. The distribution of lesion type and location varies depending upon the position of the aryl ring that is iodinated. Unlike 5-halopyrimidine nucleotides, the aryl iodides produce interstrand cross-links in duplex regions of DNA when exposed to gamma-radiolysis or UV-irradiation. Quenching studies suggest that cross-links are produced by gamma-radiolysis via capture of a solvated electron, and subsequent fragmentation to the sigma-radical. These observations suggest that aryl iodide C-nucleotide analogues may be useful as probes for excess electron transfer and radiosensitizing agents.
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Affiliation(s)
- Hui Ding
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
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23
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Loakes D, Gallego J, Pinheiro VB, Kool ET, Holliger P. Evolving a polymerase for hydrophobic base analogues. J Am Chem Soc 2009; 131:14827-37. [PMID: 19778048 PMCID: PMC2762193 DOI: 10.1021/ja9039696] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic base analogues (HBAs) have shown great promise for the expansion of the chemical and coding potential of nucleic acids but are generally poor polymerase substrates. While extensive synthetic efforts have yielded examples of HBAs with favorable substrate properties, their discovery has remained challenging. Here we describe a complementary strategy for improving HBA substrate properties by directed evolution of a dedicated polymerase using compartmentalized self-replication (CSR) with the archetypal HBA 5-nitroindole (d5NI) and its derivative 5-nitroindole-3-carboxamide (d5NIC) as selection substrates. Starting from a repertoire of chimeric polymerases generated by molecular breeding of DNA polymerase genes from the genus Thermus, we isolated a polymerase (5D4) with a generically enhanced ability to utilize HBAs. The selected polymerase. 5D4 was able to form and extend d5NI and d5NIC (d5NI(C)) self-pairs as well as d5NI(C) heteropairs with all four bases with efficiencies approaching, or exceeding, those of the cognate Watson-Crick pairs, despite significant distortions caused by the intercalation of the d5NI(C) heterocycles into the opposing strand base stack, as shown by nuclear magnetic resonance spectroscopy (NMR). Unlike Taq polymerase, 5D4 was also able to extend HBA pairs such as Pyrene: varphi (abasic site), d5NI: varphi, and isocarbostyril (ICS): 7-azaindole (7AI), allowed bypass of a chemically diverse spectrum of HBAs, and enabled PCR amplification with primers comprising multiple d5NI(C)-substitutions, while maintaining high levels of catalytic activity and fidelity. The selected polymerase 5D4 promises to expand the range of nucleobase analogues amenable to replication and should find numerous applications, including the synthesis and replication of nucleic acid polymers with expanded chemical and functional diversity.
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Affiliation(s)
- David Loakes
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - José Gallego
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Vitor B. Pinheiro
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Eric T. Kool
- Stanford University, Department of Chemistry, Stanford, CA 94305, USA
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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24
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Affiliation(s)
- Michal Hocek
- Department of Chemistry, WestChem, University of Glasgow, Glasgow G12 8QQ, United Kingdom, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, CZ-16610 Prague 6, Czech Republic
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25
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Zendlová L, Reha D, Hocek M, Hobza P. Theoretical study of the stability of the DNA duplexes modified by a series of hydrophobic base analogues. Chemistry 2009; 15:7601-10. [PMID: 19569131 DOI: 10.1002/chem.200802170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The geometries of a 13 mer of a DNA double helix (5'-GCGTACACATGCG-3') were determined by molecular dynamics simulations using a Cornell et al. empirical force field. The bases in the central base pair (shown in bold) were replaced (one or both) by a series of hydrophobic base analogues (phenyl, biphenyl, phenylnaphathalene, phenylanthracene and phenylphenanthrene). Due to the large fluctuations of the systems, an average geometry could not be determined. The interaction energies of the Model A, which consisted of three central steps of a duplex without a sugar phosphate backbone, taken from molecular dynamics simulations (geometry sampled every 1 ps), were calculated by the self-consistent charge density functional based tight-binding (SCC-DFTB-D) method and were subsequently averaged. The higher the stability of the systems the higher the aromaticity of the base analogues. To estimate the desolvation energy of the duplex, the COSMO continuum solvent model was used and the calculations were provided on a larger model, Model B (the three central steps of the duplex with a sugar phosphate backbone neutralised by H atoms), taken from molecular dynamics simulations (geometry sampled every 200 ps) and subsequently averaged. The selectivity of the base analogue pairs was ascertained (Model B) by including the desolvation energy and the interaction energy of both strands, as determined by the SCC-DFTB-D method. The highest selectivity was found for a phenylphenanthrene. Replacing the nucleic acid bases with a base analogue leads to structural changes of the central pair. Only with the smallest base analogues (phenyl) does the central base pair stay planar. When passing to larger base analogues the central base pair is usually stacked.
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Affiliation(s)
- Lucie Zendlová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2,166 10, Prague 6, Czech Republic
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26
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Bergstrom DE. Unnatural nucleosides with unusual base pairing properties. ACTA ACUST UNITED AC 2009; Chapter 1:1.4.1-1.4.32. [PMID: 19488968 DOI: 10.1002/0471142700.nc0104s37] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in biology and biotechnology. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered include base pairs with alternative H-bonding schemes, dimensionally expanded base pairs, hydrophobic base pairs, metal-ligated bases, degenerate bases, universal nucleosides, and triplex constituents.
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27
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Loakes D, Holliger P. Polymerase engineering: towards the encoded synthesis of unnatural biopolymers. Chem Commun (Camb) 2009:4619-31. [PMID: 19641798 DOI: 10.1039/b903307f] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA is not only a repository of genetic information for life, it is also a unique polymer with remarkable properties: it associates according to well-defined rules, it can be assembled into diverse nanostructures of defined geometry, it can be evolved to bind ligands and catalyse chemical reactions and it can serve as a supramolecular scaffold to arrange chemical groups in space. However, its chemical makeup is rather uniform and the physicochemical properties of the four canonical bases only span a narrow range. Much wider chemical diversity is accessible through solid-phase synthesis but oligomers are limited to <100 nucleotides and variations in chemistry can usually not be replicated and thus are not amenable to evolution. Recent advances in nucleic acid chemistry and polymerase engineering promise to bring the synthesis, replication and ultimately evolution of nucleic acid polymers with greatly expanded chemical diversity within our reach.
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Affiliation(s)
- David Loakes
- Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge, Cambridgeshire, UKCB2 0QH
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28
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Brudno Y, Liu DR. Recent progress toward the templated synthesis and directed evolution of sequence-defined synthetic polymers. ACTA ACUST UNITED AC 2009; 16:265-76. [PMID: 19318208 DOI: 10.1016/j.chembiol.2009.02.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 01/20/2009] [Accepted: 02/16/2009] [Indexed: 12/21/2022]
Abstract
Biological polymers such as nucleic acids and proteins are ubiquitous in living systems, but their ability to address problems beyond those found in nature is constrained by factors such as chemical or biological instability, limited building-block functionality, bioavailability, and immunogenicity. In principle, sequence-defined synthetic polymers based on nonbiological monomers and backbones might overcome these constraints; however, identifying the sequence of a synthetic polymer that possesses a specific desired functional property remains a major challenge. Molecular evolution can rapidly generate functional polymers but requires a means of translating amplifiable templates such as nucleic acids into the polymer being evolved. This review covers recent advances in the enzymatic and nonenzymatic templated polymerization of nonnatural polymers and their potential applications in the directed evolution of sequence-defined synthetic polymers.
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Affiliation(s)
- Yevgeny Brudno
- Department of Chemistry and Chemical Biology and the Howard Hughes Medical Institute, 12 Oxford Street, Harvard University, Cambridge, MA 02138, USA
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29
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Seo YJ, Hwang GT, Ordoukhanian P, Romesberg FE. Optimization of an unnatural base pair toward natural-like replication. J Am Chem Soc 2009; 131:3246-52. [PMID: 19256568 PMCID: PMC2901498 DOI: 10.1021/ja807853m] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Predominantly hydrophobic unnatural nucleotides that selectively pair within duplex DNA as well as during polymerase-mediated replication have recently received much attention as the cornerstone of efforts to expand the genetic alphabet. We recently reported the results of a screen and subsequent lead hit optimization that led to identification of the unnatural base pair formed between the nucleotides dMMO2 and d5SICS. This unnatural base pair is replicated by the Klenow fragment of Escherichia coli DNA polymerase I with better efficiency and fidelity than other candidates reported in the literature. However, its replication remains significantly less efficient than a natural base pair, and further optimization is necessary for its practical use. To better understand and optimize the slowest step of replication of the unnatural base pair, the insertion of dMMO2 opposite d5SICS, we synthesized two dMMO2 derivatives, d5FM and dNaM, which differ from the parent nucleobase in terms of shape, hydrophobicity, and polarizability. We find that both derivatives are inserted opposite d5SICS more efficiently than dMMO2 and that overall the corresponding unnatural base pairs are generally replicated with higher efficiency and fidelity than the pair between dMMO2 and d5SICS. In fact, in the case of the dNaM:d5SICS heteropair, the efficiency of each individual step of replication approaches that of a natural base pair, and the minimum overall fidelity ranges from 10(3) to 10(4). In addition, the data allow us to propose a generalized model of unnatural base pair replication, which should aid in further optimization of the unnatural base pair and possibly in the design of additional unnatural base pairs that are replicated with truly natural-like efficiency and fidelity.
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Affiliation(s)
- Young Jun Seo
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Gil Tae Hwang
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Phillip Ordoukhanian
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
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30
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Kopitz H, Zivković A, Engels JW, Gohlke H. Determinants of the unexpected stability of RNA fluorobenzene self pairs. Chembiochem 2009; 9:2619-22. [PMID: 18823057 DOI: 10.1002/cbic.200800461] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hannes Kopitz
- Pharmazeutisches Institut, Christian-Albrechts-Universität zu Kiel, Gutenbergstr. 76, 24118 Kiel, Germany
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31
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Lindquist BA, Furse KE, Corcelli SA. Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview. Phys Chem Chem Phys 2009; 11:8119-32. [DOI: 10.1039/b908588b] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Chelliserrykattil J, Lu H, Lee AHF, Kool ET. Polymerase amplification, cloning, and gene expression of benzo-homologous "yDNA" base pairs. Chembiochem 2008; 9:2976-80. [PMID: 19053129 PMCID: PMC2977970 DOI: 10.1002/cbic.200800339] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Indexed: 11/12/2022]
Abstract
A widened DNA base-pair architecture is studied in an effort to explore the possibility of whether new genetic system designs might possess some of the functions of natural DNA. In the "yDNA" system, pairs are homologated by addition of a benzene ring, which yields (in the present study) benzopyrimidines that are correctly paired with purines. Here we report initial tests of ability of the benzopyrimidines yT and yC to store and transfer biochemical and biological information in vitro and in bacterial cells. In vitro primer extension studies with two polymerases showed that the enzymes could insert the correct nucleotides opposite these yDNA bases, but with low selectivity. PCR amplifications with a thermostable polymerase resulted in correct pairings in 15-20 % of the cases, and more successfully when yT or yC were situated within the primers. Segments of DNA containing one or two yDNA bases were then ligated into a plasmid and tested for their ability to successfully lead the expression of an active protein in vivo. Although active at only a fraction of the activity of fully natural DNA, the unnatural bases encoded the correct codon bases in the majority of cases when singly substituted, and yielded functioning green fluorescent protein. Although the activities with native polymerases are modest with these large base pairs, this is the first example of encoding protein in vivo by an unnatural DNA base pair architecture.
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Affiliation(s)
| | - Haige Lu
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080 (USA)
| | - Alex H. F. Lee
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080 (USA)
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080 (USA)
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33
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Hwang GT, Romesberg FE. Unnatural substrate repertoire of A, B, and X family DNA polymerases. J Am Chem Soc 2008; 130:14872-82. [PMID: 18847263 DOI: 10.1021/ja803833h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
As part of an effort to develop unnatural base pairs that are stable and replicable in DNA, we examined the ability of five different polymerases to replicate DNA containing four different unnatural nucleotides bearing predominantly hydrophobic nucleobase analogs. The unnatural pairs were developed based on intensive studies using the Klenow fragment of DNA polymerase I from E. coli (Kf) and found to be recognized to varying degrees. The five additional polymerases characterized here include family A polymerases from bacteriophage T7 and Thermus aquaticus, family B polymerases from Thermococcus litoralis and Thermococcus 9(o)N-7, and the family X polymerase, human polymerase beta. While we find that some aspects of unnatural base pair recognition are conserved among the polymerases, for example, the pair formed between two d3FB nucleotides is typically well recognized, the detailed recognition of most of the unnatural base pairs is generally polymerase dependent. In contrast, we find that the pair formed between d5SICS and dMMO2 is generally well recognized by all of the polymerases examined, suggesting that the determinants of efficient and general recognition are contained within the geometric and electronic structure of these unnatural nucleobases themselves. The data suggest that while the d3FB:d3FB pair is sufficiently well recognized by several of the polymerases for in vitro applications, the d5SICS:dMMO2 heteropair is likely uniquely promising for in vivo use. T7-mediated replication is especially noteworthy due to strong mispair discrimination.
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Affiliation(s)
- Gil Tae Hwang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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34
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Watson MD, Gai XS, Gillies AT, Brewer SH, Fenlon EE. A vibrational probe for local nucleic acid environments: 5-cyano-2'-deoxyuridine. J Phys Chem B 2008; 112:13188-92. [PMID: 18816094 DOI: 10.1021/jp8067238] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitriles have been shown to be effective vibrational probes of local environments in proteins but have yet to be fully utilized for the study of nucleic acids. The potential utility of 5-cyano-2'-deoxyuridine ( 1) as a probe of local nucleic acid environment was investigated by measuring the dependence of the IR nitrile stretching frequency (nu CN), line shape, and absorbance on solvent and temperature. The nu CN was found to be sensitive to solvent with an observed blue shift of 9.2 cm (-1) in going from THF to water. The dependence of the nitrile IR absorbance band was further investigated in water-THF mixtures. Global line shape analysis, difference FTIR spectroscopy, and singular value decomposition (SVD) were used to show the presence of three distinct local environments around the nitrile group of 1 in these mixtures. A modest blue shift in nu CN was observed upon a hydrogen-bond-mediated heterodimer formation between 2 (a silyl ether analogue of 1) and 2,6-diheptanamido-pyridine ( 3a) in chloroform. The intrinsic temperature dependence of the nu CN was found to be minimal and linear over the temperature range studied. The experimental studies were complemented by density functional theory (DFT) calculations on the dependence of the nitrile stretching frequency on solute-solvent interactions and upon heterodimer formation with model systems.
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35
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Kumar TS, Madsen AS, Østergaard ME, Wengel J, Hrdlicka PJ. Nucleic acid structural engineering using pyrene-functionalized 2'-amino-alpha-L-LNA monomers and abasic sites. J Org Chem 2008; 73:7060-6. [PMID: 18710289 DOI: 10.1021/jo800551j] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Oligonucleotides (ONs) modified with a 2'-N-(pyren-1-yl)acetyl-2'-amino-alpha-L-LNA thymine monomer Y flanked on the 3'-side by an abasic site Phi (i.e., YPhi-unit) exhibit unprecedented increases in thermal affinity (DeltaT(m) values) toward target strands containing abasic sites (DeltaT(m) per YPhi unit >+33.0 degrees C in 9-mer duplexes relative to unmodified ONs). Biophysical studies along with force field calculations suggest that the conformationally locked 2-oxo-5-azabicyclo[2.2.1]heptane skeleton of monomer Y, in concert with the short rigid acetyl linker, efficiently forces the thymine and pyrene moieties to adopt an interplanar distance of approximately 3.4 A. This precisely positions the pyrene moiety in the duplex core void formed by abasic sites (Phi:Phi pair) for optimal pi-pi overlap. Duplexes with multiple YPhi: APhi units separated by one base pair are tolerated extraordinarily well, as exemplified by a 13-mer duplex containing four separated YPhi: APhi units (8 abasic sites distributed over 13 "base pairs"), which exhibit a thermal denaturation temperature of 60.5 degrees C. The YPhi probes display up to 16-fold increases in fluorescence intensity at 380 nm upon hybridization with abasic target strands, whereby self-assembly of these complex architectures can be easily monitored. This study underlines the potential of N2'-functionalized 2'-amino-alpha-L-LNA as building blocks in nucleic acid based diagnostics and nanomaterial engineering.
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Affiliation(s)
- T Santhosh Kumar
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
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36
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Havemann SA, Hoshika S, Hutter D, Benner SA. Incorporation of multiple sequential pseudothymidines by DNA polymerases and their impact on DNA duplex structure. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:261-78. [PMID: 18260010 DOI: 10.1080/15257770701853679] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Thermal denaturation and circular dichroism studies suggested that multiple (up to 12), sequential pseudothymidines, a representative C-glycoside, do not perturb the structure of a representative DNA duplex. Further, various Family A and B DNA polymerases were found to extend a primer by incorporating four sequential pseudothymidine triphosphates, and then continue the extension to generate full-length product. Detailed studies showed that Taq polymerase incorporated up to five sequential C-glycosides, but not more. These results constrain architectures for sequencing, quantitating, and analyzing DNA analogs that exploit C-glycosides, and define better the challenge of creating a synthetic biology using these with natural polymerases.
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Affiliation(s)
- Stephanie A Havemann
- Department of Microbiology & Cell Science, Space Life Sciences Laboratory, Kennedy Space Center, University of Florida, FL, USA
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37
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Bárta J, Pohl R, Klepetárová B, Ernsting NP, Hocek M. Modular synthesis of 5-substituted thiophen-2-yl C-2'-deoxyribonucleosides. J Org Chem 2008; 73:3798-806. [PMID: 18416574 DOI: 10.1021/jo800177y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new modular methodology of preparation of 5-substituted thiophene-2-yl C-nucleosides was developed. A Friedel-Crafts-type of C-glycosidation of 2-bromothiophene with toluoyl-protected methylglycoside 2 gave the desired protected 1beta-(5-bromothiophen-2-yl)-1,2-dideoxyribofuranose 4a in 60%. The key intermediate 4a was then subjected to a series of palladium-catalyzed cross-coupling reactions. The cross-coupling reactions with alkyl organometallics gave beta-(5-alkylthiophen-2-yl)-2-deoxyribonucleosides 4 and 7 in moderate yields accompanied by side-products of reduction. On the other hand, cross-couplings with arylstannanes proceeded smoothly to give a series of beta-(5-arylthiophen-2-yl)-2-deoxyribonucleosides 4 in good yields. Deprotection of toluoylated nucleosides by NaOMe in MeOH and silylated nucleosides by Et 3N.3HF gave a series of free C-nucleosides 6. Alternatively, other types of 5-arylthiophene C-nucleosides 6 were prepared in one step by the aqueous-phase cross-coupling reactions of unprotected 1beta-(5-bromothiophen-2-yl)-1,2-dideoxyribofuranose with boronic acids. Title 5-arylthiophene C-nucleosides 6 exhibit interesting fluorescent properties with emission maxima varying from 339 to 396 nm depending on the aryl group attached.
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Affiliation(s)
- Jan Bárta
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Prague 6, Czech Republic
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38
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Štefko M, Pohl R, Klepetářová B, Hocek M. A Modular Methodology for the Synthesis of 4- and 3-Substituted Benzene and Aniline C-Ribonucleosides. European J Org Chem 2008. [DOI: 10.1002/ejoc.200701168] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Leconte AM, Hwang GT, Matsuda S, Capek P, Hari Y, Romesberg FE. Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet. J Am Chem Soc 2008; 130:2336-43. [PMID: 18217762 PMCID: PMC2892755 DOI: 10.1021/ja078223d] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA is inherently limited by its four natural nucleotides. Efforts to expand the genetic alphabet, by addition of an unnatural base pair, promise to expand the biotechnological applications available for DNA as well as to be an essential first step toward expansion of the genetic code. We have conducted two independent screens of hydrophobic unnatural nucleotides to identify novel candidate base pairs that are well recognized by a natural DNA polymerase. From a pool of 3600 candidate base pairs, both screens identified the same base pair, dSICS:dMMO2, which we report here. Using a series of related analogues, we performed a detailed structure-activity relationship analysis, which allowed us to identify the essential functional groups on each nucleobase. From the results of these studies, we designed an optimized base pair, d5SICS:dMMO2, which is efficiently and selectively synthesized by Kf within the context of natural DNA.
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Affiliation(s)
- Aaron M. Leconte
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Gil Tae Hwang
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Shigeo Matsuda
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Petr Capek
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Yoshiyuki Hari
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
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40
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Tawarada R, Seio K, Sekine M. Synthesis and properties of oligonucleotides with iodo-substituted aromatic aglycons: investigation of possible halogen bonding base pairs. J Org Chem 2007; 73:383-90. [PMID: 18081343 DOI: 10.1021/jo701634t] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ab initio calculations of halogen bond energies of artificial base pairs constructed between iodinated aromatic nucleobase mimics and nitrogen-containing acceptor molecules such as pyridine and imidazole suggest that modified base pairs are converted to optimized planar base pairs with weak Delta E values of -0.19 to -3.93 kcal/mol. To evaluate the contribution of halogen bonding toward duplex stabilization of such modified nucleobase mimics introduced into artificial base pairs, we synthesized three C-nucleoside analogues 1-3 with several iodinated aromatic rings and an imidazole nucleoside derivative 4 and incorporated them into oligodeoxynucleotides. Hybridization studies of modified oligodeoxynucleotides incorporating iodoaromatic bases showed their unique universal base-like ability; however, no indication of halogen bond formation was observed. A more sophisticated design is required for the development of new base pairs stabilized by halogen bonding.
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Affiliation(s)
- Ryuya Tawarada
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan
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41
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Model systems for understanding DNA base pairing. Curr Opin Chem Biol 2007; 11:588-94. [PMID: 17967435 DOI: 10.1016/j.cbpa.2007.09.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2007] [Accepted: 09/28/2007] [Indexed: 11/23/2022]
Abstract
The fact that nucleic acid bases recognize each other to form pairs is a canonical part of the dogma of biology. However, they do not recognize each other well enough in water to account for the selectivity and efficiency that is needed in the transmission of biological information through a cell. Thus proteins assist in this recognition in multiple ways, and recent data suggest that these mechanisms of recognition can vary widely with context. To probe how the chemical differences of the four nucleobases are defined in various biological contexts, chemists and biochemists have developed modified versions that differ in their polarity, shape, size, and functional groups. This brief review covers recent advances in this field of research.
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Hainke S, Singh I, Hemmings J, Seitz O. Synthesis of C-Aryl-Nucleosides and O-Aryl-Glycosides via Cuprate Glycosylation. J Org Chem 2007; 72:8811-9. [DOI: 10.1021/jo7016185] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sven Hainke
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor Strasse 2, D-12489 Berlin, Germany
| | - Ishwar Singh
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor Strasse 2, D-12489 Berlin, Germany
| | - Jennifer Hemmings
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor Strasse 2, D-12489 Berlin, Germany
| | - Oliver Seitz
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor Strasse 2, D-12489 Berlin, Germany
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Silverman LN, Pitzer ME, Ankomah PO, Boxer SG, Fenlon EE. Vibrational stark effect probes for nucleic acids. J Phys Chem B 2007; 111:11611-3. [PMID: 17877390 PMCID: PMC2546494 DOI: 10.1021/jp0750912] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vibrational Stark effect (VSE) has proven to be an effective method for the study of electric fields in proteins via the use of infrared probes. To explore the use of VSE in nucleic acids, we investigated the Stark spectroscopy of nine structurally diverse nucleosides. These nucleosides contained nitrile or azide probes in positions that correspond to both the major and minor grooves of DNA. The nitrile probes showed better characteristics and exhibited absorption frequencies over a broad range; that is, from 2253 cm-1 for 2'-O-cyanoethyl ribonucleosides 8 and 9 to 2102 cm(-1) for a 13C-labeled 5-thiocyanatomethyl-2'-deoxyuridine 3c. The largest Stark tuning rate observed was |Deltamu| = 1.1 cm(-1)/(MV/cm) for both 5-cyano-2'-deoxyuridine 1 and N2-nitrile-2'-deoxyguanosine 7. The latter is a particularly attractive probe because of its high extinction coefficient (epsilon = 412 M-1cm-1) and ease of incorporation into oligomers.
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Affiliation(s)
- Lisa N. Silverman
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080
| | - Michael E. Pitzer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17601
| | - Peter O. Ankomah
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17601
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080
- To whom correspondence should be addressed. Stark Spectroscopy: E-mail: . Telephone: 650-723-4482. Fax: 650-723-4817. Synthesis: E-mail: . Telephone: 717-291-4201. Fax: 717-291-4343
| | - Edward E. Fenlon
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17601
- To whom correspondence should be addressed. Stark Spectroscopy: E-mail: . Telephone: 650-723-4482. Fax: 650-723-4817. Synthesis: E-mail: . Telephone: 717-291-4201. Fax: 717-291-4343
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Matsuda S, Fillo JD, Henry AA, Rai P, Wilkens SJ, Dwyer TJ, Geierstanger BH, Wemmer DE, Schultz PG, Spraggon G, Romesberg FE. Efforts toward expansion of the genetic alphabet: structure and replication of unnatural base pairs. J Am Chem Soc 2007; 129:10466-73. [PMID: 17685517 PMCID: PMC2536688 DOI: 10.1021/ja072276d] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Expansion of the genetic alphabet has been a long-time goal of chemical biology. A third DNA base pair that is stable and replicable would have a great number of practical applications and would also lay the foundation for a semisynthetic organism. We have reported that DNA base pairs formed between deoxyribonucleotides with large aromatic, predominantly hydrophobic nucleobase analogues, such as propynylisocarbostyril (dPICS), are stable and efficiently synthesized by DNA polymerases. However, once incorporated into the primer, these analogues inhibit continued primer elongation. More recently, we have found that DNA base pairs formed between nucleobase analogues that have minimal aromatic surface area in addition to little or no hydrogen-bonding potential, such as 3-fluorobenzene (d3FB), are synthesized and extended by DNA polymerases with greatly increased efficiency. Here we show that the rate of synthesis and extension of the self-pair formed between two d3FB analogues is sufficient for in vitro DNA replication. To better understand the origins of efficient replication, we examined the structure of DNA duplexes containing either the d3FB or dPICS self-pairs. We find that the large aromatic rings of dPICS pair in an intercalative manner within duplex DNA, while the d3FB nucleobases interact in an edge-on manner, much closer in structure to natural base pairs. We also synthesized duplexes containing the 5-methyl-substituted derivatives of d3FB (d5Me3FB) paired opposite d3FB or the unsubstituted analogue (dBEN). In all, the data suggest that the structure, electrostatics, and dynamics can all contribute to the extension of unnatural primer termini. The results also help explain the replication properties of many previously examined unnatural base pairs and should help design unnatural base pairs that are better replicated.
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Affiliation(s)
- Shigeo Matsuda
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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Joubert N, Pohl R, Klepetérová B, Hocek M. Modular and Practical Synthesis of 6-Substituted Pyridin-3-yl C-Nucleosides. J Org Chem 2007; 72:6797-805. [PMID: 17665955 DOI: 10.1021/jo0709504] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel modular and practical methodology for preparation of 6-substituted pyridin-3-yl C-nucleosides was developed. The Heck reaction of 2-chloro-5-iodopyridine with a 3'-TBDMS-protected glycal gave a 6-chloropyridin-3-yl nucleoside analogue, which was then desilylated, selectively reduced, and reprotected to give the TBDMS-protected 6-chloropyridin-3-yl C-2'-deoxyribonucleoside as a pure beta-anomer in a total yield of 39% over four steps. This key intermediate was then subjected to a series of palladium-catalyzed cross-coupling reactions, aminations, and alkoxylations to give a series of protected 1beta-(6-alkyl-, 6-aryl-, 6-hetaryl, 6-amino-, and 6-tert-butoxypyridin-3-yl)-2'-deoxyribonucleosides. 6-Unsubstituted pyridin-3-yl C-nucleoside was prepared by catalytic hydrogenation of the chloro derivative and 6-oxopyridine C-nucleoside by treatment of the 6-tert-butoxy derivative with TFA. Deprotection of all the silylated nucleosides by Et3N.3HF gave a series of free C-nucleosides (10 examples).
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Affiliation(s)
- Nicolas Joubert
- Gilead Sciences & IOCB Research Center, Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, CZ-16610, Prague 6, Czech Republic
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Matsuda S, Leconte AM, Romesberg FE. Minor groove hydrogen bonds and the replication of unnatural base pairs. J Am Chem Soc 2007; 129:5551-7. [PMID: 17411040 PMCID: PMC2527036 DOI: 10.1021/ja068282b] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
As part of an effort to expand the genetic alphabet, we examined the synthesis of DNA with six different unnatural nucleotides bearing methoxy-derivatized nucleobase analogues. Different nucleobase substitution patterns were used to systematically alter the nucleobase electronics, sterics, and hydrogen-bonding potential. We determined the ability of the Klenow fragment of E. coli DNA polymerase I to synthesize and extend the different unnatural base pairs and mispairs under steady-state conditions. Unlike other hydrogen-bond acceptors examined in the past, the methoxy groups do not facilitate mispairing, implying that they are not recognized by any of the hydrogen-bond donors of the natural nucleobases; however, they do facilitate replication. The more efficient replication results largely from an increase in the rate of extension of primers terminating at the unnatural base pair and, interestingly, requires that the methoxy group be at the ortho position where it is positioned in the developing minor groove and can form a functionally important hydrogen bond with the polymerase. Thus, ortho methoxy groups should be generally useful for the effort to expand the genetic alphabet.
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Kim Y, Leconte AM, Hari Y, Romesberg FE. Stability and Polymerase Recognition of Pyridine Nucleobase Analogues: Role of Minor-Groove H-Bond Acceptors. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602579] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kim Y, Leconte AM, Hari Y, Romesberg FE. Stability and Polymerase Recognition of Pyridine Nucleobase Analogues: Role of Minor-Groove H-Bond Acceptors. Angew Chem Int Ed Engl 2006; 45:7809-12. [PMID: 17075934 DOI: 10.1002/anie.200602579] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yoonkyung Kim
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Kuwahara M, Nagashima JI, Hasegawa M, Tamura T, Kitagata R, Hanawa K, Hososhima SI, Kasamatsu T, Ozaki H, Sawai H. Systematic characterization of 2'-deoxynucleoside- 5'-triphosphate analogs as substrates for DNA polymerases by polymerase chain reaction and kinetic studies on enzymatic production of modified DNA. Nucleic Acids Res 2006; 34:5383-94. [PMID: 17012278 PMCID: PMC1636466 DOI: 10.1093/nar/gkl637] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 07/28/2006] [Accepted: 08/14/2006] [Indexed: 11/26/2022] Open
Abstract
We synthesized C5-modified analogs of 2'-deoxyuridine triphosphate and 2'-deoxycytidine triphosphate and investigated them as substrates for PCRs using Taq, Tth, Vent(exo-), KOD Dash and KOD(exo-) polymerases and pUC 18 plasmid DNA as a template. These assays were performed on two different amplifying regions of pUC18 with different T/C contents that are expected to have relatively high barriers for incorporation of either modified dU or dC. On the basis of 260 different assays (26 modified triphosphates x 5 DNA polymerases x 2 amplifying regions), it appears that generation of the full-length PCR product depends not only on the chemical structures of the substitution and the nature of the polymerase but also on whether the substitution is on dU or dC. Furthermore, the template sequence greatly affected generation of the PCR product, depending on the combination of the DNA polymerase and modified triphosphate. By examining primer extension reactions using primers and templates containing C5-modified dUs, we found that a modified dU at the 3' end of the elongation strand greatly affects the catalytic efficiency of DNA polymerases, whereas a modified dU opposite the elongation site on the template strand has less of an influence on the catalytic efficiency.
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Affiliation(s)
- Masayasu Kuwahara
- Department of Applied Chemistry, Faculty of Engineering, Gunma University, Gunma 376-8515, Japan.
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Leconte AM, Matsuda S, Hwang GT, Romesberg FE. Efforts towards Expansion of the Genetic Alphabet: Pyridone and Methyl Pyridone Nucleobases. Angew Chem Int Ed Engl 2006; 45:4326-9. [PMID: 16733840 DOI: 10.1002/anie.200601272] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aaron M Leconte
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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