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Jena NR. Rare Tautomers of Artificially Expanded Genetic Letters and their Effects on the Base pair Stabilities. Chemphyschem 2022; 23:e202100908. [PMID: 35029036 DOI: 10.1002/cphc.202100908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 11/11/2022]
Abstract
To expand the existing genetic letters, it is necessary to design robust nucleotides that can function naturally in living cells. Therefore, it is desirable to examine the roles of recently proposed second-generation artificially expanded genetic letters in producing stable duplex DNA. Here, a reliable dispersion-corrected density functional theory method is used to understand the electronic structures and properties of different rare tautomers of proposed expanded genetic letters and their effects on the base pair stabilities in the duplex DNA. It is found that the rare tautomers are not only stable in the aqueous medium but can also base pair with natural bases to produce stable mispairs. Except for J and V, all the artificial genetic letters are found to produce mispairs that are about 1-7 kcal/mol more stable than their complementary counterparts. They are also appreciably more stable than the naturally occurring G:C, A:T, and G:T pairs. The higher base pair stabilities are found to be mainly because of the polarity of monomers and attractive electrostatic interactions.
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Affiliation(s)
- N R Jena
- IIITDM Jabalpur, Discipline of Natural Sciences, Dumna Airport Road, Khamaria, India, 482005, Jabalpur, INDIA
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2
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Marx A, Betz K. The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases. Chemistry 2020; 26:3446-3463. [PMID: 31544987 PMCID: PMC7155079 DOI: 10.1002/chem.201903525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Indexed: 12/16/2022]
Abstract
Unnatural base pairs (UBPs) greatly increase the diversity of DNA and RNA, furthering their broad range of molecular biological and biotechnological approaches. Different candidates have been developed whereby alternative hydrogen-bonding patterns and hydrophobic and packing interactions have turned out to be the most promising base-pairing concepts to date. The key in many applications is the highly efficient and selective acceptance of artificial base pairs by DNA polymerases, which enables amplification of the modified DNA. In this Review, computational as well as experimental studies that were performed to characterize the pairing behavior of UBPs in free duplex DNA or bound to the active site of KlenTaq DNA polymerase are highlighted. The structural studies, on the one hand, elucidate how base pairs lacking hydrogen bonds are accepted by these enzymes and, on the other hand, highlight the influence of one or several consecutive UBPs on the structure of a DNA double helix. Understanding these concepts facilitates optimization of future UBPs for the manifold fields of applications.
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Affiliation(s)
- Andreas Marx
- Department of ChemistryKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078464KonstanzGermany
| | - Karin Betz
- Department of ChemistryKonstanz Research School Chemical BiologyUniversity of KonstanzUniversitätsstrasse 1078464KonstanzGermany
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3
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Zhang L, Wang S, Yang Z, Hoshika S, Xie S, Li J, Chen X, Wan S, Li L, Benner SA, Tan W. An Aptamer-Nanotrain Assembled from Six-Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells. Angew Chem Int Ed Engl 2019; 59:663-668. [PMID: 31650689 DOI: 10.1002/anie.201909691] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Expanding the number of nucleotides in DNA increases the information density of functional DNA molecules, creating nanoassemblies that cannot be invaded by natural DNA/RNA in complex biological systems. Here, we show how six-letter GACTZP DNA contributes this property in two parts of a nanoassembly: 1) in an aptamer evolved from a six-letter DNA library to selectively bind liver cancer cells; and 2) in a six-letter self-assembling GACTZP nanotrain that carries the drug doxorubicin. The aptamer-nanotrain assembly, charged with doxorubicin, selectively kills liver cancer cells in culture, as the selectivity of the aptamer binding directs doxorubicin into the aptamer-targeted cells. The assembly does not kill untransformed cells that the aptamer does not bind. This architecture, built with an expanded genetic alphabet, is reminiscent of antibodies conjugated to drugs, which presumably act by this mechanism as well, but with the antibody replaced by an aptamer.
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Affiliation(s)
- Liqin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China.,Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Sai Wang
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.,Current address: College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Box 7, Alachua, FL, 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL, 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Box 7, Alachua, FL, 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL, 32615, USA
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Jin Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
| | - Xigao Chen
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Shuo Wan
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Long Li
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Box 7, Alachua, FL, 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Box 17, Alachua, FL, 32615, USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China.,Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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4
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Zhang L, Wang S, Yang Z, Hoshika S, Xie S, Li J, Chen X, Wan S, Li L, Benner SA, Tan W. An Aptamer‐Nanotrain Assembled from Six‐Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Liqin Zhang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Sai Wang
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
- Current address: College of Food Science and Engineering Ocean University of China Qingdao Shandong 266003 China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard, Box 7 Alachua FL 32615 USA
- Firebird Biomolecular Sciences LLC 13709 Progress Boulevard, Box 17 Alachua FL 32615 USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard, Box 7 Alachua FL 32615 USA
- Firebird Biomolecular Sciences LLC 13709 Progress Boulevard, Box 17 Alachua FL 32615 USA
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Jin Li
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
| | - Xigao Chen
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Shuo Wan
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Long Li
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution 13709 Progress Boulevard, Box 7 Alachua FL 32615 USA
- Firebird Biomolecular Sciences LLC 13709 Progress Boulevard, Box 17 Alachua FL 32615 USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering College of Biology, Aptamer Engineering Center of Hunan Province Hunan University Changsha Hunan 410082 China
- Department of Chemistry Department of Physiology and Functional Genomics UF Health Cancer Center UF Genetics Institute University of Florida Gainesville FL 32611 USA
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Levi-Acobas F, Röthlisberger P, Sarac I, Marlière P, Herdewijn P, Hollenstein M. On the Enzymatic Formation of Metal Base Pairs with Thiolated and pK a -Perturbed Nucleotides. Chembiochem 2019; 20:3032-3040. [PMID: 31216100 DOI: 10.1002/cbic.201900399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Indexed: 12/15/2022]
Abstract
The formation of artificial metal base pairs is an alluring and versatile method for the functionalization of nucleic acids. Access to DNA functionalized with metal base pairs is granted mainly by solid-phase synthesis. An alternative, yet underexplored method, envisions the installation of metal base pairs through the polymerization of modified nucleoside triphosphates. Herein, we have explored the possibility of using thiolated and pKa -perturbed nucleotides for the enzymatic construction of artificial metal base pairs. The thiolated nucleotides S2C, S6G, and S4T as well as the fluorinated analogue 5FU are readily incorporated opposite a templating S4T nucleotide through the guidance of metal cations. Multiple incorporation of the modified nucleotides along with polymerase bypass of the unnatural base pairs are also possible under certain conditions. The thiolated nucleotides S4T, S4T, S2C, and S6G were also shown to be compatible with the synthesis of modified, high molecular weight single-stranded (ss)DNA products through TdT-mediated tailing reactions. Thus, sulfur-substitution and pKa perturbation represent alternative strategies for the design of modified nucleotides compatible with the enzymatic construction of metal base pairs.
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Affiliation(s)
- Fabienne Levi-Acobas
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Pascal Röthlisberger
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Ivo Sarac
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbruères, 91030, Evry, France
| | - Piet Herdewijn
- Department of Medicinal Chemistry, Institute for Medical Research, KU Leuven, Herestraat, 49, Leuven, 3000, Belgium
| | - Marcel Hollenstein
- Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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Novosjolova I, Kennedy SD, Rozners E. 2-Methoxypyridine as a Thymidine Mimic in Watson-Crick Base Pairs of DNA and PNA: Synthesis, Thermal Stability, and NMR Structural Studies. Chembiochem 2017; 18:2165-2170. [PMID: 28858428 PMCID: PMC5920655 DOI: 10.1002/cbic.201700400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Indexed: 12/21/2022]
Abstract
The development of nucleic acid base-pair analogues that use new modes of molecular recognition is important both for fundamental research and practical applications. The goal of this study was to evaluate 2-methoxypyridine as a cationic thymidine mimic in the A-T base pair. The hypothesis was that including protonation in the Watson-Crick base pairing scheme would enhance the thermal stability of the DNA double helix without compromising the sequence selectivity. DNA and peptide nucleic acid (PNA) sequences containing the new 2-methoxypyridine nucleobase (P) were synthesized and studied by using UV thermal melting and NMR spectroscopy. Introduction of P nucleobase caused a loss of thermal stability of ≈10 °C in DNA-DNA duplexes and ≈20 °C in PNA-DNA duplexes over a range of mildly acidic to neutral pH. Despite the decrease in thermal stability, the NMR structural studies showed that P-A formed the expected protonated base pair at pH 4.3. Our study demonstrates the feasibility of cationic unnatural base pairs; however, future optimization of such analogues will be required.
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Affiliation(s)
- Irina Novosjolova
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
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Jiang Y, Shi M, Liu Y, Wan S, Cui C, Zhang L, Tan W. Aptamer/AuNP Biosensor for Colorimetric Profiling of Exosomal Proteins. Angew Chem Int Ed Engl 2017; 56:11916-11920. [PMID: 28834063 PMCID: PMC5912341 DOI: 10.1002/anie.201703807] [Citation(s) in RCA: 346] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 12/30/2022]
Abstract
Exosomes constitute an emerging biomarker for cancer diagnosis because they carry multiple proteins that reflect the origins of parent cells. Assessing exosome surface proteins provides a powerful means of identifying a combination of biomarkers for cancer diagnosis. We report a sensor platform that profiles exosome surface proteins in minutes by the naked eye. The sensor consists of a gold nanoparticle (AuNP) complexed with a panel of aptamers. The complexation of aptamers with AuNPs protects the nanoparticles from aggregating in a high-salt solution. In the presence of exosomes, the non-specific and weaker binding between aptamers and the AuNP is broken, and the specific and stronger binding between exosome surface protein and the aptamer displaces aptamers from the AuNP surface and results in AuNP aggregation. This aggregation results in a color change and generates patterns for the identification of multiple proteins on the exosome surface.
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Affiliation(s)
- Ying Jiang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Muling Shi
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Yuan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Shuo Wan
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Cheng Cui
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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