2
|
Müller D, Trucks S, Schwalbe H, Hengesbach M. Genetic Code Expansion Facilitates Position-Selective Modification of Nucleic Acids and Proteins. Chempluschem 2020; 85:1233-1243. [PMID: 32515171 DOI: 10.1002/cplu.202000150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/11/2020] [Indexed: 12/12/2022]
Abstract
Transcription and translation obey to the genetic code of four nucleobases and 21 amino acids evolved over billions of years. Both these processes have been engineered to facilitate the use of non-natural building blocks in both nucleic acids and proteins, enabling researchers with a decent toolbox for structural and functional analyses. Here, we review the most common approaches for how labeling of both nucleic acids as well as proteins in a site-selective fashion with either modifiable building blocks or spectroscopic probes can be facilitated by genetic code expansion. We emphasize methodological approaches and how these can be adapted for specific modifications, both during as well as after biomolecule synthesis. These modifications can facilitate, for example, a number of different spectroscopic analysis techniques and can under specific circumstances even be used in combination.
Collapse
Affiliation(s)
- Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| |
Collapse
|
5
|
Zhang L, Yang Z, Le Trinh T, Teng IT, Wang S, Bradley KM, Hoshika S, Wu Q, Cansiz S, Rowold DJ, McLendon C, Kim MS, Wu Y, Cui C, Liu Y, Hou W, Stewart K, Wan S, Liu C, Benner SA, Tan W. Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution. Angew Chem Int Ed Engl 2016; 55:12372-5. [PMID: 27601357 DOI: 10.1002/anie.201605058] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/01/2016] [Indexed: 01/11/2023]
Abstract
Laboratory in vitro evolution (LIVE) might deliver DNA aptamers that bind proteins expressed on the surface of cells. In this work, we used cell engineering to place glypican 3 (GPC3), a possible marker for liver cancer theranostics, on the surface of a liver cell line. Libraries were then built from a six-letter genetic alphabet containing the standard nucleobases and two added nucleobases (2-amino-8H-imidazo[1,2-a][1,3,5]triazin-4-one and 6-amino-5-nitropyridin-2-one), Watson-Crick complements from an artificially expanded genetic information system (AEGIS). With counterselection against non-engineered cells, eight AEGIS-containing aptamers were recovered. Five bound selectively to GPC3-overexpressing cells. This selection-counterselection scheme had acceptable statistics, notwithstanding the possibility that cells engineered to overexpress GPC3 might also express different off-target proteins. This is the first example of such a combination.
Collapse
Affiliation(s)
- Liqin Zhang
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Thu Le Trinh
- Department of Pathology, Immunology, and Laboratory Medicine, Gainesville, FL, 32611, USA
| | - I-Ting Teng
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Sai Wang
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Qunfeng Wu
- Department of Pathology, Immunology, and Laboratory Medicine, Gainesville, FL, 32611, USA
| | - Sena Cansiz
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Diane J Rowold
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Christopher McLendon
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Myong-Sang Kim
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA
| | - Yuan Wu
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA.,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Cheng Cui
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Yuan Liu
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Weijia Hou
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Kimberly Stewart
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Shuo Wan
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Chen Liu
- Department of Pathology, Immunology, and Laboratory Medicine, Gainesville, FL, 32611, USA.
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, Alachua, FL, 32615, USA.
| | - Weihong Tan
- Departments of Chemistry, Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL, 32611, USA. .,Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China.
| |
Collapse
|
6
|
Zhang L, Yang Z, Le Trinh T, Teng IT, Wang S, Bradley KM, Hoshika S, Wu Q, Cansiz S, Rowold DJ, McLendon C, Kim MS, Wu Y, Cui C, Liu Y, Hou W, Stewart K, Wan S, Liu C, Benner SA, Tan W. Aptamers against Cells Overexpressing Glypican 3 from Expanded Genetic Systems Combined with Cell Engineering and Laboratory Evolution. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Liqin Zhang
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Collaborative Innovation Center for Chemistry and Molecular Medicine; Hunan University; Changsha 410082 China
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Thu Le Trinh
- Department of Pathology, Immunology, and Laboratory Medicine; Gainesville FL 32611 USA
| | - I-Ting Teng
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Sai Wang
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Kevin M. Bradley
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Qunfeng Wu
- Department of Pathology, Immunology, and Laboratory Medicine; Gainesville FL 32611 USA
| | - Sena Cansiz
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Diane J. Rowold
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Christopher McLendon
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Myong-Sang Kim
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Yuan Wu
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Collaborative Innovation Center for Chemistry and Molecular Medicine; Hunan University; Changsha 410082 China
| | - Cheng Cui
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Yuan Liu
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Weijia Hou
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Kimberly Stewart
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Shuo Wan
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
| | - Chen Liu
- Department of Pathology, Immunology, and Laboratory Medicine; Gainesville FL 32611 USA
| | - Steven A. Benner
- Foundation for Applied Molecular Evolution; Firebird Biomolecular Sciences LLC; 13709 Progress Boulevard Alachua FL 32615 USA
| | - Weihong Tan
- Departments of Chemistry, Physiology and Functional Genomics; Center for Research at the Bio/Nano Interface; UF Health Cancer Center; UF Genetics Institute and McKnight Brain Institute; University of Florida; Gainesville FL 32611 USA
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics; College of Chemistry and Chemical Engineering; College of Biology; Collaborative Innovation Center for Chemistry and Molecular Medicine; Hunan University; Changsha 410082 China
| |
Collapse
|