1
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Harusawa S, Shioiri T. Diethyl phosphorocyanidate (DEPC): a versatile reagent for organic synthesis. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.09.070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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2
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Zhang Y, Wang MQ, Zhang J, Zhang DW, Lin HH, Yu XQ. Synthesis, DNA binding, and cleavage studies of novel PNA binding cyclen complexes. Chem Biodivers 2011; 8:827-40. [PMID: 21560231 DOI: 10.1002/cbdv.201000084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A novel coumarin-appended PNA binding cyclen derivative ligand, C1, and its copper(II) complex, C2, have been synthesized and characterized. The interaction of these compounds with DNA was systematically investigated by absorption, fluorescence, and viscometric titration, and DNA-melting and gel-electrophoresis experiments. DNA Melting and viscometric titration experiments indicate that the binding mode of C1 is a groove binding, and C2 is a multiple binding mode that involves groove binding and electrostatic binding. From the absorption-titration data, we can state that the primary interaction between CT DNA and the two compounds may be H-bonds between nucleobases. Fluorescence studies indicate that the binding ability of C1 to d(A)(9) is as twice or thrice as that of other oligodeoxynucleotides. Agarose gel-electrophoresis experiments demonstrate that C2 is an excellent chemical nuclease, which can cleave plasmid DNA completely within 24 h.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, P. R. China
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3
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Synthesis, DNA binding and cleavage studies of the copper(II) complexes of PNA-cyclen conjugates. Sci China Chem 2011. [DOI: 10.1007/s11426-010-4169-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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Kodama K, Nakayama H, Sakamoto K, Fukuzawa S, Kigawa T, Yabuki T, Kitabatake M, Takio K, Yokoyama S. Site-specific incorporation of 4-Iodo-l-phenylalanine through opal suppression. ACTA ACUST UNITED AC 2010; 148:179-87. [DOI: 10.1093/jb/mvq051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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5
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Ye S, Ann Berger A, Petzold D, Reimann O, Matt B, Koksch B. Chemical aminoacylation of tRNAs with fluorinated amino acids for in vitro protein mutagenesis. Beilstein J Org Chem 2010; 6:40. [PMID: 20502658 PMCID: PMC2874332 DOI: 10.3762/bjoc.6.40] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 03/23/2010] [Indexed: 01/11/2023] Open
Abstract
This article describes the chemical aminoacylation of the yeast phenylalanine suppressor tRNA with a series of amino acids bearing fluorinated side chains via the hybrid dinucleotide pdCpA and ligation to the corresponding truncated tRNA species. Aminoacyl-tRNAs can be used to synthesize biologically relevant proteins which contain fluorinated amino acids at specific sites by means of a cell-free translation system. Such engineered proteins are expected to contribute to our understanding of discrete fluorines’ interaction with canonical amino acids in a native protein environment and to enable the design of fluorinated proteins with arbitrary desired properties.
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Affiliation(s)
- Shijie Ye
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry - Organic Chemistry, Takustrasse 3, 14195 Berlin, Germany
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6
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Ohta A, Yamagishi Y, Suga H. Synthesis of biopolymers using genetic code reprogramming. Curr Opin Chem Biol 2008; 12:159-67. [PMID: 18249198 DOI: 10.1016/j.cbpa.2007.12.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 12/27/2007] [Indexed: 11/25/2022]
Abstract
Genetic code reprogramming is a new emerging methodology that enables us to synthesize non-standard peptides containing multiple non-proteinogenic amino acids using translation machinery. This review describes the historical background of this methodology and what distinguishes it from the classical 'nonsense suppression' methodology, followed by a discussion of recent developments in combining this methodology with other compatible technologies. Specifically, we discuss in detail the combination of genetic code reprogramming with flexizymes, de novo tRNA acylation ribozymes that facilitate the charging process of a variety of non-proteinogenic amino acids onto tRNAs bearing designated anticodons, and summarize some of the recent demonstrations of the synthesis of non-standard peptides with cyclic structure or/and altered backbones employing this technology.
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Affiliation(s)
- Atsushi Ohta
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 113-8656 Tokyo, Japan
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7
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Liu M, Jinmei H, Abe H, Ito Y. Chemical Aminoacylation of RNA by an Intermolecular Adenosine Transfer Reaction. CHEM LETT 2008. [DOI: 10.1246/cl.2008.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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8
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Hartman MCT, Josephson K, Lin CW, Szostak JW. An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides. PLoS One 2007; 2:e972. [PMID: 17912351 PMCID: PMC1989143 DOI: 10.1371/journal.pone.0000972] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 09/12/2007] [Indexed: 11/23/2022] Open
Abstract
Background The application of in vitro translation to the synthesis of unnatural peptides may allow the production of extremely large libraries of highly modified peptides, which are a potential source of lead compounds in the search for new pharmaceutical agents. The specificity of the translation apparatus, however, limits the diversity of unnatural amino acids that can be incorporated into peptides by ribosomal translation. We have previously shown that over 90 unnatural amino acids can be enzymatically loaded onto tRNA. Methodology/Principal Findings We have now used a competition assay to assess the efficiency of tRNA-aminoacylation of these analogs. We have also used a series of peptide translation assays to measure the efficiency with which these analogs are incorporated into peptides. The translation apparatus tolerates most side chain derivatives, a few α,α disubstituted, N-methyl and α-hydroxy derivatives, but no β-amino acids. We show that over 50 unnatural amino acids can be incorporated into peptides by ribosomal translation. Using a set of analogs that are efficiently charged and translated we were able to prepare individual peptides containing up to 13 different unnatural amino acids. Conclusions/Significance Our results demonstrate that a diverse array of unnatural building blocks can be translationally incorporated into peptides. These building blocks provide new opportunities for in vitro selections with highly modified drug-like peptides.
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Affiliation(s)
- Matthew C. T. Hartman
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kristopher Josephson
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Chi-Wang Lin
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Simches Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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9
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Taki M, Matsushita J, Sisido M. Expanding the genetic code in a mammalian cell line by the introduction of four-base codon/anticodon pairs. Chembiochem 2006; 7:425-8. [PMID: 16440374 DOI: 10.1002/cbic.200500360] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Masumi Taki
- Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
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10
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Phelps SS, Gaudin C, Yoshizawa S, Benitez C, Fourmy D, Joseph S. Translocation of a tRNA with an extended anticodon through the ribosome. J Mol Biol 2006; 360:610-22. [PMID: 16787653 DOI: 10.1016/j.jmb.2006.05.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/04/2006] [Accepted: 05/04/2006] [Indexed: 11/18/2022]
Abstract
Coordinated translocation of the tRNA-mRNA complex by the ribosome occurs in a precise, stepwise movement corresponding to a distance of three nucleotides along the mRNA. Frameshift suppressor tRNAs generally contain an extra nucleotide in the anticodon loop and they subvert the normal mechanisms used by the ribosome for frame maintenance. The mechanism by which suppressor tRNAs traverse the ribosome during translocation is poorly understood. Here, we demonstrate translocation of a tRNA by four nucleotides from the A site to the P site, and from the P site to the E site. We show that translocation of a punctuated mRNA is possible with an extra, unpaired nucleotide between codons. Interestingly, the NMR structure of the four nucleotide anticodon stem-loop reveals a conformation different from the canonical tRNA structure. Flexibility within the loop may allow conformational adjustment upon A site binding and for interacting with the four nucleotide codon in order to shift the mRNA reading frame.
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MESH Headings
- Anticodon/genetics
- Anticodon/metabolism
- Base Sequence
- Escherichia coli
- Hydrogen-Ion Concentration
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Nucleic Acid Conformation/drug effects
- Pliability/drug effects
- Protein Biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/genetics
- RNA, Transfer, Met/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/genetics
- RNA, Transfer, Val/metabolism
- Reading Frames/genetics
- Ribosomes/genetics
- Ribosomes/metabolism
- Salts/pharmacology
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Affiliation(s)
- Steven S Phelps
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0314, USA
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11
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Ma LJ, Zhang GL, Chen SY, Wu B, You JS, Xia CQ, Yu XQ. The first synthesis of chiral PNA monomer-cyclen conjugates. J Pept Sci 2006; 11:812-7. [PMID: 16103987 DOI: 10.1002/psc.685] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A synthetic route to novel chiral PNA monomer-cyclen conjugates was described for the first time, the targeted products were obtained in high yields under mild reaction conditions. The preliminary results demonstrated that the uracil-PNA monomer-cyclen conjugates can rapidly bind Zn2+ in aqueous solution, and the structure of the Zn(II) complex was confirmed facilely by HRMS spectra, 1H NMR spectra and elemental analysis.
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Affiliation(s)
- Li-Jian Ma
- Department of Chemistry, Key Laboratory of Green Chemistry and Technology (Ministry of Education), Sichuan University, Chengdu 610064, P. R. China
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12
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Ohtsuki T, Manabe T, Sisido M. Multiple incorporation of non-natural amino acids into a single protein using tRNAs with non-standard structures. FEBS Lett 2005; 579:6769-74. [PMID: 16310775 DOI: 10.1016/j.febslet.2005.11.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Accepted: 11/01/2005] [Indexed: 11/28/2022]
Abstract
The ability to introduce non-natural amino acids into proteins opens up new vistas for the study of protein structure and function. This approach requires suppressor tRNAs that deliver the non-natural amino acid to a ribosome associated with an mRNA containing an expanded codon. The suppressor tRNAs must be absolutely protected from aminoacylation by any of the aminoacyl-tRNA synthetases in the protein synthesizing system, or a natural amino acid will be incorporated instead of the non-natural amino acid. Here, we found that some tRNAs with non-standard structures could work as efficient four-base suppressors fulfilling the above orthogonal conditions. Using these tRNAs, we successfully demonstrated incorporation of three different non-natural amino acids into a single protein.
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Affiliation(s)
- Takashi Ohtsuki
- Department of Bioscience and Biotechnology, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan
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13
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Sisido M, Ninomiya K, Ohtsuki T, Hohsaka T. Four-base codon/anticodon strategy and non-enzymatic aminoacylation for protein engineering with non-natural amino acids. Methods 2005; 36:270-8. [PMID: 16076453 DOI: 10.1016/j.ymeth.2005.04.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Accepted: 04/28/2005] [Indexed: 11/19/2022] Open
Abstract
Techniques for position-specific incorporation of non-natural amino acids in an in vitro protein synthesizing system are described. First, a PNA-assisted non-enzymatic tRNA aminoacylation with a variety of natural and non-natural amino acids is described. With this technique, one can aminoacylate a specific tRNA simply by adding a preformed amino acid activated ester-PNA conjugate into an in vitro protein biosynthesizing system. Second, the genetic code is expanded by introducing 4-base codons that can be exclusively translated to non-natural amino acids. The most advantageous point of the 4-base codon strategy is to introduce multiple amino acids into specific positions in single proteins by using mutually orthogonal 4-base codons and orthogonal tRNAs. An easy and quick method for preparation of tRNAs possessing 4-base anticodons is also described. Combination of the non-enzymatic aminoacylation and the 4-base codon/anticodon strategy gives an easy and widely applicable technique for incorporating a variety of non-natural amino acids into proteins in vitro.
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Affiliation(s)
- Masahiko Sisido
- Department of Bioscience and Biotechnology, Okayama University, 3-1-1 Tsushimanaka, Okayama 700-8530, Japan.
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14
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Porcher S, Meyyappan M, Pitsch S. Spontaneous Aminoacylation of a RNA Sequence Containing a 3′-Terminal 2′-Thioadenosine. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Hashimoto N, Ninomiya K, Endo T, Sisido M. Simple and quick chemical aminoacylation of tRNA in cationic micellar solution under ultrasonic agitation. Chem Commun (Camb) 2005:4321-3. [PMID: 16113735 DOI: 10.1039/b508194g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and quick method for direct aminoacylation of a tRNA with a non-natural amino acid was developed by using an N-protected amino acid cyanomethyl ester as a substrate solubilized in CTACl micelle under ultrasonic agitation.
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Affiliation(s)
- Naoto Hashimoto
- Department of Bioscience and Biotechnology, Okayama University, 3-1-1 Tsushimanaka, Okayama, 700-8530, Japan.
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