1
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Murase H, Lee J, Togo N, Taniguchi Y, Sasaki S. The selective chemical modification of the 6-amino group of adenosine of the premature termination codon induces readthrough to produce full-length peptide in the reconstituted E. Coli translation system. Bioorg Med Chem 2024; 111:117868. [PMID: 39137475 DOI: 10.1016/j.bmc.2024.117868] [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: 07/03/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024]
Abstract
Nonsense mutations in the coding region turn amino acid codons into termination codons, resulting in premature termination codons (PTCs). In the case of the in-frame PTC, if translation does not stop at the PTC but continues to the natural termination codon (NTC) with the insertion of an amino acid, known as readthrough, the full-length peptide is formed, albeit with a single amino acid mutation. We have previously developed the functionality-transfer oligonucleotide (FT-Probe), which forms a hybrid complex with RNA of a complementary sequence to transfer the functional group, resulting in modification of the 4-amino group of cytosine or the 6-amino group of adenine. In this study, the FT-Probe was used to chemically modify the adenosines of the PTC (UAA, UAG, and UGA) of mRNA, which were assayed for the readthrough in a reconstituted Escherichia coli translation system. The third adenosine-modified UAA produced three readthrough peptides incorporating tyrosine, glutamine and lysine at the UAA site. It should be noted that the additional modification with a cyclodextrin only induced glutamine incorporation. The adenosine modified UGA induced readthrough very efficiently with selective tryptophan incorporation. Readthrough of the modified UGA is caused by inhibition of the RF2 function. This study has demonstrated that the chemical modification of the adenosine 6-amino group of the PTC is a strategy for effective readthrough in a prokaryotic translation system.
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Affiliation(s)
- Hirotaka Murase
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch Machi, Sasebo 859-3298, Japan; RINAT Imaging, Inc., 1-1, Kurume Hundred Years Park, Kurume 839-0064, Japan
| | - Jeongsu Lee
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch Machi, Sasebo 859-3298, Japan
| | - Norihiro Togo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yosuke Taniguchi
- RINAT Imaging, Inc., 1-1, Kurume Hundred Years Park, Kurume 839-0064, Japan; Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch Machi, Sasebo 859-3298, Japan; RINAT Imaging, Inc., 1-1, Kurume Hundred Years Park, Kurume 839-0064, Japan.
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2
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Togo N, Murase H, Lee J, Taniguchi Y, Sasaki S. Application of the Functionality Transfer Oligodeoxynucleotide for the Site-Selective Modification of RNA with a Divers Molecule. Chem Pharm Bull (Tokyo) 2022; 70:498-504. [PMID: 35786569 DOI: 10.1248/cpb.c22-00288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Due to the importance of the RNA chemical modifications, methods for the selective chemical modification at a predetermined site of the internal position of RNA have attracted much attention. We have developed functional artificial nucleic acids that modify a specific site of RNA in a site- and base-selective manner. In addition, the copper-catalyzed azide-alkyne cycloaddition (CuAAC) has been shown to introduce additional molecules on the alkynes attached to the pyridine ring. However, it was found that some azide compounds produced the cycloadduct in lower yields. Therefore, in this study, we synthesized the pyridinyl transfer group with the alkyne attached via a polyethylene glycol (PEG) linker with a different length and optimized its structure for both the transfer and CuAAC reaction. Three new transfer groups were synthesized by introducing an alkyne group at the end of the triethylene (11), tetraethylene (12) or pentaethylen glycol linker (13) at the 5-position of the pyridine ring of (E)-3-iodo-1-(pyridin-2-yl)prop-2-en-1-one. These transfer groups were introduced to the 6-thioguanine base in the oligodeoxynucleotide (ODN) in high yields. The transfer groups 11 and 12 more efficiently underwent the cytosine modification. For the CuAAC reaction, although 7 showed low adduct yields with the anionic azide compound, the new transfer groups, especially 12 and 13, significantly improved the yields. In conclusion, the transfer groups 12 and 13 were determined to be promising compounds for the modification of long RNAs.
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Affiliation(s)
- Norihiro Togo
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Hirotaka Murase
- Graduate School of Pharmaceutical Sciences, Nagasaki International University
| | - Jeongsu Lee
- Graduate School of Pharmaceutical Sciences, Nagasaki International University
| | | | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Nagasaki International University
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3
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Zhou H, Li Y, Gan Y, Wang R. Total RNA Synthesis and its Covalent Labeling Innovation. Top Curr Chem (Cham) 2022; 380:16. [PMID: 35218412 DOI: 10.1007/s41061-022-00371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
Abstract
RNA plays critical roles in a wide range of physiological processes. For example, it is well known that RNA plays an important role in regulating gene expression, cell proliferation, and differentiation, and many other chemical and biological processes. However, the research community still suffers from limited approaches that can be applied to readily visualize a specific RNA-of-interest (ROI). Several methods can be used to track RNAs; these rely mainly on biological properties, namely, hybridization, aptamer, reporter protein, and protein binding. With respect to covalent approaches, very few cases have been reported. Happily, several new methods for efficient labeling studies of ROIs have been demonstrated successfully in recent years. Additionally, methods employed for the detection of ROIs by RNA modifying enzymes have also proved feasible. Several approaches, namely, phosphoramidite chemistry, in vitro transcription reactions, co-transcription reactions, chemical post-modification, RNA modifying enzymes, ligation, and other methods targeted at RNA labeling have been revealed in the past decades. To illustrate the most recent achievements, this review aims to summarize the most recent research in the field of synthesis of RNAs-of-interest bearing a variety of unnatural nucleosides, the subsequent RNA labeling research via biocompatible ligation, and beyond.
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Affiliation(s)
- Hongling Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Youfang Gan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Natural Product and Resource, Shanghai Institute of Organic Chemistry, Shanghai, 230030, China.
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4
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Ito Y, Hari Y. Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution. CHEM REC 2022; 22:e202100325. [PMID: 35119181 DOI: 10.1002/tcr.202100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/21/2022] [Indexed: 11/11/2022]
Abstract
Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.
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Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
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5
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Abstract
Fast and efficient site-specific labeling of long RNAs is one of the main bottlenecks limiting distance measurements by means of Förster resonance energy transfer (FRET) or electron paramagnetic resonance (EPR) spectroscopy. Here, we present an optimized protocol for dual end-labeling with different fluorophores at the same time meeting the restrictions of highly labile and degradation-sensitive RNAs. We describe in detail the dual-labeling of a catalytically active wild-type group II intron as a typical representative of long functional RNAs. The modular procedure chemically activates the 5'-phosphate and the 3'-ribose for bioconjugation with a pair of fluorophores, as shown herein, or with spin labels. The mild reaction conditions preserve the structural and functional integrity of the biomacromolecule and results in covalent, dual-labeled RNA in its pre-catalytic state in yields suitable for both ensemble and single-molecule FRET experiments.
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Affiliation(s)
- Esra Ahunbay
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Fabio D Steffen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
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6
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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7
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O'Hagan MP, Morales JC, Galan MC. Binding and Beyond: What Else Can G-Quadruplex Ligands Do? European J Org Chem 2019. [DOI: 10.1002/ejoc.201900692] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Juan C. Morales
- Instituto de Parasitología y Biomedicina “López Neyra”; Consejo Superior de Investigaciones Científicas (CSIC); PTS Granada; Avenida del Conocimiento 17 18016 Armilla, Granada Spain
| | - M. Carmen Galan
- School of Chemistry; University of Bristol; Cantock's Close BS8 1TS UK
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8
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Sasaki S. Development of Novel Functional Molecules Targeting DNA and RNA. Chem Pharm Bull (Tokyo) 2019; 67:505-518. [PMID: 31155555 DOI: 10.1248/cpb.c19-00169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleic acid therapeutics such as antisense and small interfering RNA (siRNA) have attracted increasing attention as innovative medicines that interfere with and/or modify gene expression systems. We have developed new functional oligonucleotides that can target DNA and RNA with high efficiency and selectivity. This review summarizes our achievements, including (1) the formation of non-natural triplex DNA for sequence-specific inhibition of transcription; (2) artificial receptor molecules for 8-oxidized-guanosine nucleosides; and (3) reactive oligonucleotides with a cross-linking agent or a functionality-transfer nucleoside for RNA pinpoint modification.
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Affiliation(s)
- Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University
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9
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Monakhova MV, Kubareva EA, Romanova EA, Semkina AS, Naberezhnov DS, Rao DN, Zatsepin TS, Oretskaya TS. Synthesis of β-Diketone DNA Derivatives for Affinity Modification of Proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019020079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Gillingham D, Geigle S, Anatole von Lilienfeld O. Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics. Chem Soc Rev 2017; 45:2637-55. [PMID: 26992131 DOI: 10.1039/c5cs00271k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developments in epigenomics, toxicology, and therapeutic nucleic acids all rely on a precise understanding of nucleic acid properties and chemical reactivity. In this review we discuss the properties and chemical reactivity of each nucleobase and attempt to provide some general principles for nucleic acid targeting or engineering. For adenine-thymine and guanine-cytosine base pairs, we review recent quantum chemical estimates of their Watson-Crick interaction energy, π-π stacking energies, as well as the nuclear quantum effects on tautomerism. Reactions that target nucleobases have been crucial in the development of new sequencing technologies and we believe further developments in nucleic acid chemistry will be required to deconstruct the enormously complex transcriptome.
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Affiliation(s)
- Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
| | - Stefanie Geigle
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
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11
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Padilha G, Birmann PT, Domingues M, Kaufman TS, Savegnago L, Silveira CC. Convenient Michael addition/β-elimination approach to the synthesis of 4-benzyl- and 4-aryl-selenyl coumarins using diselenides as selenium sources. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.01.084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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12
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Li Y, Fin A, McCoy L, Tor Y. Polymerase-Mediated Site-Specific Incorporation of a Synthetic Fluorescent Isomorphic G Surrogate into RNA. Angew Chem Int Ed Engl 2017; 56:1303-1307. [PMID: 28000329 PMCID: PMC5241218 DOI: 10.1002/anie.201609327] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/10/2016] [Indexed: 12/22/2022]
Abstract
An enzyme-mediated approach for the assembly of singly modified RNA constructs in which specific G residues are replaced with th G, an emissive isomorphic G surrogate, is reported. Transcription in the presence of th G and native nucleoside triphosphates enforces initiation with the unnatural analogue, yielding 5'-end modified transcripts that can be mono-phosphorylated and ligated to provide longer site-specifically modified RNA constructs. The scope of this unprecedented enzymatic approach to non-canonical purine-containing RNAs is explored via the assembly of several altered hammerhead (HH) ribozymes and a singly modified HH substrate. By strategically modifying key positions, a mechanistic insight into the ribozyme-mediated cleavage is gained. Additionally, the emissive features of the modified nucleoside and its responsiveness to environmental changes can be used to monitor cleavage in real time by steady state fluorescence spectroscopy.
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Affiliation(s)
- Yao Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Lisa McCoy
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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13
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Li Y, Fin A, McCoy L, Tor Y. Polymerase‐Mediated Site‐Specific Incorporation of a Synthetic Fluorescent Isomorphic G Surrogate into RNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yao Li
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Andrea Fin
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Lisa McCoy
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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14
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Egloff D, Oleinich IA, Zhao M, König SLB, Sigel RKO, Freisinger E. Sequence-Specific Post-Synthetic Oligonucleotide Labeling for Single-Molecule Fluorescence Applications. ACS Chem Biol 2016; 11:2558-67. [PMID: 27409145 DOI: 10.1021/acschembio.6b00343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The sequence-specific fluorescence labeling of nucleic acids is a prerequisite for various methods including single-molecule Förster resonance energy transfer (smFRET) for the detailed study of nucleic acid folding and function. Such nucleic acid derivatives are commonly obtained by solid-phase methods; however, yields decrease rapidly with increasing length and restrict the practicability of this approach for long strands. Here, we report a new labeling strategy for the postsynthetic incorporation of a bioorthogonal group into single stranded regions of both DNA and RNA of unrestricted length. A 12-alkyne-etheno-adenine modification is sequence-selectively formed using DNA-templated synthesis, followed by conjugation of the fluorophore Cy3 via a copper-catalyzed azide-alkyne cycloaddition (CuAAC). Evaluation of the labeled strands in smFRET measurements shows that the strategy developed here has the potential to be used for the study of long functional nucleic acids by (single-molecule) fluorescence or other methods. To prove the universal use of the method, its application was successfully extended to the labeling of a short RNA single strand. As a proof-of-concept, also the labeling of a large RNA molecule in form of a 633 nucleotide long construct derived from the Saccharomyces cerevisiae group II intron Sc.ai5γ was performed, and covalent attachment of the Cy3 fluorophore was shown with gel electrophoresis.
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Affiliation(s)
- David Egloff
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Igor A. Oleinich
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Meng Zhao
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Sebastian L. B. König
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Roland K. O. Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
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15
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Liu Y, Sousa R, Wang YX. Specific labeling: An effective tool to explore the RNA world. Bioessays 2015; 38:192-200. [DOI: 10.1002/bies.201500119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
| | - Rui Sousa
- Department of Biochemistry; University of Texas Health Science Center; San Antonio TX USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
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16
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Oshiro I, Jitsuzaki D, Onizuka K, Nishimoto A, Taniguchi Y, Sasaki S. Site-specific modification of the 6-amino group of adenosine in RNA by an interstrand functionality-transfer reaction with an s-functionalized 4-thiothymidine. Chembiochem 2015; 16:1199-204. [PMID: 25940822 DOI: 10.1002/cbic.201500084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Indexed: 11/06/2022]
Abstract
Non-natural RNA modifications have been widely used to study the function and structure of RNA. Expanding the study of RNA further requires versatile and efficient tools for site-specific RNA modification. We recently established a new strategy for the site-specific modification of RNA based on a functionality-transfer reaction between an oligodeoxynucleotide (ODN) probe and an RNA substrate. 2'-Deoxy-6-thioguanosine was used to anchor the transfer group, and the 4-amino group of cytosine or the 2-amino group of guanine was specifically modified. In this study, 2'-deoxy-4-thiothymidine was adopted as a new platform to target the 6-amino group of adenosine. The (E)-pyridinyl vinyl keto transfer group was attached to the 4-thioT in the ODN probe, and it was efficiently and specifically transferred to the 6-amino group of the opposing adenosine in RNA in the presence of CuCl2 . This method expands the available RNA target sites for specific modification.
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Affiliation(s)
- Ikuya Oshiro
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan).,CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012 (Japan)
| | - Daichi Jitsuzaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan).,CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012 (Japan)
| | - Kazumitsu Onizuka
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan).,CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012 (Japan)
| | - Atsushi Nishimoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan).,CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012 (Japan)
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan).,CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012 (Japan)
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan).,CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012 (Japan)
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17
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Jitsuzaki D, Onizuka K, Nishimoto A, Oshiro I, Taniguchi Y, Sasaki S. Remarkable acceleration of a DNA/RNA inter-strand functionality transfer reaction to modify a cytosine residue: the proximity effect via complexation with a metal cation. Nucleic Acids Res 2014; 42:8808-15. [PMID: 24957600 PMCID: PMC4117767 DOI: 10.1093/nar/gku538] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Modified nucleosides in natural RNA molecules are essential for their functions. Non-natural nucleoside analogues have been introduced into RNA to manipulate its structure and function. We have recently developed a new strategy for the in situ modification of RNA based on the functionality transfer reaction between an oligodeoxynucleotide probe and an RNA substrate. 2′-Deoxy-6-thioguanosine (6-thio-dG) was used as the platform to anchor the transfer group. In this study, a pyridinyl vinyl ketone moiety was newly designed as the transfer group with the expectation that a metal cation would form a chelate complex with the pyridinyl-2-keto group. It was demonstrated that the (E)-pyridinyl vinyl keto group was efficiently and specifically transferred to the 4-amino group of the opposing cytosine in RNA in the presence of NiCl2 with more than 200-fold accelerated rate compared with the previous system with the use of the diketo transfer group. Detailed mechanistic studies suggested that NiCl2 forms a bridging complex between the pyridinyl keto moiety and the N7 of the purine residue neighboring the cytosine residue of the RNA substrate to bring the groups in close proximity.
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Affiliation(s)
- Daichi Jitsuzaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 Japan, and CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012, Japan
| | - Kazumitsu Onizuka
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 Japan, and CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012, Japan
| | - Atsushi Nishimoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 Japan, and CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuya Oshiro
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 Japan, and CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012, Japan
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 Japan, and CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 Japan, and CREST, Japan Science and Technology Agency, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012, Japan
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Büttner L, Javadi-Zarnaghi F, Höbartner C. Site-specific labeling of RNA at internal ribose hydroxyl groups: terbium-assisted deoxyribozymes at work. J Am Chem Soc 2014; 136:8131-7. [PMID: 24825547 DOI: 10.1021/ja503864v] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A general and efficient single-step method was established for site-specific post-transcriptional labeling of RNA. Using Tb(3+) as accelerating cofactor for deoxyribozymes, various labeled guanosines were site-specifically attached to 2'-OH groups of internal adenosines in in vitro transcribed RNA. The DNA-catalyzed 2',5'-phosphodiester bond formation proceeded efficiently with fluorescent, spin-labeled, biotinylated, or cross-linker-modified guanosine triphosphates. The sequence context of the labeling site was systematically analyzed by mutating the nucleotides flanking the targeted adenosine. Labeling of adenosines in a purine-rich environment showed the fastest reactions and highest yields. Overall, practically useful yields >70% were obtained for 13 out of 16 possible nucleotide (nt) combinations. Using this approach, we demonstrate preparative labeling under mild conditions for up to ~160-nt-long RNAs, including spliceosomal U6 small nuclear RNA and a cyclic-di-AMP binding riboswitch RNA.
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Affiliation(s)
- Lea Büttner
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
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19
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Futamura A, Uemura A, Imoto T, Kitamura Y, Matsuura H, Wang CX, Ichihashi T, Sato Y, Teramae N, Nishizawa S, Ihara T. Rational design for cooperative recognition of specific nucleobases using β-cyclodextrin-modified DNAs and fluorescent ligands on DNA and RNA scaffolds. Chemistry 2013; 19:10526-35. [PMID: 23821253 DOI: 10.1002/chem.201300985] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Indexed: 01/10/2023]
Abstract
We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β-cyclodextrin (β-CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase-specific heterocycle and an environment-sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β-CyD. Three reporter ligands, MNDS (naphthyridine-dansyl linked ligand), MNDB (naphthyridine-DBD), and DPDB (pyridine-DBD), were used for DNA and RNA probing with 3'-end or 5'-end modified β-CyD-ODN conjugates. For the DNA target, the β-CyD tethered to the 3'-end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site (MNDS and DPDB). Meanwhile the β-CyD on the 5'-end of the ODN interacted with the fluorophore in the minor groove (MNDB and DPDB). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules.
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Affiliation(s)
- Akika Futamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
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20
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Gorska K, Winssinger N. Reactions templated by nucleic acids: more ways to translate oligonucleotide-based instructions into emerging function. Angew Chem Int Ed Engl 2013; 52:6820-43. [PMID: 23794204 DOI: 10.1002/anie.201208460] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Indexed: 12/30/2022]
Abstract
The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.
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Affiliation(s)
- Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Universite de Strasbourg-CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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Gorska K, Winssinger N. Reaktionen an Nucleinsäuretemplaten: mehr Methoden zur Übersetzung Oligonucleotid-basierter Informationen in neue Funktionen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208460] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Tishinov K, Schmidt K, Häussinger D, Gillingham DG. Structure-selective catalytic alkylation of DNA and RNA. Angew Chem Int Ed Engl 2012; 51:12000-4. [PMID: 23090851 DOI: 10.1002/anie.201205201] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Indexed: 01/17/2023]
Affiliation(s)
- Kiril Tishinov
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
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23
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Tishinov K, Schmidt K, Häussinger D, Gillingham DG. Structure-Selective Catalytic Alkylation of DNA and RNA. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205201] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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24
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Sasaki S, Onizuka K, Taniguchi Y. Oligodeoxynucleotide containing s-functionalized 2'-deoxy-6-thioguanosine: facile tools for base-selective and site-specific internal modification of RNA. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.49.1-16. [PMID: 22395968 DOI: 10.1002/0471142700.nc0449s48] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chemically modified oligonucleotides play a significant role for genomic research. Modified nucleosides, such as with a fluorescent dye, can be obtained by chemical synthesis. Site-specifically modified long nucleic acids are obtained by ligation of chemically modified short oligonucleotides with enzyme, photochemistry, or catalytic DNA. The functionality-transfer ODN (FT-ODN), which contains 2'-deoxy-6-thioguanosine (6-thio-dG) functionalized with the 2-methyliden-1,3-diketone group, is hybridized with the target RNA to trigger the selective functionalization of the 4-amino group of the cytosine base at pH 7 or the 2-amino group of the guanine base at pH 9.4 or at pH 7.4 in the presence of NiCl(2). In particular, the functionality-transfer reaction (FTR) under the alkaline conditions or neutral conditions in the presence of NiCl(2) proceeds rapidly and selectively to lead to the modification of the target guanine. The transfer reaction of the acetylene-containing diketone group produces the acetylene-modified RNA, which can be subjected to the Cu(I)-catalyzed "click chemistry" with a variety of azide compounds for highly specific, internal modification of RNA.
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25
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Tomkuviene M, Clouet-d'Orval B, Cerniauskas I, Weinhold E, Klimasauskas S. Programmable sequence-specific click-labeling of RNA using archaeal box C/D RNP methyltransferases. Nucleic Acids Res 2012; 40:6765-73. [PMID: 22564896 PMCID: PMC3413156 DOI: 10.1093/nar/gks381] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Biophysical and mechanistic investigation of RNA function requires site-specific incorporation of spectroscopic and chemical probes, which is difficult to achieve using current technologies. We have in vitro reconstituted a functional box C/D small ribonucleoprotein RNA 2′-O-methyltransferase (C/D RNP) from the thermophilic archaeon Pyrococcus abyssi and demonstrated its ability to transfer a prop-2-ynyl group from a synthetic cofactor analog to a series of preselected target sites in model tRNA and pre-mRNA molecules. Target selection of the RNP was programmed by changing a dodecanucleotide guide sequence in a 64-nt C/D guide RNA leading to efficient derivatization of three out of four new targets in each RNA substrate. We also show that the transferred terminal alkyne can be further appended with a fluorophore using a bioorthogonal azide-alkyne 1,3-cycloaddition (click) reaction. The described approach for the first time permits synthetically tunable sequence-specific labeling of RNA with single-nucleotide precision.
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Affiliation(s)
- Migle Tomkuviene
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-02241, Lithuania
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26
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Winz ML, Samanta A, Benzinger D, Jäschke A. Site-specific terminal and internal labeling of RNA by poly(A) polymerase tailing and copper-catalyzed or copper-free strain-promoted click chemistry. Nucleic Acids Res 2012; 40:e78. [PMID: 22344697 PMCID: PMC3378897 DOI: 10.1093/nar/gks062] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The modification of RNA with fluorophores, affinity tags and reactive moieties is of enormous utility for studying RNA localization, structure and dynamics as well as diverse biological phenomena involving RNA as an interacting partner. Here we report a labeling approach in which the RNA of interest—of either synthetic or biological origin—is modified at its 3′-end by a poly(A) polymerase with an azido-derivatized nucleotide. The azide is later on conjugated via copper-catalyzed or strain-promoted azide–alkyne click reaction. Under optimized conditions, a single modified nucleotide of choice (A, C, G, U) containing an azide at the 2′-position can be incorporated site-specifically. We have identified ligases that tolerate the presence of a 2′-azido group at the ligation site. This azide is subsequently reacted with a fluorophore alkyne. With this stepwise approach, we are able to achieve site-specific, internal backbone-labeling of de novo synthesized RNA molecules.
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Affiliation(s)
- Marie-Luise Winz
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany
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27
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Onizuka K, Nishioka T, Li Z, Jitsuzaki D, Taniguchi Y, Sasaki S. An efficient and simple method for site-selective modification of O6-methyl-2′-deoxyguanosine in DNA. Chem Commun (Camb) 2012; 48:3969-71. [DOI: 10.1039/c2cc17621a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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28
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29
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Wong OY, Mulcrone AE, Silverman SK. DNA-catalyzed reductive amination. Angew Chem Int Ed Engl 2011; 50:11679-84. [PMID: 21994131 DOI: 10.1002/anie.201104976] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/22/2011] [Indexed: 11/12/2022]
Affiliation(s)
- On Yi Wong
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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30
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Sasaki S, Onizuka K, Taniguchi Y. The oligodeoxynucleotide probes for the site-specific modification of RNA. Chem Soc Rev 2011; 40:5698-706. [PMID: 21647493 DOI: 10.1039/c1cs15066a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As the knowledge of the biological functions of RNA expands, the demand for research tools to investigate intracellular RNA is increasing. Oligonucleotides can be rationally designed for the target RNA sequence, and therefore, have become a reliable platform for the development of specific molecules for RNA. The chemical modification of RNA has a strong impact on RNA research; the fluorescent labeling of RNA is useful to monitor RNA production, processing, relocation in the cell, interaction with other intracellular components and degradation, etc. Chemical modification may affect the RNA function through a variety of pathways, and therefore, would be potentially useful for biological research, therapeutic approach and artificial manipulation of the RNA function. This tutorial review starts with an introduction of the biological relevance of modified RNA, and focuses on the recent progress of the oligodeoxynucleotide probes for the covalent modifications of RNA. The prospects of this new technology are also discussed.
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Affiliation(s)
- Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan.
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31
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Erben A, Grossmann TN, Seitz O. DNA-instructed acyl transfer reactions for the synthesis of bioactive peptides. Bioorg Med Chem Lett 2011; 21:4993-7. [PMID: 21664815 DOI: 10.1016/j.bmcl.2011.05.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 05/06/2011] [Accepted: 05/09/2011] [Indexed: 01/31/2023]
Abstract
We present a method which allows for the translation of nucleic acid information into the output of molecules that interfere with disease-related protein-protein interactions. The method draws upon a nucleic acid-templated reaction, in which adjacent binding of reactive conjugates triggers the transfer of an aminoacyl or peptidyl group from a donating thioester-linked PNA-peptide hybrid to a peptide-PNA acceptor. We evaluated the influence of conjugate structures on reactivity and sequence specificity. The DNA-triggered peptide synthesis proceeded sequence specifically and showed catalytic turnover in template. The affinity of the formed peptide conjugates for the BIR3 domain of the X-linked inhibitor of apoptosis protein (XIAP) is discussed.
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Affiliation(s)
- Anne Erben
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin 12489, Germany
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32
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Onizuka K, Shibata A, Taniguchi Y, Sasaki S. Pin-point chemical modification of RNA with diverse molecules through the functionality transfer reaction and the copper-catalyzed azide-alkyne cycloaddition reaction. Chem Commun (Camb) 2011; 47:5004-6. [PMID: 21431191 DOI: 10.1039/c1cc10582e] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The internal modification of RNA has been successfully achieved by the functionality transfer reaction (FTR) and following click chemistry with diverse azide compounds. The benefits of the FTR have been demonstrated by its specificity, rapidity, broad applicability, and procedure simplicity.
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Affiliation(s)
- Kazumitsu Onizuka
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan
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33
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Erben A, Grossmann TN, Seitz O. DNA-triggered synthesis and bioactivity of proapoptotic peptides. Angew Chem Int Ed Engl 2011; 50:2828-32. [PMID: 21387498 DOI: 10.1002/anie.201007103] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Indexed: 11/11/2022]
Affiliation(s)
- Anne Erben
- Institut für Chemie der Humboldt Universität zu Berlin, Germany
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34
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Erben A, Grossmann TN, Seitz O. DNA‐gesteuerte Synthese und Bioaktivität proapoptotischer Peptide. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Anne Erben
- Institut für Chemie der Humboldt Universität zu Berlin, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland), Fax: (+49) 30‐2093‐7266
| | - Tom N. Grossmann
- Institut für Chemie der Humboldt Universität zu Berlin, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland), Fax: (+49) 30‐2093‐7266
| | - Oliver Seitz
- Institut für Chemie der Humboldt Universität zu Berlin, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland), Fax: (+49) 30‐2093‐7266
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35
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Onizuka K, Taniguchi Y, Sasaki S. Activation and alteration of base selectivity by metal cations in the functionality-transfer reaction for RNA modification. Bioconjug Chem 2011; 21:1508-12. [PMID: 20586420 DOI: 10.1021/bc100131j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previously, we reported that the 2-methylidene-1,3-diketone unit of 6-thioguanosine transferred selectively to the amino group of cytosine at pH 7.0 and that its selectivity was changed to the guanine base at pH 9.6. In this study, it was found that the functionality-transfer reaction enhanced selectivity for the guanine base in the presence of divalent transition metal cations such as Ni(2+) and Co(2+) at pH 7.4.
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Affiliation(s)
- Kazumitsu Onizuka
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Japan
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36
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Jahn K, Olsen EM, Nielsen MM, Tørring T, MohammadZadegan R, Andersen ES, Gothelf KV, Kjems J. Site-Specific Chemical Labeling of Long RNA Molecules. Bioconjug Chem 2010; 22:95-100. [DOI: 10.1021/bc100422k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kasper Jahn
- Danish National Research Foundation, Center for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Eva Maria Olsen
- Danish National Research Foundation, Center for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Morten Muhlig Nielsen
- Danish National Research Foundation, Center for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Thomas Tørring
- Danish National Research Foundation, Center for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Reza MohammadZadegan
- Danish National Research Foundation, Center for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Ebbe Sloth Andersen
- Danish National Research Foundation, Center for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Kurt Vesterager Gothelf
- Danish National Research Foundation, Center for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Jørgen Kjems
- Danish National Research Foundation, Center for DNA Nanotechnology (CDNA) at Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
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Onizuka K, Taniguchi Y, Sasaki S. A new odorless procedure for the synthesis of 2'-deoxy-6-thioguanosine and its incorporation into oligodeoxynucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:752-60. [PMID: 20183614 DOI: 10.1080/15257770903155576] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
6-S-[2-[(2-ethylhexyl)oxycarbonyl]ethyl)}-3',5'-O-bis(tert-butyldimethylsilyl)-2'-deoxy-6-thiogua nosine (2) was synthesized in high yield from the corresponding 6-O-mesitylenesulfonyl derivative by the reaction with 2-ethylhexyl 3-mercapto-propionate. The phosphoramidite precursor derived from 2 was successfully applied to an automated DNA synthesizer to produce 2'-deoxy-6-thioguanosine containing ODN. The results showed that 2-ethylhexyl 3-mercaptopropionate is useful as an odor less reagent and also as an S-protecting group of 2'-deoxy-6-thioguanosine.
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Affiliation(s)
- Kazumitsu Onizuka
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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38
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Onizuka K, Taniguchi Y, Sasaki S. A new usage of functionalized oligodeoxynucleotide probe for site-specific modification of a guanine base within RNA. Nucleic Acids Res 2010; 38:1760-6. [PMID: 20123727 PMCID: PMC2836579 DOI: 10.1093/nar/gkp930] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Site-specific modification of RNA is of great significance to investigate RNA structure, function and dynamics. Recently, we reported a new method for sequence- and cytosine-selective chemical modification of RNA based on the functional group transfer reaction of the 1-phenyl-2-methylydene-1,3-diketone unit of the 6-thioguanosine base incorporated in the oligodeoxynucleotide probe. In this study, we describe that the functionality transfer rate is greatly enhanced and the selectivity is shifted to the guanine base when the reaction is performed under alkaline conditions. Detailed investigation indicated that the 2-amino group of the enolate form of rG is the reactant of the functionality transfer reaction. As a potential application of this efficient functionality transfer reaction, a pyrene group as a relatively large fluorescent group was successfully transferred to the target guanine base of RNA with a high guanine and site selectivity. This functionality transfer reaction with high efficiency and high site-selectivity would provide a new opportunity as a unique tool for the study of RNA.
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Affiliation(s)
- Kazumitsu Onizuka
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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