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Nakamura A, Wang D, Komatsu Y. Analysis of GTP addition in the reverse (3'-5') direction by human tRNA His guanylyltransferase. RNA (NEW YORK, N.Y.) 2021; 27:665-675. [PMID: 33758037 PMCID: PMC8127990 DOI: 10.1261/rna.078287.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Human tRNAHis guanylyltransferase (HsThg1) catalyzes the 3'-5' addition of guanosine triphosphate (GTP) to the 5'-end (-1 position) of tRNAHis, producing mature tRNAHis In human cells, cytoplasmic and mitochondrial tRNAHis have adenine (A) or cytidine (C), respectively, opposite to G-1 Little attention has been paid to the structural requirements of incoming GTP in 3'-5' nucleotidyl addition by HsThg1. In this study, we evaluated the incorporation efficiencies of various GTP analogs by HsThg1 and compared the reaction mechanism with that of Candida albicans Thg1 (CaThg1). HsThg1 incorporated GTP opposite A or C in the template most efficiently. In contrast to CaThg1, HsThg1 could incorporate UTP opposite A, and guanosine diphosphate (GDP) opposite C. These results suggest that HsThg1 could transfer not only GTP, but also other NTPs, by forming Watson-Crick (WC) hydrogen bonds between the incoming NTP and the template base. On the basis of the molecular mechanism, HsThg1 succeeded in labeling the 5'-end of tRNAHis with biotinylated GTP. Structural analysis of HsThg1 was also performed in the presence of the mitochondrial tRNAHis Structural comparison of HsThg1 with other Thg1 family enzymes suggested that the structural diversity of the carboxy-terminal domain of the Thg1 enzymes might be involved in the formation of WC base-pairing between the incoming GTP and template base. These findings provide new insights into an unidentified biological function of HsThg1 and also into the applicability of HsThg1 to the 5'-terminal modification of RNAs.
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Affiliation(s)
- Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Daole Wang
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yasuo Komatsu
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
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Jiang S, Li L, Li L, Zheng X, Li Z, Song X. The products from fermentation of wheat bran fiber by Auricularia polytricha strain and the effects of the products on rheological properties of dough sheet. Food Sci Nutr 2020; 8:1345-1354. [PMID: 32180944 PMCID: PMC7063353 DOI: 10.1002/fsn3.1366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/10/2022] Open
Abstract
Being classified within the Basidiomycota, Auricularia polytricha has been proved to degrade lignocellulose, a major component of wheat bran fiber. During the fermentation of lignocellulose by A. polytricha strain, a large number of intermediate products are produced, which affect the further degradation of lignocellulose. Therefore, it is essential to analyze the fermentation intermediates for study on the degradation mechanism of wheat bran fiber. In this study, the effectiveness of fermentation of wheat bran fiber by A. polytricha strain was confirmed via scanning electron microscopy. Additionally, the results of gas chromatography-mass spectrometry indicated that the A. polytricha strain could degrade wheat bran fiber and produce several aromatic compounds, and that the number of products obtained after 7 days of fermentation was significantly lower than that after 3 days of fermentation. It has also been demonstrated that diisooctyl phthalate and 9-octadecenamide belong to metabolites produced during the fermentation of wheat bran fiber, by culturing A. polytricha with wheat bran fiber and glucose as carbon source, respectively. Moreover, by conducting an ultraviolet wavelength scanning of the culture liquid containing vanillin fermented by A. polytricha, it has been indicated that the strain could degrade vanillin and further demonstrated that the strain has the ability to degrade wheat bran fiber. Furthermore, adding the products of wheat bran fiber fermented for 3 days by A. polytricha could improve the elasticity of the dough sheet.
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Affiliation(s)
- Shiyu Jiang
- College of Grain and Food Science Henan University of Technology Zhengzhou China
| | - Li Li
- College of Grain and Food Science Henan University of Technology Zhengzhou China
| | - Limin Li
- College of Grain and Food Science Henan University of Technology Zhengzhou China
| | - Xueling Zheng
- College of Grain and Food Science Henan University of Technology Zhengzhou China
| | - Zhengzhe Li
- College of Grain and Food Science Henan University of Technology Zhengzhou China
| | - Xin Song
- College of Grain and Food Science Henan University of Technology Zhengzhou China
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Kowata K, Kojima N, Komatsu Y. Development of a 3'-amino linker with high conjugation activity and its application to conveniently cross-link blunt ends of a duplex. Bioorg Med Chem 2016; 24:2108-13. [PMID: 27041396 DOI: 10.1016/j.bmc.2016.03.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 11/19/2022]
Abstract
The 2-aminoethyl carbamate linker (ssH linker) exhibits high activity in modifying the 5'-termini of oligonucleotides; however, the ssH linker is not appropriate for 3'-terminal modification because it undergoes intramolecular trans-acylation under heat-aqueous ammonia conditions. We developed an N-(2-aminoethyl)carbamate linker (revH linker), in which the carbamate is oriented in the reverse direction relative to that in 2-aminoethyl carbamate. The revH linker was tolerant to heat-alkaline conditions and retained its high reactivity in conjugation with exogenous molecules. The 3'-revH linker was efficiently linked with the 5'-ssH linker at the termini of complementary double strands with a bifunctional molecule, producing a synthetic loop structure. An anti-microRNA oligonucleotide (AMO) was prepared from the chemical ligation of three-stranded 2'-O-methyl RNAs, and the AMO with two alkyl loops exhibited high inhibition activity toward miRNA function. The revH linker is not only useful for 3'-terminal modification of oligonucleotides but also expands the utility range in combination with the 5'-ssH linker.
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Affiliation(s)
- Keiko Kowata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Naoshi Kojima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Tsukuba Central 6, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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Kojima N, Komatsu Y. Synthesis and application of highly reactive amino linkers for functional oligonucleotides. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.48.1-23. [PMID: 22395967 DOI: 10.1002/0471142700.nc0448s48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Oligonucleotides are functionalized by conjugation with a variety of molecules, and aliphatic amino linkers have been frequently used as a tether for their modifications. This unit describes the syntheses and applications of novel amino linkers having a carbamate structure. Two major chemical properties of the primary amine are induced by the neighboring effect of the carbamate group, which are found to be optimum in an aminoethyl carbamate structure. First, the hydrophobic monomethoxytrityl group can be rapidly removed from the aminoethyl carbamate under very mild acidic conditions, while the deprotection is not completed in standard aliphatic amines even under high acid concentration. This significant feature enables the convenient purification of amino-modified oligonucleotides by using the hydrophobic interaction of the monomethoxytrityl group with a reverse-phase resin. Second, the introduction of the carbamate linkage reduces the pK(a) value of the neighboring primary amine, resulting in an increase in the conjugation yields with various functional molecules, such as those having active esters. The novel amino linkers that have an aminoethyl carbamate linkage indicate potent activity and are applicable for the preparation of various functional oligonucleotides.
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Affiliation(s)
- Naoshi Kojima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
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Engelhart AE, Cafferty BJ, Okafor CD, Chen MC, Williams LD, Lynn DG, Hud NV. Nonenzymatic Ligation of DNA with a Reversible Step and a Final Linkage that Can Be Used in PCR. Chembiochem 2012; 13:1121-4. [DOI: 10.1002/cbic.201200167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Indexed: 11/10/2022]
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Liu J, Liu J, Yang L, Chen X, Zhang M, Meng F, Luo T, Li M. Nanomaterial-assisted signal enhancement of hybridization for DNA biosensors: a review. SENSORS 2009; 9:7343-64. [PMID: 22399999 PMCID: PMC3290467 DOI: 10.3390/s90907343] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 08/31/2009] [Accepted: 09/07/2009] [Indexed: 11/16/2022]
Abstract
Detection of DNA sequences has received broad attention due to its potential applications in a variety of fields. As sensitivity of DNA biosensors is determined by signal variation of hybridization events, the signal enhancement is of great significance for improving the sensitivity in DNA detection, which still remains a great challenge. Nanomaterials, which possess some unique chemical and physical properties caused by nanoscale effects, provide a new opportunity for developing novel nanomaterial-based signal-enhancers for DNA biosensors. In this review, recent progress concerning this field, including some newly-developed signal enhancement approaches using quantum-dots, carbon nanotubes and their composites reported by our group and other researchers are comprehensively summarized. Reports on signal enhancement of DNA biosensors by non-nanomaterials, such as enzymes and polymer reagents, are also reviewed for comparison. Furthermore, the prospects for developing DNA biosensors using nanomaterials as signal-enhancers in future are also indicated.
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Affiliation(s)
- Jinhuai Liu
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86 551 5591142; Fax: +86 551 5591142
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Kojima N, Takebayashi T, Mikami A, Ohtsuka E, Komatsu Y. Efficient synthesis of oligonucleotide conjugates on solid-support using an (aminoethoxycarbonyl)aminohexyl group for 5'-terminal modification. Bioorg Med Chem Lett 2009; 19:2144-7. [PMID: 19303292 DOI: 10.1016/j.bmcl.2009.02.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 02/17/2009] [Accepted: 02/27/2009] [Indexed: 11/19/2022]
Abstract
Solid-support conjugation at the 5'-terminal primary amine of oligonucleotides is a convenient and powerful method for introducing various functional groups. However, conventional aliphatic amines do not necessarily provide conjugates with sufficient yields. To improve the modification efficacy, we used the amino-linker (aminoethoxycarbonyl)aminohexyl group (ssH-linker), for solid-support conjugation. In the ssH-linker terminal modification, reactive free amino group could be easily presented onto a solid-support due to rapid removal of the amino-protecting group, and activated amino acids or cholesterol molecules could be covalently connected more efficiently than to typical 6-aminohexyl-linkers. Based on these results, the ssH-linker can be a useful terminal modification for the solid-support conjugation of functional molecules.
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Affiliation(s)
- Naoshi Kojima
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, Tsukisamu-Higashi, Sapporo, Japan
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Komatsu Y, Kojima N, Sugino M, Mikami A, Nonaka K, Fujinawa Y, Sugimoto T, Sato K, Matsubara K, Ohtsuka E. Novel amino linkers enabling efficient labeling and convenient purification of amino-modified oligonucleotides. Bioorg Med Chem 2007; 16:941-9. [PMID: 17950606 DOI: 10.1016/j.bmc.2007.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 10/01/2007] [Accepted: 10/04/2007] [Indexed: 11/17/2022]
Abstract
We developed new amino linker reagents for an oligonucleotide (ONT) terminus. These reagents consist of an aminoethyl carbamate main linkage and a side-chain residue, which was a naphthylmethoxymethyl, methoxymethyl, or methyl group or a hydrogen atom. The primary amine was protected with a monomethoxytrityl (MMT) group. The chemical properties of ONTs containing these amino-modifications were investigated. The MMT group of these amino-modifications could be quite rapidly removed from the amine under very mild acidic conditions, which are not strong enough for the deprotection of a conventional aliphatic amine. This significant feature enabled the amino-modified ONTs to be conveniently purified with a reverse phase column. Furthermore, the amino-modifications efficiently reacted to active esters, as compared with other amino-modifications. We also found that the pK(a) values of the amino-modifications were lower than that of the aliphatic amine. All of the experimental results showed that these chemical properties are closely related to their structures. We report here the chemical properties and the availability of the new amino linker reagents.
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Affiliation(s)
- Yasuo Komatsu
- Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science & Technology (AIST Hokkaido), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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Smith EE, McClean JN, Cooke LA, Duprey JL, McCourt M, Fabani MM, Tucker JH, Vyle JS. A novel structural class of photoswitchable oligonucleotide. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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