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Matsuura K. Construction of Functional Biomaterials by Biomolecular Self-Assembly. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170133] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552
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Ries A, Kumar R, Lou C, Kosbar T, Vengut-Climent E, Jørgensen PT, Morales JC, Wengel J. Synthesis and Biophysical Investigations of Oligonucleotides Containing Galactose-Modified DNA, LNA, and 2'-Amino-LNA Monomers. J Org Chem 2016; 81:10845-10856. [PMID: 27736097 DOI: 10.1021/acs.joc.6b01917] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Galactose-modified thymidine, LNA-T, and 2'-amino-LNA-T nucleosides were synthesized, converted into the corresponding phosphoramidite derivatives and introduced into short oligonucleotides. Compared to the unmodified control strands, the galactose-modified oligonucleotides in general, and the N2'-functionalized 2'-amino-LNA derivatives in particular, showed improved duplex thermal stability against DNA and RNA complements and increased ability to discriminate mismatches. In addition, the 2'-amino-LNA-T derivatives induced remarkable 3'-exonuclease resistance. These results were further investigated using molecular modeling studies.
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Affiliation(s)
- Annika Ries
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Rajesh Kumar
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Chenguang Lou
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Tamer Kosbar
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Empar Vengut-Climent
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark.,Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC Universidad de Sevilla , Americo Vespucio 49, 41092 Sevilla, Spain
| | - Per T Jørgensen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Juan C Morales
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC Universidad de Sevilla , Americo Vespucio 49, 41092 Sevilla, Spain.,Department of Biochemistry and Molecular Pharmacology, Institute of Parasitology and Biomedicine López Neyra , CSIC Avenida del conocimiento 17, 18016 Granada, Spain
| | - Jesper Wengel
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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Affiliation(s)
- Kazunori Matsuura
- Department of Chemistry and Biochemisry, Graduate School of Engineering, Kyushu University
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Zatsepin TS, Oretskaya TS. Synthesis and applications of oligonucleotide-carbohydrate conjugates. Chem Biodivers 2007; 1:1401-17. [PMID: 17191787 DOI: 10.1002/cbdv.200490104] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nowadays, oligonucleotide-carbohydrate conjugates are used in antisense biotechnology and in the study of glycosylated DNA functioning in vitro. The application of mono- and disaccharide phosphoramidites, solid-phase supports with immobilized carbohydrates, glycosylated nucleoside phosphoramidites, and postsynthetic conjugation of reactive sugar derivatives with oligonucleotides for preparation of oligonucleotide-carbohydrate conjugates have been systematically studied. The advantages and disadvantages of these approaches are considered. Possible strategies for synthesis of glycoclusters with different topologies conjugated to DNA are discussed. Applications of oligonucleotide-carbohydrate conjugates are highlighted. Studies of interactions of glycosylated oligonucleotides with proteins and effective cell-specific delivery of oligonucleotide-carbohydrate conjugates are discussed.
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Affiliation(s)
- Timofei S Zatsepin
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory, Moscow, Russia, 119992
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Matsui M, Nishiyama Y, Ueji SI, Ebara Y. Construction of saccharide-modified DNAs by DNA polymerase. Bioorg Med Chem Lett 2006; 17:456-60. [PMID: 17064895 DOI: 10.1016/j.bmcl.2006.10.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2006] [Revised: 09/30/2006] [Accepted: 10/10/2006] [Indexed: 11/22/2022]
Abstract
Novel deoxyribonucleotide triphosphates bearing maltose or lactose groups were synthesized as substrates for DNA polymerase. The incorporation efficiencies of these modified substrates were investigated in both primer extension reactions and PCR. The stability and conformation of saccharide-modified dsDNAs were assessed by UV absorbance melting experiments and CD analysis. Enzymatic incorporation of saccharide-modified substrates can be used for the efficient production of saccharide-modified DNAs.
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Affiliation(s)
- Masayuki Matsui
- Graduate School of Science and Technology, Kobe University, 3-11 Tsurukabuto, Kobe 657-8501, Japan
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Matsuura K, Hayashi K, Kobayashi K. On−Off Switching of Gene Expression Regulated with Carbohydrate−Lectin Interaction. Biomacromolecules 2005; 6:2533-40. [PMID: 16153090 DOI: 10.1021/bm050255a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel strategy for artificial regulation system of gene expression applying the specific molecular recognition between carbohydrate and lectin is proposed. Plasmid-lactose conjugates (pActin-lactose and pGFP-lactose) prepared via diazocoupling maintained the transcription activity with T7 RNA polymerase. Gel-shift assay showed that the pActin-lactose conjugates were specifically complexed with galactose-specific lectin RCA(120) with a strong binding affinity (K(a) = 7.6 x 10(5) M(-1) per Lac-unit). The complexes were observed to form aggregates of sub-several micrometer size by means of transmission electron microscopy (TEM) and atomic force microscopy (AFM). The activities of transcription and expression of the conjugates were evaluated, respectively, on the basis of the amount of transcript of pActin and the fluorescent intensity of the expressed GFP. These activities were repressed in the presence of an increasing concentration of RCA120, and then recovered by adding lactose, lactosylceramide-containing liposomes, and lactose-carrying polymers to the conjugate-RCA120 complex. Gel-shift assay and TEM observation revealed that the aggregation form of the complex was relaxed partially in the presence of the lactose derivatives, which increased the accessibility of T7 RNA polymerase to result in the recovery of transcription activity.
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Affiliation(s)
- Kazunori Matsuura
- Department of Molecular Design, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.
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Yamada Y, Matsuura K, Kobayashi K. Cooperative lectin recognition of periodical glycoclusters along DNA duplexes: alternate hybridization and full hybridization. Bioorg Med Chem 2005; 13:1913-22. [PMID: 15727847 DOI: 10.1016/j.bmc.2005.01.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2004] [Revised: 01/14/2005] [Accepted: 01/14/2005] [Indexed: 11/23/2022]
Abstract
We describe herein the construction of periodically, spatially controlled glycoclusters along DNA duplexes and their cooperative lectin recognition. Site-specifically alpha-mannosylated oligodeoxynucleotide 20-mer (Man-ODN20) was synthesized via the phosphoramidite solid-phase synthesis. Alternate hybridization of the Man-ODN20 with the half-sliding complementary ODN 20-mer (hscODN20) gave an alternately prolonged Man-cluster Man-ODN20/hscODN20. The binding of the Man-cluster to FITC-labeled ConA lectin showed sigmoidal fluorescence dependency on the concentration of Man-ODN, indicating that some mannose residues along the repeating DNA duplex were cooperatively bound to ConA (apparent affinity constant: K(af)=2.4 x 10(4)M(-1) and Hill coefficient: n=3.5). The duplex of Man-ODN20 with full complementary ODN 20-mer (fcODN20) was little bound to ConA. The binding behavior of Man-ODN20/hscODN20 is compared with that of the alternately prolonged Gal-cluster Gal-ODN20/hscODN20 previously reported. Duplexes 20-mer, 40-mer, and 60-mer presenting one, two, and three periodic galactoses were also prepared by full hybridization of 20-mer beta-galactosylated oligodeoxynucleotide (Gal-ODN20) with the periodically repeating full complementary 20-mer, 40-mer, and 60-mer ODNs. RCA(120) lectin was found to little bind the 20-mer and 40-mer duplexes and to bind weakly and non-cooperatively the 60-mer duplex (K(af)=1.1 x 10(4)M(-1)). The cooperative lectin recognition of these glycoclusters in relation with the degree of association (DA) of ODN and the numbers of glycosides along the DNA duplex is discussed.
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Affiliation(s)
- Yoshinao Yamada
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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Adinolfi M, De Napoli L, Di Fabio G, Iadonisi A, Montesarchio D, Piccialli G. Solid phase synthesis of oligonucleotides tethered to oligo-glucose phosphate tails. Tetrahedron 2002. [DOI: 10.1016/s0040-4020(02)00684-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Matsuura K, Hibino M, Yamada Y, Kobayashi K. Construction of glyco-clusters by self-organization of site-specifically glycosylated oligonucleotides and their cooperative amplification of lectin-recognition. J Am Chem Soc 2001; 123:357-8. [PMID: 11456533 DOI: 10.1021/ja001945j] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K Matsuura
- Department of Molecular Design Graduate School of Engineering Nagoya University, Chikusa, Nagoya 464-8603, Japan
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