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Tang Z, Gao M, Gong F, Shan X, Yang Y, Zhang Y, Chen L, Wang F, Ji X, Zhou F, He Z. Quantum Dot Reporters Designed for CRISPR-Based Detection of Viral Nucleic Acids. Anal Chem 2024. [PMID: 39324802 DOI: 10.1021/acs.analchem.4c03541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Diagnostic methods based on CRISPR technology have shown great potential due to their highly specific, efficient, and sensitive detection capabilities. Although the majority of the current studies rely on fluorescent dye-quencher reporters, the limitations of fluorescent dyes, such as poor photostability and small Stokes shifts, urgently necessitate the optimization of reporters. In this study, we developed innovative quantum dot (QD) reporters for the CRISPR/Cas systems, which not only leveraged the advantages of high photoluminescence quantum yield and large Stokes shifts of QDs but were also easily synthesized through a simple one-step hydrothermal method. Based on the trans-cleavage characteristics of Cas12a and Cas13a, two types of QD reporters were designed, the short DNA strand and the hybridization-based QD reporters, achieving the detection of DNA and RNA at the pM level, respectively, and validating the performance in the analysis of clinical samples. Furthermore, based on the unique property of QDs that allowed multicolor emission under one excitation, the application potential for simultaneous detection of diseases was further investigated. Taken together, this work proposed novel QD reporters that could be applied to the various CRISPR/Cas systems, providing a new toolbox to expand the diagnosis of bioanalytical and biomedical fields.
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Affiliation(s)
- Ziwen Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Menglu Gao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Feng Gong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoyun Shan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yeling Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yaran Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Liangjun Chen
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Fubing Wang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Center for Single-Cell Omics and Tumor Liquid Biopsy, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
| | - Xinghu Ji
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Fuxiang Zhou
- Department of Radiation and Medical Oncology, Hubei Key Laboratory of Tumor Biological Behaviors, and Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan 430072, China
| | - Zhike He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, China
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Ranjan P, Chakraborty B, Chakraborty T. A systematic computational study of acridine derivatives through conceptual density functional theory. Mol Divers 2022:10.1007/s11030-022-10486-6. [PMID: 35781180 DOI: 10.1007/s11030-022-10486-6] [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: 05/02/2022] [Accepted: 06/14/2022] [Indexed: 12/18/2022]
Abstract
A detailed computational analysis of acridine derivatives viz. acridone, 9-amino acridine hydrochloride hydrate, proflavin, acridine orange and acridine yellow is done in terms of conceptual density functional theory (CDFT). CDFT-based global descriptors-ionization potential, electron affinity, HOMO-LUMO gap, hardness, softness, electronegativity and electrophilicity index of acridine derivatives for ground state as well as excited state are estimated with the help of different hybrid functionals B3LYP/6-31G (d, p), B3LYP/6-311G (d, p), B3LYP/DGDZVP and B3LYP/LANL2DZ. Acridine derivatives show higher values of ionization potential and electron affinity in excited state as compared to ground state, indicating that these compounds are willing to accept electrons in excited state rather than donating electron. Acridone shows the maximum HOMO-LUMO energy gap in ground and excited state which implies that one-way electron transfer is most feasible with this compound. Our computed results emphasize the pronounced electron acceptor behaviour of the acridine derivatives in the excited state which has already been experimentally verified. It is observed that the trend in the computed values of the descriptors is not much improved on refinement of the basis set.
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Affiliation(s)
- Prabhat Ranjan
- Department of Mechatronics Engineering, Manipal University Jaipur, Dehmi Kalan, Jaipur, 303007, India
| | - Brotati Chakraborty
- Department of Chemistry, Bejoy Narayan Mahavidyalaya, Itachuna, Hooghly, West Bengal, 712147, India.
| | - Tanmoy Chakraborty
- Department of Chemistry and Biochemistry, School of Basic Sciences and Research, Sharda University, Greater Noida, 201310, India.
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3
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Liu Z, Wang S, Tapeinos C, Torrieri G, Känkänen V, El-Sayed N, Python A, Hirvonen JT, Santos HA. Non-viral nanoparticles for RNA interference: Principles of design and practical guidelines. Adv Drug Deliv Rev 2021; 174:576-612. [PMID: 34019958 DOI: 10.1016/j.addr.2021.05.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/04/2021] [Accepted: 05/15/2021] [Indexed: 02/08/2023]
Abstract
Ribonucleic acid interference (RNAi) is an innovative treatment strategy for a myriad of indications. Non-viral synthetic nanoparticles (NPs) have drawn extensive attention as vectors for RNAi due to their potential advantages, including improved safety, high delivery efficiency and economic feasibility. However, the complex natural process of RNAi and the susceptible nature of oligonucleotides render the NPs subject to particular design principles and requirements for practical fabrication. Here, we summarize the requirements and obstacles for fabricating non-viral nano-vectors for efficient RNAi. To address the delivery challenges, we discuss practical guidelines for materials selection and NP synthesis in order to maximize RNA encapsulation efficiency and protection against degradation, and to facilitate the cytosolic release of oligonucleotides. The current status of clinical translation of RNAi-based therapies and further perspectives for reducing the potential side effects are also reviewed.
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Luige O, Murtola M, Ghidini A, Strömberg R. Further Probing of Cu 2+-Dependent PNAzymes Acting as Artificial RNA Restriction Enzymes. Molecules 2019; 24:molecules24040672. [PMID: 30769777 PMCID: PMC6412939 DOI: 10.3390/molecules24040672] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 11/16/2022] Open
Abstract
Peptide nucleic acid (PNA)-neocuproine conjugates have been shown to efficiently catalyse the cleavage of RNA target sequences in the presence of Cu2+ ions in a site-specific manner. These artificial enzymes are designed to force the formation of a bulge in the RNA target, the sequence of which has been shown to be key to the catalytic activity. Here, we present a further investigation into the action of Cu2+-dependent PNAzymes with respect to the dependence on bulge composition in 3- and 4-nucleotide bulge systems. Cu2+-dependent PNAzymes were shown to have a clear preference for 4-nucleotide bulges, as the cleavage of 3-nucleotide bulge-forming RNA sequences was significantly slower, which is illustrated by a shift in the half-lives from approximately 30 min to 24 h. Nonetheless, the nucleotide preferences at different positions in the bulge displayed similar trends in both systems. Moreover, the cleavage site was probed by introducing critical chemical modifications to one of the cleavage site nucleotides of the fastest cleaved 4-nucleotide RNA bulge. Namely, the exclusion of the exocyclic amine of the central adenine and the replacement of the 2′-hydroxyl nucleophile with 2′-H or 2′-OMe substituents in the RNA severely diminished the rate of RNA cleavage by the Cu2+-dependent PNAzyme, giving insight into the mechanism of cleavage. Moreover, the shorter recognition arm of the RNA/PNAzyme complex was modified by extending the PNAzyme by two additional nucleobases. The new PNAzyme was able to efficiently promote the cleavage of RNA when fully hybridised to a longer RNA target and even outperform the previous fastest PNAzyme. The improvement was demonstrated in cleavage studies with stoichiometric amounts of either PNAzyme present, and the extended PNAzyme was also shown to give turnover with a 10-fold excess of the RNA target.
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Affiliation(s)
- Olivia Luige
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
| | - Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland.
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
- Institut für Pharmazeutische Wissenschaften (IPW), Eidgenössische Technische Hochschule Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, 141 83 Huddinge, Stockholm, Sweden.
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Kuzuya A, Machida K, Shi Y, Tanaka K, Komiyama M. Site-Selective RNA Activation by Acridine-Modified Oligodeoxynucleotides in Metal-Ion Catalyzed Hydrolysis: A Comprehensive Study. ACS OMEGA 2017; 2:5370-5377. [PMID: 31457805 PMCID: PMC6644747 DOI: 10.1021/acsomega.7b00966] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/21/2017] [Indexed: 06/10/2023]
Abstract
Various types of acridine were conjugated to DNA and used for site-selective RNA scission together with another unmodified DNA and a Lu(III) ion. The target phosphodiester linkage in the substrate RNA was selectively and efficiently activated, and was hydrolyzed by the free Lu(III) ion. Among the investigated 14 conjugates, the conjugate bearing 9-amino-2-isopropoxy-6-nitroacridine was the best RNA-activator. Systematic evaluation of the RNA-activating ability of the acridines showed that (1) the acridines act as an acid catalyst within the RNA activation, (2) the amino-group at the 9-position of acridine is essential to modulate the acidity of acridine, (3) the electron-withdrawing group at the 3-position further enhances the acid catalysis, and (4) the substituent at the 2-position sterically modulates the orientation of acridine-intercalation favorably for the catalysis. Moreover, it is revealed that the opposite base of acridine does not inhibit direct interaction of acridine with the target phosphodiester linkage.
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Affiliation(s)
- Akinori Kuzuya
- Department
of Chemistry and Materials Engineering, Kansai University, 3-3-35
Yamate, Suita, Osaka 564-8680, Japan
| | - Kenzo Machida
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Yun Shi
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Keita Tanaka
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Makoto Komiyama
- International
Center for Materials Nanoarchitechtonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
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Kuah E, Toh S, Yee J, Ma Q, Gao Z. Enzyme Mimics: Advances and Applications. Chemistry 2016; 22:8404-30. [PMID: 27062126 DOI: 10.1002/chem.201504394] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Indexed: 12/29/2022]
Abstract
Enzyme mimics or artificial enzymes are a class of catalysts that have been actively pursued for decades and have heralded much interest as potentially viable alternatives to natural enzymes. Aside from having catalytic activities similar to their natural counterparts, enzyme mimics have the desired advantages of tunable structures and catalytic efficiencies, excellent tolerance to experimental conditions, lower cost, and purely synthetic routes to their preparation. Although still in the midst of development, impressive advances have already been made. Enzyme mimics have shown immense potential in the catalysis of a wide range of chemical and biological reactions, the development of chemical and biological sensing and anti-biofouling systems, and the production of pharmaceuticals and clean fuels. This Review concerns the development of various types of enzyme mimics, namely polymeric and dendrimeric, supramolecular, nanoparticulate and proteinic enzyme mimics, with an emphasis on their synthesis, catalytic properties and technical applications. It provides an introduction to enzyme mimics and a comprehensive summary of the advances and current standings of their applications, and seeks to inspire researchers to perfect the design and synthesis of enzyme mimics and to tailor their functionality for a much wider range of applications.
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Affiliation(s)
- Evelyn Kuah
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Seraphina Toh
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Jessica Yee
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Qian Ma
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax
| | - Zhiqiang Gao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Fax.
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Kupryushkin MS, Pyshnyi DV. Oligonucleotide derivatives in nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insertion. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012. [DOI: 10.1134/s106816201206009x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Kuzuya A, Tanaka K, Komiyama M. Photoswitching of site-selective RNA scission by sequential incorporation of azobenzene and acridine residues in a DNA oligomer. J Nucleic Acids 2011; 2011:162452. [PMID: 21941627 PMCID: PMC3177363 DOI: 10.4061/2011/162452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/06/2011] [Indexed: 11/20/2022] Open
Abstract
Photoresponsive systems for site-selective RNA scission have been prepared by combining Lu(III) ions with acridine/azobenzene dual-modified DNA. The modified DNA forms a heteroduplex with substrate RNA, and the target phosphodiester linkages in front of the acridine residue is selectively activated so that Lu(III) ion rapidly cleaves the linkage. Azobenzene residue introduced adjacent to the acridine residue acts as a photoresponsive switch, which triggers the site-selective scission upon UV irradiation. A trans isomer of azobenzene efficiently suppresses the scission, whereas the cis isomer formed by UV irradiation hardly affects the scission. As a result, 1.7-2.4-fold acceleration of the cleavage was achieved simply by irradiating UV for 3 min to the mixture prior to the reaction. Considering the yield of photoisomerization, the intrinsic activity of a cis isomer is up to 14.5-fold higher than that of the trans isomer.
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Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Chemistry and Materials Engineering, Kansai University, 3-3-35 Kamiyamate-cho, Suita, Osaka 564-8680, Japan
| | - Keita Tanaka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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10
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Qi X, Xia T, Roberts RW. Acridine-N peptide conjugates display enhanced affinity and specificity for boxB RNA targets. Biochemistry 2010; 49:5782-9. [PMID: 20527807 DOI: 10.1021/bi100634h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Arginine-rich peptides and small-molecule intercalating agents utilize distinct molecular mechanisms for RNA recognition. Here, we combined these distinct binding modules in an effort to create conjugate ligands with enhanced affinity and specificity using the bacteriophage lambda N peptide-boxB interaction as a model system. We first designed and synthesized a series of peptide-acridine conjugates using portions of the RNA-binding domain of N protein (11- and 22- residue peptide segments) and then compared the binding affinity, specificity, salt dependence, and structural properties of the RNA-peptide and RNA-peptide-acridine conjugate complexes using steady-state fluorescence, CD spectroscopy, NMR, and native gel mobility shift assays (GMSAs). These analyses revealed that the full-length peptide-acridine conjugate displayed substantially improved RNA binding affinity ( approximately 80-fold; K(d) approximately 15 pM) relative to that of the peptide alone (K(d) approximately 1.2 nM). In accordance, we also observed specificity enhancement ( approximately 25-fold) as determined via comparison of the binding of the best conjugate to a cognate lambda boxB RNA with that to a noncognate P22 RNA hairpin (80-fold vs 3.2-fold enhancement). Furthermore, the observed binding enhancement was unique to the full-length conjugate with a flexible linker, implying that the structural context of the acridine presentation was critical. Taken together, our observations support the idea that peptide- and intercalation-based binding can be combined to create a new class of high-affinity, high-specificity RNA-binding ligands.
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Affiliation(s)
- Xin Qi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Mail-code 147-75, Pasadena, California 91125, USA
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Shao Y, Ding Y, Xu W, Wei L, Liu F, Lu G. DNA Binding and Cleavage Activity of Zinc(II) Complex ofN,N′-Bis(2-guanidinoethyl)-2,6-pyridinedicarboxamide. CHINESE J CHEM 2009. [DOI: 10.1002/cjoc.200990290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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12
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Kuzuya A, Shi Y, Tanaka K, Machida K, Komiyama M. Efficient Site-selective RNA Activation and Scission Achieved by Geometry Control of Acridine Intercalation in RNA/DNA Heteroduplex. CHEM LETT 2009. [DOI: 10.1246/cl.2009.432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Sugimoto N. Designable DNA Functions toward New Nanobiotechnology. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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14
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15
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Tanaka K, Yamamoto Y, Kuzuya A, Komiyama M. Synthesis of photo-responsive acridine-modified DNA and its application to site-selective RNA scission. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:1175-85. [PMID: 18788047 DOI: 10.1080/15257770802400099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Photo-responsive phosphoramidite monomers, which bear an azobenzene between acridine and the phosphoramidite unit, were synthesized, and incorporated into oligonucleotides. Upon UV irradiation, the azobenzene in the modified DNA efficiently isomerized from the trans isomer into the cis isomer. Although the T(m) values of their duplexes with complementary DNA were not much changed by the isomerization, site-selective RNA scission was significantly accelerated by the UV irradiation when Mn(II) ion was used as the catalyst for RNA scission.
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Affiliation(s)
- Keita Tanaka
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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16
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Bazzicalupi C, Bencini A, Bonaccini C, Giorgi C, Gratteri P, Moro S, Palumbo M, Simionato A, Sgrignani J, Sissi C, Valtancoli B. Tuning the Activity of Zn(II) Complexes in DNA Cleavage: Clues for Design of New Efficient Metallo-Hydrolases. Inorg Chem 2008; 47:5473-84. [DOI: 10.1021/ic800085n] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Carla Bazzicalupi
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Andrea Bencini
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Claudia Bonaccini
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Claudia Giorgi
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Paola Gratteri
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Stefano Moro
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Manlio Palumbo
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Alessandro Simionato
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Jacopo Sgrignani
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Claudia Sissi
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Barbara Valtancoli
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
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17
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Dijk EW, Feringa BL, Roelfes G. DNA in Metal Catalysis. TOP ORGANOMETAL CHEM 2008. [DOI: 10.1007/3418_2008_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Cacciapaglia R, Casnati A, Mandolini L, Peracchi A, Reinhoudt DN, Salvio R, Sartori A, Ungaro R. Efficient and selective cleavage of RNA oligonucleotides by calix[4]arene-based synthetic metallonucleases. J Am Chem Soc 2007; 129:12512-20. [PMID: 17880217 DOI: 10.1021/ja0737366] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Di- and trinuclear copper(II) complexes of [12]aneN3 macrocycles anchored at the upper rim of cone calix[4]arenes in 1,2-, 1,3-, and 1,2,3-positions were investigated as cleaving agents of 6-, 7-, and 17-meric oligoribonucleotides. A kinetic investigation of the cleavage reactions was carried out using gel electrophoresis to separate and analyze reactants and products having a radioactive phosphate label in the terminal 5'-position. The degree of cooperation was assessed on the basis of a comparison with rates of cleavage by mononuclear controls. A remarkable selectivity of cleavage of the CpA phosphodiester bond was observed for all metal complexes, in sharp contrast with the UpU and UpG selectivity previously observed in the cleavage of diribonucleoside monophosphates by the same metal complexes. The highest rate acceleration, brought about in the cleavage of the 5'-pCpA bond in hexanucleotide 9 by 50 muM trinuclear complex 5-Cu3 (water solution, pH 7.4, 50 degrees C), amounts to 5 x 105-fold, as based on the estimated background reactivity of the CpA dimer. Selectivity in the cleavage of oligoribonucleotides by copper(II) complexes closely resembles that experienced by ribonuclease A and by a number of metal-independent RNase A mimicks. The possible role of the dianionic phosphate at the 5'-terminal positions as a primary anchoring site for the metal catalyst is discussed.
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Affiliation(s)
- Roberta Cacciapaglia
- Dipartimento di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Università La Sapienza, Box 34 - Roma 62, 00185 Roma, Italy
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19
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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20
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Li Y, Sheng X, Shao Y, Lu GY. DNA Cleavage Promoted by Cu2+ Complex of N,N′-Bis(2-aminoethyl)-2,6-pyridinedicarboxamide. CHINESE J CHEM 2007. [DOI: 10.1002/cjoc.200790182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Peluffo F, Torres J, Kremer C, Domínguez S, Mederos A, Kremer E. Phosphodiesterolytic activity of samarium(III) mixed ligand complexes containing crown ethers and α-amino acids. Inorganica Chim Acta 2006. [DOI: 10.1016/j.ica.2005.12.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Sasayama T, Kato M, Aburatani H, Kuzuya A, Komiyama M. Simultaneous genotyping of indels and SNPs by mass spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:3-8. [PMID: 16338145 DOI: 10.1016/j.jasms.2005.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 08/20/2005] [Accepted: 08/26/2005] [Indexed: 05/05/2023]
Abstract
Nucleotide insertion/deletion polymorphisms (indels) in ApoE gene were precisely genotyped using artificial ribonucleases and MALDI-TOF MS. The RNA fragments for MS analysis were prepared by treating RNA specimens with our artificial ribonucleases, which consist of LuCl(3) (molecular scissors) and oligonucleotides bearing two acridine groups (RNA-activator for site-selective scission). RNA scission by Lu(III) ion always occurred at the phosphodiester linkages in front of the two acridines, even when the RNA specimens involved consecutive cytidine sequences of different lengths. Thus, even complicated mixtures of these indel specimens were completely genotyped by using only one acridine-bearing oligonucleotide and by subjecting the reaction mixture to single MS measurement. Moreover, single nucleotide polymorphism (SNP) in the consecutive sequences could be genotyped simultaneously with the indels.
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Affiliation(s)
- Takuro Sasayama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan
| | - Mayu Kato
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan
| | - Hiroyuki Aburatani
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan
| | - Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, 153-8904, Tokyo, Japan.
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23
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Nakano SI, Uotani Y, Uenishi K, Fujii M, Sugimoto N. DNA base flipping by a base pair-mimic nucleoside. Nucleic Acids Res 2005; 33:7111-9. [PMID: 16361269 PMCID: PMC1316115 DOI: 10.1093/nar/gki1018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
On the basis of non-covalent bond interactions in nucleic acids, we synthesized the deoxyadenosine derivatives tethering a phenyl group (X) and a naphthyl group (Z) by an amide linker, which mimic a Watson–Crick base pair. Circular dichroism spectra indicated that the duplexes containing X and Z formed a similar conformation regardless of the opposite nucleotide species (A, G, C, T and an abasic site analogue F), which was not observed for the natural duplexes. The ΔG370 values among the natural duplexes containing the A/A, A/G, A/C, A/T and A/F pairs differed by 5.2 kcal mol−1 while that among the duplexes containing X or Z in place of the adenine differed by only 1.9 or 2.8 kcal mol−1, respectively. Fluorescence quenching experiments confirmed that 2-amino purine opposite X adopted an unstacked conformation. The structural and thermodynamic analyses suggest that the aromatic hydrocarbon group of X and Z intercalates into a double helix, resulting in the opposite nucleotide base flipping into an unstacked position regardless of the nucleotide species. This observation implies that modifications at the aromatic hydrocarbon group and the amide linker may expand the application of the base pair-mimic nucleosides for molecular biology and biotechnology.
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Affiliation(s)
- Shu-ichi Nakano
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
| | - Yuuki Uotani
- Department of Chemistry, Faculty of Science and Engineering, Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
| | - Kazuya Uenishi
- Molecular Engineering Institute, Kinki University11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Masayuki Fujii
- Molecular Engineering Institute, Kinki University11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
- Department of Environmental and Biological Chemistry, Kinki University11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
- Department of Chemistry, Faculty of Science and Engineering, Konan University8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
- To whom correspondence should be addressed. Tel: +81 78 435 2497; Fax: +81 78 435 2539;
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24
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Chen W, Komiyama M. Site-selective DNA hydrolysis by Ce(IV)-EDTA with the use of one oligonucleotide additive bearing two monophosphates. Chembiochem 2005; 6:1825-30. [PMID: 16196014 DOI: 10.1002/cbic.200500119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two deoxyuridine derivatives each bearing a monophosphate group at the 5-position with a C3 linker, were incorporated into an oligonucleotide. By using this modified oligonucleotide, a bulge was formed at a predetermined position in a DNA substrate, and two monophosphate groups were placed at both junctions of the bulge. Upon treatment of the mixture with Ce(IV)-EDTA at pH 7.0, the phosphodiester linkages at the bulge site were selectively and efficiently hydrolyzed. The monophosphate groups introduced into the bulge site greatly accelerated site-selective DNA scission. Compared with the previously reported two-additive system, which combines two oligonucleotide additives each with a monophosphate at their termini, the present one-additive system is simpler and more convenient. Furthermore, site-selective DNA hydrolysis by using this one-additive system is successful even at high reaction temperatures (e.g., 55 degrees C). This reflects the thermodynamic stability of the duplexes formed between the substrate and the additive DNA.
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Affiliation(s)
- Wen Chen
- Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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25
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Abstract
Mimicking the action of enzymes by simpler and more robust man-made catalysts has long inspired bioorganic chemists. During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, or, more precisely, mimics of ribozymes that cleave RNA in sequence-selective rather than base-selective manner, have received special attention. These artificial ribonucleases are typically oligonucleotides (or their structural analogs) that bear a catalytically active conjugate group and catalyze sequence-selective hydrolysis of RNA phosphodiester bonds.
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Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland
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26
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Torres J, Brusoni M, Peluffo F, Kremer C, Domínguez S, Mederos A, Kremer E. Phosphodiesterolytic activity of lanthanide (III) complexes with α-amino acids. Inorganica Chim Acta 2005. [DOI: 10.1016/j.ica.2005.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Komiyama M, Arishima H, Yokoyama M, Kitamura Y, Yamamoto Y. Oligonucleotide bearing ethylenediamine-N,N,N'-Triacetates for gap-selective DNA hydrolysis by Ce4+/EDTA. Chembiochem 2005; 6:192-6. [PMID: 15540227 DOI: 10.1002/cbic.200400220] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
With the use of two oligonucleotides bearing ethylenediamine-N,N,N'-triacetate groups as additives, gap sites were formed at predetermined sites in substrate DNA. Upon treating these systems with a Ce(4+)/EDTA complex at pH 7.0 and 37 degrees C, the phosphodiester linkages at the gap site were selectively hydrolyzed. The DNA scission was greatly promoted by the introduction of ethylenediaminetriacetate groups, and the scission efficiency increased as the number of these groups increased. Even a one-base gap was successfully hydrolyzed when three ethylenediaminetriacetate groups were placed consecutively at both edges of the gap, although the scission was minimal in the absence of these groups. The site-selective scission could be also achieved at higher temperatures without any significant loss of site-selectivity.
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Affiliation(s)
- Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
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28
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Shi Y, Machida K, Kuzuya A, Komiyama M. Design of phosphoramidite monomer for optimal incorporation of functional intercalator to main chain of oligonucleotide. Bioconjug Chem 2005; 16:306-11. [PMID: 15769083 DOI: 10.1021/bc049698m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chirally pure phosphoramidite monomers bearing 9-amino-6-chloro-2-methoxyacridine were synthesized from D- or L-threoninol and omega-aminocarboxylic acid, and incorporated into oligonucleotides. These acridine-DNA conjugates formed stable duplexes with complementary RNA because of intercalation of the acridine to DNA/RNA heteroduplexes. The stability of duplexes was not very dependent on either the chirality of the central carbon bearing the acridine or the length of the side chain. However, the ability for site-selective activation of the phosphodiester linkage in front of the acridine, which induced Lu(III)-promoted RNA scission, was strongly dependent on these two factors. The largest activation was achieved when the monomer unit was prepared from L-threoninol and 4-aminobutyric acid and the acridine was bound to the amino group. By attaching the more acidic 9-amino-2-methoxy-6-nitroacridine to this optimized scaffold, a quite effective acridine-DNA conjugate for site-selective RNA scission was obtained.
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Affiliation(s)
- Yun Shi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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29
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Ogawa A, Tomita N, Kikuchi N, Sando S, Aoyama Y. Aptamer selection for the inhibition of cell adhesion with fibronectin as target. Bioorg Med Chem Lett 2005; 14:4001-4. [PMID: 15225715 DOI: 10.1016/j.bmcl.2004.05.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Revised: 05/19/2004] [Accepted: 05/19/2004] [Indexed: 10/26/2022]
Abstract
An affinity column immobilizing a decapeptide H(2)N-RGDSPASSKP-CO(2)H was used to select RGD-binding aptamers from a pool of 86-mer single-strand oligodeoxynucleotides (ODNs) containing a random 40-mer sequence. The enriched library thus obtained was further selected against adsorbed fibronectin and individual aptamers were monocloned in E. coli and sequenced to give a couple of highly homologous ODNs, which indeed inhibited fibronectin-integrin mediated cell adhesion.
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Affiliation(s)
- Atsushi Ogawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-Ku, Kyoto 615-8510, Japan
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30
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Kuzuya A, Shi Y, Sasayama T, Komiyama M. Cooperation of metal-ion fixation and target-site activation for efficient site-selective RNA scission. J Biol Inorg Chem 2005; 10:270-4. [PMID: 15772817 DOI: 10.1007/s00775-005-0638-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Accepted: 02/21/2005] [Indexed: 10/25/2022]
Abstract
Iminodiacetate-DNA conjugates and acridine-DNA conjugates were synthesized and combined for site-selective RNA hydrolysis by Lu(III). When these conjugates form a ternary complex with complementary RNA, the Lu(III)-iminodiacetate complex is placed near the target phosphodiester linkage of RNA which is in front of the acridine and is activated by noncovalent interactions. The site-selective hydrolysis by these combinations is several times as fast as that achieved by combining unmodified DNA (without iminodiacetate) and the acridine-DNA conjugate.
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Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, 153-8904, Japan
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31
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Kuznetsova IL, Zenkova MA, Gross HJ, Vlassov VV. Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease. Nucleic Acids Res 2005; 33:1201-12. [PMID: 15731340 PMCID: PMC549568 DOI: 10.1093/nar/gki264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cleavage of phosphodiester bonds by small ribonuclease mimics within different bulge-loops of RNA was investigated. Bulge-loops of different size (1–7 nt) and sequence composition were formed in a 3′ terminal fragment of influenza virus M2 RNA (96 nt) by hybridization of complementary oligodeoxynucleotides. Small bulges (up to 4 nt) were readily formed upon oligonucleotide hybridization, whereas hybridization of the RNA to the oligonucleotides designed to produce larger bulges resulted in formation of several alternative structures. A synthetic ribonuclease mimic displaying Pyr–Pu cleavage specificity cleaved CpA motifs located within bulges faster than similar motifs within the rest of the RNA. In the presence of 10 mM MgCl2, 75% of the cleavage products resulted from the attack of this motif. Thus, selective RNA cleavage at a single target phosphodiester bond was achieved by using bulge forming oligonucleotides and a small ribonuclease A mimic.
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Affiliation(s)
| | - Marina A. Zenkova
- To whom correspondence should be addressed. Tel: +7 3832 333761; Fax: +7 3832 333761;
| | - Hans J. Gross
- Institute of Biochemistry, BiocenterAm Hubland, D-97074 Würzburg, Germany
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32
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Nakano SI, Uotani Y, Uenishi K, Fujii M, Sugimoto N. Site-Selective RNA Cleavage by DNA Bearing a Base Pair-Mimic Nucleoside. J Am Chem Soc 2004; 127:518-9. [PMID: 15643864 DOI: 10.1021/ja045445s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We have synthesized the deoxyadenosine derivative tethering a phenyl group (X), which mimics the Watson-Crick A/T base pair. The RNA/DNA hybrid duplexes containing X in the middle of the DNA sequence showed a similar thermal stability regardless of the ribonucleotide species (A, G, C, or U) opposite to X, probably because of the phenyl group stacking inside of the duplex accompanied by the opposite ribonucleotide base flipped in an extrahelical position. The RNA strand hybridized with the DNA strand bearing X was cleaved on the 3'-side of the ribonucleotide opposite to X in the presence of MgCl2, and the RNA sequence to be cleaved was not restricted. The site-specific RNA hydrolysis suggests that the DNA strand bearing X has the advantage of the site-selective base flipping in the target sequence and the development of a "universal deoxyribozyme" to exclusively cleave a target RNA sequence.
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Affiliation(s)
- Shu-ichi Nakano
- Frontier Institute for Biomolecular Engineering Research and Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan
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33
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Abstract
Synthetic metallonucleases are versatile metal ion catalysts that use multiple catalytic strategies for the cleavage of RNA. Recent work in the design of more active metallonucleases combines a single metal ion with functional groups that interact with RNA, including amino acid fragments or additional metal ions. Rate enhancements by multifunctional catalysts for cleavage of simple model substrates with good leaving groups are as high as 10(6) but somewhat lower (10(5)) for real RNA. However, cleavage of RNA substrates is complicated by different binding modes and steric interactions that can interfere with catalysis. Antisense oligonucleotides, peptides and small molecules that act as RNA recognition agents increase the strength of substrate binding, but not necessarily the catalytic rate constant. In general, catalytic strategies used by synthetic metallonucleases are probably not optimized. A better grasp of the mechanism of RNA cleavage by metal ions and more effort on positioning the metal ion complex with respect to the cleavage site may lead to improved catalysts.
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Affiliation(s)
- Janet R Morrow
- Department of Chemistry, University at Buffalo, State University of New York, Amherst, NY 14260-3000, USA.
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34
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Shi Y, Niikura F, Kuzuya A, Komiyama M. Noncovalent Combination of Oligoamine and Oligonucleotide as Totally Organic Site-selective RNA Cutter. CHEM LETT 2004. [DOI: 10.1246/cl.2004.1012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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35
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Kuzuya A, Mizoguchi R, Sasayama T, Zhou JM, Komiyama M. Selective activation of two sites in RNA by acridine-bearing oligonucleotides for clipping of designated RNA fragments. J Am Chem Soc 2004; 126:1430-6. [PMID: 14759201 DOI: 10.1021/ja0389568] [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] [Indexed: 11/29/2022]
Abstract
Artificial enzymes for selective scission of RNA at two designated sites, which are valuable for advanced RNA science, have been prepared by combining lanthanide(III) ion with an oligonucleotide bearing two acridine groups. When these modified oligonucleotides form heteroduplexes with substrate RNA, the two phosphodiester linkages in front of the acridines are selectively activated and preferentially hydrolyzed by lanthanide ion. This two-site RNA scission does not require any specific RNA sequence at the scission sites, and the length of clipped RNA fragment is easily and precisely controllable by changing the distance between two acridine groups in the modified oligonucleotide. The two-site scission is also successful even when the substrate RNA has higher-order structures. By using these two-site RNA cutters, RNA fragments of predetermined length were obtained from long RNA substrates and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Single nucleotide polymorphisms in homozygous and heterozygous samples were accurately and easily detected in terms of the difference in mass number. Multiplex analyses of in vitro transcripts from human genome were also successful.
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Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan
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36
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Shi Y, Kuzuya A, Machida K, Komiyama M. Crucial role of linker portion in acridine-bearing oligonucleotides for highly efficient site-selective RNA scission. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.03.102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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37
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Chen W, Igawa T, Sumaoka J, Komiyama M. Monophosphate as Eminent Ligand to Bind Ce(IV)/EDTA Complex for Site-selective DNA Hydrolysis. CHEM LETT 2004. [DOI: 10.1246/cl.2004.300] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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38
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Yamamoto Y, Tsuboi W, Komiyama M. Oligoamine-acridine conjugates for promotion of gap-selective DNA hydrolysis by Ce(IV)/EDTA complex. Nucleic Acids Res 2003; 31:4497-502. [PMID: 12888510 PMCID: PMC169895 DOI: 10.1093/nar/gkg634] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Oligoamines (spermidine, dipropylenetriamine and propylenediamine) were covalently attached to acridine via a hexamethylene linker. These oligoamine-acridine conjugates were efficiently bound to gap sites in substrate DNA, and promoted the DNA hydrolysis by a homogeneous Ce(IV)/ethylenediamine-N,N,N',N'-tetraacetate (EDTA) complex at these sites. In contrast, the hydrolysis of the double-stranded portion in the DNA was little affected by these conjugates, although they were strongly bound thereto by the intercalation of their acridine moieties. As a result, the gap site was selectively and efficiently hydrolyzed by combining the Ce(IV)/EDTA complex with the oligoamine--acridine conjugate. Either the oligoamine or the acridine was only poorly active for the purpose, substantiating the essential role of cooperation between them. The promotion of gap-selective DNA hydrolysis by the conjugates has been ascribed to electrostatic stabilization of a negatively charged transition state by their positive charges.
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Affiliation(s)
- Yoji Yamamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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39
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Shi Y, Kuzuya A, Komiyama M. Stereochemically Pure Acridine-modified DNA for Site-selective Activation and Scission of RNA. CHEM LETT 2003. [DOI: 10.1246/cl.2003.464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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40
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Whitney A, Gavory G, Balasubramanian S. Site-specific cleavage of human telomerase RNA using PNA-neocuproine.Zn(II) derivatives. Chem Commun (Camb) 2003:36-7. [PMID: 12610953 DOI: 10.1039/b210135a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we report the synthesis of a novel PNA based neocuproine.Zn RNA cleaving agent; we demonstrate that such agents sequence specifically cleave a synthetic RNA target and in particular the RNA component of human telomerase.
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Affiliation(s)
- Andrew Whitney
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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42
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43
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Komiyama M, Kuzuya A, Mizoguchi R. Site-Selective Activation of RNA Leading to Sequence-Selective RNA Cutters. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2002. [DOI: 10.1246/bcsj.75.2547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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44
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Kuzuya A, Machida K, Komiyama M. A highly acidic acridine for efficient site-selective activation of RNA leading to an eminent ribozyme mimic. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)02017-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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45
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Kitamura Y, Komiyama M. Preferential hydrolysis of gap and bulge sites in DNA by Ce(IV)/EDTA complex. Nucleic Acids Res 2002; 30:e102. [PMID: 12364619 PMCID: PMC140562 DOI: 10.1093/nar/gnf101] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A new strategy for site-selective DNA hydrolysis, which takes advantage of the difference in reactivity between the phosphodiester linkages at the target site and the others, is presented. As the molecular scissors, homogeneous Ce(IV)/ethylenediamine-N,N,N',N'-tetraacetate (EDTA) complex is used without being bound to any sequence-recognizing moiety. When a gap structure is formed at the target site by using two short oligonucleotides and the composite is treated with the Ce(IV)/EDTA complex at pH 7.0 and 37 degrees C, the gap site in the substrate DNA is preferentially hydrolyzed over the double-stranded portion of the DNA. Site-selective DNA scission is also achieved by forming a bulge structure at the target site with the use of the appropriate oligonucleotide. These site-selective scissions are based on the following two factors: (i) the phosphodiester linkages in a single-stranded DNA are far more susceptible to the hydrolysis by the Ce(IV) complex than are the linkages in double-stranded DNA, and (ii) the phosphodiester linkages in the bulge sites are still more reactive than those in single-stranded DNA. In both cases, the addition of spermine significantly accelerates the scission.
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Affiliation(s)
- Yoshihito Kitamura
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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