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Komiyama M. Ce-based solid-phase catalysts for phosphate hydrolysis as new tools for next-generation nanoarchitectonics. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2023; 24:2250705. [PMID: 37701758 PMCID: PMC10494760 DOI: 10.1080/14686996.2023.2250705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/06/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023]
Abstract
This review comprehensively covers synthetic catalysts for the hydrolysis of biorelevant phosphates and pyrophosphates, which bridge between nanoarchitectonics and biology to construct their interdisciplinary hybrids. In the early 1980s, remarkable catalytic activity of Ce4+ ion for phosphate hydrolysis was found. More recently, this finding has been extended to Ce-based solid catalysts (CeO2 and Ce-based metal-organic frameworks (MOFs)), which are directly compatible with nanoarchitectonics. Monoesters and triesters of phosphates, as well as pyrophosphates, were effectively cleaved by these catalysts. With the use of either CeO2 nanoparticles or elegantly designed Ce-based MOF, highly stable phosphodiester linkages were also hydrolyzed. On the surfaces of all these solid catalysts, Ce4+ and Ce3+ coexist and cooperate for the catalysis. The Ce4+ activates phosphate substrates as a strong acid, whereas the Ce3+ provides metal-bound hydroxide as an eminent nucleophile. Applications of these Ce-based catalysts to practical purposes are also discussed.
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Affiliation(s)
- Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo, Japan
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Du J, Qi S, Chen J, Yang Y, Fan T, Zhang P, Zhuo S, Zhu C. Fabrication of highly active phosphatase-like fluorescent cerium-doped carbon dots for in situ monitoring the hydrolysis of phosphate diesters. RSC Adv 2020; 10:41551-41559. [PMID: 35516543 PMCID: PMC9057792 DOI: 10.1039/d0ra07429b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/07/2020] [Indexed: 12/13/2022] Open
Abstract
The hydrolytic cleavage of BNPP was catalyzed and monitored by the fluorescent CeCDs.
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Affiliation(s)
- Jinyan Du
- Anhui Key Laboratory of Chemo-Biosensing
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Shuangqing Qi
- Anhui Key Laboratory of Chemo-Biosensing
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Juan Chen
- Anhui Key Laboratory of Chemo-Biosensing
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Ying Yang
- Anhui Key Laboratory of Chemo-Biosensing
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Tingting Fan
- Anhui Key Laboratory of Chemo-Biosensing
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Ping Zhang
- Anhui Key Laboratory of Chemo-Biosensing
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Shujuan Zhuo
- Anhui Key Laboratory of Chemo-Biosensing
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- College of Chemistry and Materials Science
- Anhui Normal University
| | - Changqing Zhu
- Anhui Key Laboratory of Chemo-Biosensing
- Key Laboratory of Functional Molecular Solids
- Ministry of Education
- College of Chemistry and Materials Science
- Anhui Normal University
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Sugiyama T, Hasegawa G, Niikura C, Kuwata K, Imamura Y, Demizu Y, Kurihara M, Kittaka A. PNA monomers fully compatible with standard Fmoc-based solid-phase synthesis of pseudocomplementary PNA. Bioorg Med Chem Lett 2017; 27:3337-3341. [PMID: 28610975 DOI: 10.1016/j.bmcl.2017.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 11/18/2022]
Abstract
Here we report the synthesis of new PNA monomers for pseudocomplementary PNA (pcPNA) that are fully compatible with standard Fmoc chemistry. The thiocarbonyl group of the 2-thiouracil (sU) monomer was protected with the 4-methoxy-2-methybenzyl group (MMPM), while the exocyclic amino groups of diaminopurine (D) were protected with Boc groups. The newly synthesized monomers were incorporated into a 10-mer PNA oligomer using standard Fmoc chemistry for solid-phase synthesis. Oligomerization proceeded smoothly and the HPLC and MALDI-TOF MS analyses indicated that there was no remaining MMPM on the sU nucleobase. The new PNA monomers reported here would facilitate a wide range of applications, such as antigene PNAs and DNA nanotechnologies.
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Affiliation(s)
- Toru Sugiyama
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
| | - Genki Hasegawa
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Chie Niikura
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa-ku, Nagoya 464-8601, Japan
| | - Yasutada Imamura
- Faculty of Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Ministry of Health and Welfare, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan
| | - Masaaki Kurihara
- School of Pharmacy, International University of Health and Welfare, 2600-1, Kitakanemaru, Ohtawara, Tochigi 324-8501, Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi-ku, Tokyo 173-8605, Japan.
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Komiyama M. Design of Highly Active Ce(IV) Catalysts for DNA Hydrolysis and Their Applications. CHEM LETT 2016. [DOI: 10.1246/cl.160786] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Asanuma H, Niwa R, Akahane M, Murayama K, Kashida H, Kamiya Y. Strand-invading linear probe combined with unmodified PNA. Bioorg Med Chem 2016; 24:4129-4137. [PMID: 27394693 DOI: 10.1016/j.bmc.2016.06.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/23/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022]
Abstract
Efficient strand invasion by a linear probe to fluorescently label double-stranded DNA has been implemented by employing a probe and unmodified PNA. As a fluorophore, we utilized ethynylperylene. Multiple ethynylperylene residues were incorporated into the DNA probe via a d-threoninol scaffold. The ethynylperylene did not significantly disrupt hybridization with complementary DNA. The linear probe self-quenched in the absence of target DNA and did not hybridize with PNA. A gel-shift assay revealed that linear probe and PNA combination invaded the central region of double-stranded DNA upon heat-shock treatment to form a double duplex. To further suppress the background emission and increase the stability of the probe/DNA duplex, a probe containing anthraquinones as well as ethynylperylene was synthesized. This probe and PNA invader pair detected an internal sequence in a double-stranded DNA with high sensitivity when heat shock treatment was used. The probe and PNA pair was able to invade at the terminus of a long double-stranded DNA at 40°C at 100mM NaCl concentration.
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Affiliation(s)
- Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
| | - Rie Niwa
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Mariko Akahane
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yukiko Kamiya
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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Futai K, Sumaoka J, Komiyama M. Fabrication of DNA/RNA Hybrids Through Sequence-Specific Scission of Both Strands by pcPNA-S1 Nuclease Combination. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 35:233-44. [PMID: 27057646 DOI: 10.1080/15257770.2015.1131294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
By combining two strands of pseudo-complementary peptide nucleic acid (pcPNA) with S1 nuclease, a tool for site-selective and dual-strand scission of DNA/RNA hybrids has been developed. Both of the DNA and the RNA strands in the hybrids are hydrolyzed at desired sites to provide unique sticky ends. The scission fragments are directly ligated with other DNA/RNA hybrids by using T4 DNA ligase, resulting in the formation of desired recombinant DNA/RNA hybrids.
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Kameshima W, Ishizuka T, Minoshima M, Yamamoto M, Sugiyama H, Xu Y, Komiyama M. Conjugation of peptide nucleic acid with a pyrrole/imidazole polyamide to specifically recognize and cleave DNA. Angew Chem Int Ed Engl 2013; 52:13681-4. [PMID: 24155125 DOI: 10.1002/anie.201305489] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/03/2013] [Indexed: 11/06/2022]
Abstract
Cut loose: A pseudocomplementary peptide nucleic acid was tethered to a pyrrole/imidazole hairpin polyamide, and was used to selectively target a specific DNA sequence. Binding even occurs under high salt conditions. Furthermore, the conjugate facilitated sequence-specific scission of long dsDNA. This simple approach promises to resolve the technical difficulties in targeting DNA sequences with PNA.
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Affiliation(s)
- Wataru Kameshima
- 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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Kameshima W, Ishizuka T, Minoshima M, Yamamoto M, Sugiyama H, Xu Y, Komiyama M. Conjugation of Peptide Nucleic Acid with a Pyrrole/Imidazole Polyamide to Specifically Recognize and Cleave DNA. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Matsumoto K, Nakata E, Tamura T, Saito I, Aizawa Y, Morii T. A peptide nucleic acid (PNA) heteroduplex probe containing an inosine-cytosine base pair discriminates a single-nucleotide difference in RNA. Chemistry 2013; 19:5034-40. [PMID: 23494894 DOI: 10.1002/chem.201204183] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Indexed: 11/07/2022]
Abstract
Selective discrimination of a single-nucleotide difference in single-stranded DNA or RNA remains a challenge with conventional DNA or RNA probes. A peptide nucleic acid (PNA)-derived probe, in which PNA forms a pseudocomplementary heteroduplex with inosine-containing DNA or RNA, effectively discriminates a single-nucleotide difference in a closely related group of sequences of single-stranded DNA and/or RNA. The pseudocomplementary PNA heteroduplex is easily converted to a fluorescent probe that distinctively detects a member of highly homologous let-7 microRNAs.
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Komiyama M. Cut-and-Paste of DNA Using an Artificial Restriction DNA Cutter. Int J Mol Sci 2013; 14:3343-57. [PMID: 23385238 PMCID: PMC3588047 DOI: 10.3390/ijms14023343] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/28/2013] [Accepted: 01/30/2013] [Indexed: 12/29/2022] Open
Abstract
DNA manipulations using a completely chemistry-based DNA cutter (ARCUT) have been reviewed. This cutter, recently developed by the authors, is composed of Ce(IV)/EDTA complex and two strands of pseudo-complementary peptide nucleic acid. The site-selective scission proceeds via hydrolysis of targeted phosphodiester linkages, so that the resultant scission fragments can be easily ligated with other fragments by using DNA ligase. Importantly, scission-site and site-specificity of the cutter are freely tuned in terms of the Watson-Crick rule. Thus, when one should like to manipulate DNA according to the need, he or she does not have to think about (1) whether appropriate "restriction enzyme sites" exist near the manipulation site and (2) whether the site-specificity of the restriction enzymes, if any, are sufficient to cut only the aimed position without chopping the DNA at non-targeted sites. Even the human genome can be manipulated, since ARCUT can cut the genome at only one predetermined site. Furthermore, the cutter is useful to promote homologous recombination in human cells, converting a site to desired sequence. The ARCUT-based DNA manipulation should be promising for versatile applications.
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Affiliation(s)
- Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.
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Komiyama M, Sumaoka J. Design and Applications of Artificial Restriction DNA Cutters for Site-Selective Scission of Genomes. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20110318] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo
| | - Jun Sumaoka
- Research Center for Advanced Science and Technology, The University of Tokyo
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12
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Abstract
The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is still a fascinating challenge. Over the years, many examples have been reported reproducing part of the behaviour of the corresponding natural enzymes. Eventually, even the possibility to apply such systems to the manipulation of DNA of higher organisms has been demonstrated. However, efficiency of enzymes is still unrivalled. This feature article discusses the progress reported toward the realization of synthetic nucleases with particular attention to the comprehension of the reaction mechanisms and to the strategies that need to be addressed to obtain more efficient systems.
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Affiliation(s)
- Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, I -35131 Padova, Italy.
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Wang Y, Zhu Y, Wang Y, Chen G. Structural analysis of zinc-finger (TTK) + [Cu(BPA)]2+ /[Cu(IDB)]2+ + DNA complexes: an investigation by molecular dynamics simulation. J Mol Recognit 2011; 24:981-94. [PMID: 22038805 DOI: 10.1002/jmr.1146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the present study, the molecular dynamics simulation technique is employed to investigate the hydrogen abstraction possibility from sugar of DNA in two designed complexes of copper-based chemical nuclease [Cu(BPA)](2+) bis(2-pyridylmethyl) amine (BPA) or [Cu(IDB)](2+) N,N-bis(2-benzimidazolylmethyl) amine (IDB) bound to the zinc finger protein Tramtrack (TTK). The simulated results show that each of the designed complexes can form a stable conformation within 30 ns of simulation time with the substrate OOH(-) and an 18-base pair (bp) DNA segment and is located in the major groove of the DNA segment. The active terminal O atom of the OOH(-) substrate is found in close proximity to the target C2'H, C3'H, C4'H or C5'H proton of the DNA in TTK + [Cu(BPA)OOH](+) + DNA or TTK + [Cu(IDB)OOH](+) + DNA complex, which is crucial to propose the hydrogen abstraction possibility that is responsible for the DNA cleavage. The positions of copper-based chemical nucleases bound to TTK may substantially influence the hydrogen abstraction possibility. The structures and sizes of ligands in copper-based nucleases are also found to have influence on the order of difficulty of the hydrogen abstraction from the sugars of DNA.
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Affiliation(s)
- Yaru Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
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Wang MQ, Liu JL, Wang JY, Zhang DW, Zhang J, Streckenbach F, Tang Z, Lin HH, Liu Y, Zhao YF, Yu XQ. Site-selective DNA hydrolysis induced by a metal-free peptide nucleic acid-cyclen conjugate. Chem Commun (Camb) 2011; 47:11059-61. [PMID: 21901188 DOI: 10.1039/c1cc14185f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A metal-free artificial restriction DNA cutter which is composed of cyclen and classical peptide nucleic acid (PNA) was synthesized. Analysis of DNA cleavage products indicates the site-selective hydrolysis.
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Affiliation(s)
- Ming-Qi Wang
- Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu, 610064, PR China
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Doyle SR, Chan CK, Grant WN. Enhanced annealing of mismatched oligonucleotides using a novel melting curve assay allows efficient in vitro discrimination and restriction of a single nucleotide polymorphism. BMC Biotechnol 2011; 11:83. [PMID: 21875442 PMCID: PMC3175457 DOI: 10.1186/1472-6750-11-83] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 08/30/2011] [Indexed: 11/25/2022] Open
Abstract
Background Many SNP discrimination strategies employ natural restriction endonucleases to discriminate between allelic states. However, SNPs are often not associated with a restriction site and therefore, a number of attempts have been made to generate sequence-adaptable restriction endonucleases. In this study, a simple, sequence-adaptable SNP discrimination mechanism between a 'wild-type' and 'mutant' template is demonstrated. This model differs from other artificial restriction endonuclease models as cis- rather than trans-orientated regions of single stranded DNA were generated and cleaved, and therefore, overcomes potential issues of either inefficient or non-specific binding when only a single variant is targeted. Results A series of mismatch 'bubbles' that spanned 0-5-bp surrounding a point mutation was generated and analysed for sensitivity to S1 nuclease. In this model, generation of oligonucleotide-mediated ssDNA mismatch 'bubbles' in the presence of S1 nuclease resulted in the selective degradation of the mutant template while maintaining wild-type template integrity. Increasing the size of the mismatch increased the rate of mutant sequence degradation, until a threshold above which discrimination was lost and the wild-type sequence was degraded. This level of fine discrimination was possible due to the development of a novel high-resolution melting curve assay to empirically determine changes in Tm (~5.0°C per base-pair mismatch) and to optimise annealing conditions (~18.38°C below Tm) of the mismatched oligonucleotide sets. Conclusions The in vitro 'cleavage bubble' model presented is sequence-adaptable as determined by the binding oligonucleotide, and hence, has the potential to be tailored to discriminate between any two or more SNPs. Furthermore, the demonstrated fluorometric assay has broad application potential, offering a rapid, sensitive and high-throughput means to determine Tm and annealing rates as an alternative to conventional hybridisation detection strategies.
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Affiliation(s)
- Stephen R Doyle
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.
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Aiba Y, Sumaoka J, Komiyama M. Artificial DNA cutters for DNA manipulation and genome engineering. Chem Soc Rev 2011; 40:5657-68. [PMID: 21566825 DOI: 10.1039/c1cs15039a] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This tutorial review provides recent developments in artificial cutters for site-selective scission of DNA with the focus on chemistry-based DNA cutters. They are useful tools for molecular biology and biotechnology, since their site-selectivity of scission is much higher than that of naturally occurring restriction enzymes and also their scission site is freely chosen. In order to prepare these cutters, a DNA-cutting molecule is combined with a sequence-recognizing molecule in a covalent or non-covalent way. At targeted sites in single-stranded and double-stranded DNAs, the scission occurs via either oxidative cleavage of nucleotides or hydrolysis of phosphodiester linkages. Among many successful examples, an artificial restriction DNA cutter, prepared from Ce(iv)/EDTA and pseudo-complementary peptide nucleic acid, hydrolyzed double-stranded DNA at the target site. The scission site and scission specificity are determined simply in terms of the Watson-Crick rule so that even the whole genome of human beings was selectively cut at one predetermined site. Consistently, homologous recombination in human cells was successfully promoted by this tool. For the purpose of comparison, protein-based DNA cutters (e.g., zinc finger nucleases) are also briefly described. The potential applications of these cutters and their future aspects are discussed.
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Affiliation(s)
- Yuichiro Aiba
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
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Ullrich S, Nazir Z, Büsing A, Scheffer U, Wirth D, Bats JW, Dürner G, Göbel MW. Cleavage of phosphodiesters and of DNA by a bis(guanidinium)naphthol acting as a metal-free anion receptor. Chembiochem 2011; 12:1223-9. [PMID: 21500334 DOI: 10.1002/cbic.201100022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Indexed: 11/07/2022]
Abstract
Phosphoric acid diesters form anions at neutral pH. As a result of charge repulsion they are notoriously resistant to hydrolysis. Nucleophilic attack, however, can be promoted by different types of electrophilic catalysts that bind to the anions and reduce their negative charge density. Although in most cases phosphodiester-cleaving enzymes and synthetic catalysts rely on Lewis acidic metal ions, some exploit the guanidinium residues of arginine as metal-free electrophiles. Here we report that a combination of two guanidines and a hydroxy group yields highly reactive receptor molecules that can attack a broad range of phosphodiester substrates by nucleophilic displacement at phosphorus in a single-turnover mode. Some stable O-phosphates were isolated and characterized further by NMR spectroscopy. The bis(guanidinium)naphthols also cleave plasmid DNA, presumably by a transphosphorylation mechanism.
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Affiliation(s)
- Stefan Ullrich
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany
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Ito K, Katada H, Shigi N, Komiyama M. Site-selective scission of human genome by artificial restriction DNA cutter. Chem Commun (Camb) 2009:6542-4. [PMID: 19865643 DOI: 10.1039/b911208a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By using an artificial restriction DNA cutter which is composed of Ce(iv)/EDTA and two pseudo-complementary peptide nucleic acid strands (pcPNAs), only one target site in the whole genome of human beings (one site in the X chromosome) was selectively hydrolyzed.
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Affiliation(s)
- Kenichiro Ito
- 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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Miyajima Y, Ishizuka T, Yamamoto Y, Sumaoka J, Komiyama M. Origin of high fidelity in target-sequence recognition by PNA-Ce(IV)/EDTA combinations as site-selective DNA cutters. J Am Chem Soc 2009; 131:2657-62. [PMID: 19199631 DOI: 10.1021/ja808290e] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Double-duplex invasion of pseudocomplementary peptide nucleic acid (pcPNA) is one of the most important strategies for recognizing a specific site in double-stranded DNA (Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11804-11808). This strategy has recently been used to develop artificial restriction DNA cutters (ARCUTs) for site-selective scission of double-stranded DNA, in which a hot spot formed by double-duplex invasion of PNA was hydrolyzed by Ce(IV)/EDTA (Nat. Protoc. 2008, 3, 655-662). The present paper shows how and where the target sequence in double-stranded DNA is recognized by the PNA-Ce(IV)/EDTA combinations for site-selective scission. The mismatch-recognizing activities in both the invasion process and the whole scission process are evaluated. When both pcPNA additives are completely complementary to each strand of the DNA, site-selective scission is the most efficient, as expected. Upon exchange of one DNA base pair at the invasion site with another base pair, which introduces mismatches between the pcPNAs and the DNA, the site-selective scission by the ARCUT is notably diminished. Mismatches in (or near) the central double-invasion region are especially fatal, showing that Watson-Crick pairings of the DNA bases in this region with the pcPNA strands are essential for precise recognition of the target sequence. Both gel-shift assays and melting temperature measurements on the double-duplex invasion process have confirmed that the fidelity in this process primarily governs the fidelity of the DNA scission. According to these systematic analyses, the typical ARCUT involving two 15-mer pcPNAs precisely recognizes 14-16 base pairs in substrate DNA. This remarkable fidelity is accomplished at rather high salt concentrations that are similar to the values in cells.
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Affiliation(s)
- Yoshitaka Miyajima
- 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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Ihara T, Sasahara D, Shimizu M, Jyo A. DNA conjugates bearing a ferrocenyl group in backbone and their electrochemical behaviour. Supramol Chem 2009. [DOI: 10.1080/10610270802468405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Toshihiro Ihara
- a Department of Applied Chemistry and Biochemistry , Graduate School of Science and Technology, Kumamoto University , Kumamoto, Japan
| | - Daisuke Sasahara
- a Department of Applied Chemistry and Biochemistry , Graduate School of Science and Technology, Kumamoto University , Kumamoto, Japan
| | - Masamichi Shimizu
- a Department of Applied Chemistry and Biochemistry , Graduate School of Science and Technology, Kumamoto University , Kumamoto, Japan
| | - Akinori Jyo
- a Department of Applied Chemistry and Biochemistry , Graduate School of Science and Technology, Kumamoto University , Kumamoto, Japan
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Belousoff MJ, Ung P, Forsyth CM, Tor Y, Spiccia L, Graham B. New macrocyclic terbium(III) complex for use in RNA footprinting experiments. J Am Chem Soc 2009; 131:1106-14. [PMID: 19119812 PMCID: PMC2633772 DOI: 10.1021/ja807301r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Reaction of terbium triflate with a heptadentate ligand derivative of cyclen, L1 = 2-[7-ethyl-4,10-bis(isopropylcarbamoylmethyl)-1,4,7,10-tetraazacyclododec-1-yl]-N-isopropyl-acetamide, produced a new synthetic ribonuclease, [Tb(L1)(OTf)(OH(2))](OTf)(2).MeCN (C1). X-ray crystal structure analysis indicates that the terbium(III) center in C1 is 9-coordinate, with a capped square-antiprism geometry. While the terbium(III) center is tightly bound by the L1 ligand, two of the coordination sites are occupied by labile water and triflate ligands. In water, the triflate ligand is likely to be displaced, forming [Tb(L1)(OH(2))(2)](3+), which is able to effectively promote RNA cleavage. This complex greatly accelerates the rate of intramolecular transesterification of an activated model RNA phosphodiester, uridine-3'-p-nitrophenylphosphate (UpNP), with k(obs) = 5.5(1) x 10(-2) s(-1) at 21 degrees C and pH 7.5, corresponding to an apparent second-order rate constant of 277(5) M(-1) s(-1). By contrast, the analogous complex of an octadentate derivative of cyclen featuring only a single labile coordination site, [Tb(L2)(OH(2))](OTf)(3) (C2), where L2 = 2-[4,7,10-tris(isopropylcarbamoylmethyl)-1,4,7,10-tetraazacyclododec-1-yl]-N-isopropyl-acetamide, is inactive. [Tb(L1)(OH(2))(2)](3+) is also capable of hydrolyzing short transcripts of the HIV-1 transactivation response (TAR) element, HIV-1 dimerization initiation site (DIS) and ribosomal A-site, as well as formyl methionine tRNA (tRNA(fMet)), albeit at a considerably slower rate than UpNP transesterification (k(obs) = 2.78(8) x 10(-5) s(-1) for TAR cleavage at 37 degrees C, pH 6.5, corresponding to an apparent second-order rate constant of 0.56(2) M(-1)s(-1)). Cleavage is concentrated at the single-stranded "bulge" regions of these RNA motifs. Exploiting this selectivity, [Tb(L1)(OH(2))(2)](3+) was successfully employed in footprinting experiments, in which binding of the Tat peptide and neomycin B to the bulge region of the TAR stem-loop was confirmed.
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Affiliation(s)
- Matthew J. Belousoff
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
| | - Phuc Ung
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
| | - Craig M. Forsyth
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
| | - Leone Spiccia
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
| | - Bim Graham
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
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23
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Zhu Y, Wang Y, Chen G. Molecular Dynamics Simulations on Binding Models of Dervan-Type Polyamide + Cu(II) Nuclease Ligands to DNA. J Phys Chem B 2008; 113:839-48. [DOI: 10.1021/jp8091545] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanyan Zhu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Yan Wang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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24
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Komiyama M, Aiba Y, Yamamoto Y, Sumaoka J. Artificial restriction DNA cutter for site-selective scission of double-stranded DNA with tunable scission site and specificity. Nat Protoc 2008; 3:655-62. [PMID: 18388948 DOI: 10.1038/nprot.2008.7] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The artificial restriction DNA cutter (ARCUT) method to cut double-stranded DNA at designated sites has been developed. The strategy at the base of this approach, which does not rely on restriction enzymes, is comprised of two stages: (i) two strands of pseudo-complementary peptide nucleic acid (pcPNA) anneal with DNA to form 'hot spots' for scission, and (ii) the Ce(IV)/EDTA complex acts as catalytic molecular scissors. The scission fragments, obtained by hydrolyzing target phosphodiester linkages, can be connected with foreign DNA using DNA ligase. The location of the scission site and the site-specificity are almost freely tunable, and there is no limitation to the size of DNA substrate. This protocol, which does not include the synthesis of pcPNA strands, takes approximately 10 d to complete. The synthesis and purification of the pcPNA, which are covered by a related protocol by the same authors, takes an additional 7 d, but pcPNA can also be ordered from custom synthesis companies if necessary.
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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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25
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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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26
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Yamamoto Y, Uehara A, Miura K, Watanabe A, Aburatani H, Komiyama M. Development of artificial restriction DNA cutter composed of Ce(Iv)/EDTA and PNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1265-8. [PMID: 18066765 DOI: 10.1080/15257770701528321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
An artificial restriction enzyme, which we developed recently by combining Ce(IV)/EDTA and peptide nucleic acids, was used for PCR-free construction of a fusion protein. The fusion protein was successfully expressed in mammalian cells. This artificial DNA cutter can be also applied to site-selective scission of huge DNAs. Promising features of this novel tool were concretely evidenced.
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Affiliation(s)
- Yoji Yamamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Muguro-ku, Tokyo, Japan
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27
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Ishizuka T, Yoshida J, Yamamoto Y, Sumaoka J, Tedeschi T, Corradini R, Sforza S, Komiyama M. Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences. Nucleic Acids Res 2008; 36:1464-71. [PMID: 18203747 PMCID: PMC2275137 DOI: 10.1093/nar/gkm1154] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 12/12/2007] [Accepted: 12/12/2007] [Indexed: 11/12/2022] Open
Abstract
Invasion of two PNA strands to double-stranded DNA is one of the most promising methods to recognize a predetermined site in double-stranded DNA (PNA = peptide nucleic acid). In order to facilitate this 'double-duplex invasion', a new type of PNA was prepared by using chiral PNA monomers in which a nucleobase was bound to the alpha-nitrogen of N-(2-aminoethyl)-d-lysine. These positively charged monomer units, introduced to defined positions in Nielsen's PNAs (poly[N-(2-aminoethyl)glycine] derivatives), promoted the invasion without impairing mismatch-recognizing activity. When pseudo-complementary nucleobases 2,6-diaminopurine and 2-thiouracil were bound to N-(2-aminoethyl)-d-lysine, the invasion successfully occurred even at highly G-C-rich regions [e.g. (G/C)7(A/T)3 and (G/C)8(A/T)2] which were otherwise hardly targeted. Thus, the scope of sequences available as the target site has been greatly expanded. In contrast with the promotion by the chiral PNA monomers derived from N-(2-aminoethyl)-d-lysine, their l-isomers hardly invaded, showing crucial importance of the d-chirality. The promotion of double-duplex invasion by the chiral (d) PNA monomer units was ascribed to both destabilization of PNA/PNA duplex and stabilization of PNA/DNA duplexes.
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Affiliation(s)
- Takumi Ishizuka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Junya Yoshida
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Yoji Yamamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Jun Sumaoka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Tullia Tedeschi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Roberto Corradini
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Stefano Sforza
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
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28
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Katada H, Seino H, Mizobe Y, Sumaoka J, Komiyama M. Crystal structure of Ce(IV)/dipicolinate complex as catalyst for DNA hydrolysis. J Biol Inorg Chem 2007; 13:249-55. [PMID: 17987328 DOI: 10.1007/s00775-007-0315-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 10/25/2007] [Indexed: 11/28/2022]
Abstract
The structures of Ce(4+) complexes that are active for DNA hydrolysis were determined for the first time by X-ray crystallography. The crystals were prepared from a 1:2 mixture of Ce(NH(4))(2)(NO(3))(6) and dipicolinic acid (2,6-pyridinedicarboxylic acid). Depending on the recrystallization conditions, three types of crystals were obtained. Some of the Ce(4+) ions in these complexes have enough coordinated water molecules that can directly and indirectly participate in the catalysis. The distances between the Ce(4+) and the dipicolinate ligand are considerably shorter than those in the corresponding La(3+) and Ce(3+) complexes. On the other hand, the distances between the Ce(4+) and its coordinated water are similar to those for the La(3+) and Ce(3+) complexes. In a proposed mechanism of DNA hydrolysis, the scissile phosphodiester linkage is notably activated by coordination to Ce(4+) and attacked by the Ce(4+)-bound hydroxide. The process is further assisted by acid catalysis of Ce(4+)-bound water.
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Affiliation(s)
- Hitoshi Katada
- The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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29
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Kim KH, Nielsen PE, Glazer PM. Site-directed gene mutation at mixed sequence targets by psoralen-conjugated pseudo-complementary peptide nucleic acids. Nucleic Acids Res 2007; 35:7604-13. [PMID: 17977869 PMCID: PMC2190703 DOI: 10.1093/nar/gkm666] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Sequence-specific DNA-binding molecules such as triple helix-forming oligonucleotides (TFOs) provide a means for inducing site-specific mutagenesis and recombination at chromosomal sites in mammalian cells. However, the utility of TFOs is limited by the requirement for homopurine stretches in the target duplex DNA. Here, we report the use of pseudo-complementary peptide nucleic acids (pcPNAs) for intracellular gene targeting at mixed sequence sites. Due to steric hindrance, pcPNAs are unable to form pcPNA–pcPNA duplexes but can bind to complementary DNA sequences by Watson–Crick pairing via double duplex-invasion complex formation. We show that psoralen-conjugated pcPNAs can deliver site-specific photoadducts and mediate targeted gene modification within both episomal and chromosomal DNA in mammalian cells without detectable off-target effects. Most of the induced psoralen-pcPNA mutations were single-base substitutions and deletions at the predicted pcPNA-binding sites. The pcPNA-directed mutagenesis was found to be dependent on PNA concentration and UVA dose and required matched pairs of pcPNAs. Neither of the individual pcPNAs alone had any effect nor did complementary PNA pairs of the same sequence. These results identify pcPNAs as new tools for site-specific gene modification in mammalian cells without purine sequence restriction, thereby providing a general strategy for designing gene targeting molecules.
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Affiliation(s)
- Ki-Hyun Kim
- Department of Therapeutic Radiology, Yale University School of Medicine, P.O. Box 208040, New Haven, CT 06520-8040, USA
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30
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Aiba Y, Yamamoto Y, Komiyama M. Activation of Double-stranded DNA by One pcPNA Strand for Its Site-selective Scission with CeIV/EDTA. CHEM LETT 2007. [DOI: 10.1246/cl.2007.780] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Yamamoto Y, Mori M, Aiba Y, Tomita T, Chen W, Zhou JM, Uehara A, Ren Y, Kitamura Y, Komiyama M. Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA. Nucleic Acids Res 2007; 35:e53. [PMID: 17376805 PMCID: PMC1874645 DOI: 10.1093/nar/gkm052] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A monophosphate group was attached to the terminus of pseudo-complementary peptide nucleic acid (pcPNA), and two of thus modified pcPNAs were combined with Ce(IV)/EDTA for site-selective hydrolysis of double-stranded DNA. The site-selective DNA scission was notably accelerated by this chemical modification of pcPNAs. These second-generation artificial restriction DNA cutters (ARCUTs) differentiated the target sequence so strictly that no scission occurred even when only one DNA base-pair was altered to another. By using two of the activated ARCUTs simultaneously, DNA substrate was selectively cut at two predetermined sites, and the desired fragment was clipped and cloned. The DNA scission by ARCUT was also successful even when the target site was methylated by methyltransferase and protected from the corresponding restriction enzyme. Furthermore, potentiality of ARCUT for manipulation of huge DNA has been substantiated by site-selective scission of genomic DNA of Escherichia coli (composed of 4,600,000 bp) at the target site. All these results indicate promising applications of ARCUTs for versatile purposes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Makoto Komiyama
- *To whom correspondence should be addressed. +81 3 5452 5200+81 3 5452 5209
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32
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Yamamoto Y, Uehara A, Watanabe A, Aburatani H, Komiyama M. Chemical-reaction-based site-selective DNA cutter for PCR-free gene manipulation. Chembiochem 2006; 7:673-7. [PMID: 16491499 DOI: 10.1002/cbic.200500402] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An artificial restriction DNA cutter (ARCUT), recently developed by the authors, was used to construct a fusion protein. The gene of WW-domain-containing oxidoreductase (WWOX) was cut by ARCUT just before its stop codon, and ligated to fuse the gene of enhanced green fluorescent protein (EGFP). The reading frames of two genes were adjusted to coincide each other. Throughout the manipulation, no PCR was employed. The fluorescent fusion protein was successfully expressed in mammalian cells, and showed entirely different subcellular localization from EGFP itself. Apparently, the DNA was kept completely intact during the manipulation. The man-made tool ARCUT has promising features for future biotechnology and molecular biology.
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Affiliation(s)
- Yoji Yamamoto
- Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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33
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Yamamoto Y, Miura K, Komiyama M. Site-specific Scission of Lambda Phage Genomic DNA by Ce(IV)/EDTA-based Artificial Restriction DNA Cutter. CHEM LETT 2006. [DOI: 10.1246/cl.2006.594] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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34
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Binnemans K. Chapter 229 Applications of tetravalent cerium compounds. HANDBOOK ON THE PHYSICS AND CHEMISTRY OF RARE EARTHS 2006. [DOI: 10.1016/s0168-1273(06)36003-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Lundin KE, Good L, Strömberg R, Gräslund A, Smith CIE. Biological activity and biotechnological aspects of peptide nucleic acid. ADVANCES IN GENETICS 2006; 56:1-51. [PMID: 16735154 DOI: 10.1016/s0065-2660(06)56001-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
During the latest decades a number of different nucleic acid analogs containing natural nucleobases on a modified backbone have been synthesized. An example of this is peptide nucleic acid (PNA), a DNA mimic with a noncyclic peptide-like backbone, which was first synthesized in 1991. Owing to its flexible and neutral backbone PNA displays very good hybridization properties also at low-ion concentrations and has subsequently attracted large interest both in biotechnology and biomedicine. Numerous modifications have been made, which could be of value for particular settings. However, the original PNA does so far perform well in many diverse applications. The high biostability makes it interesting for in vivo use, although the very limited diffusion over lipid membranes requires further modifications in order to make it suitable for treatment in eukaryotic cells. The possibility to use this nucleic acid analog for gene regulation and gene editing is discussed. Peptide nucleic acid is now also used for specific genetic detection in a number of diagnostic techniques, as well as for site-specific labeling and hybridization of functional molecules to both DNA and RNA, areas that are also discussed in this chapter.
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Affiliation(s)
- Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center Karolinska Institutet, Karolinska University Hospital, Huddinge 141 86 Stockholm, Sweden
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36
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Kitamura Y, Mori S, Chen W, Sumaoka J, Komiyama M. Recombination of the GFP gene to the BFP gene using a man-made site-selective DNA cutter. J Biol Inorg Chem 2005; 11:13-6. [PMID: 16341899 DOI: 10.1007/s00775-005-0063-8] [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] [Received: 09/14/2005] [Accepted: 11/11/2005] [Indexed: 11/26/2022]
Abstract
By using the recently developed man-made DNA cutter [a combination of Ce(IV)/EDTA and two DNA additives], green fluorescent protein (GFP) was converted to closely related blue fluorescent protein (BFP). The phosphodiester linkages at T196-A200 in the sense strand of GFP were hydrolyzed by the cutter, and the A1-T196 fragment in the product was selectively connected with the downstream fragment (C197-A720) of BFP by T4 DNA ligase. This recombination changed three codons in the GFP gene (TGC at 196-198, TAT at 199-201, and ACC at 502-504) to TCT, CAT, and ATC in BFP, and accordingly three amino acids in GFP (Cys65, Tyr66, and Thr167) were altered to Ser65, His66, and Ile167. The recombinant gene was successfully expressed in Escherichia coli and emitted blue fluorescence, confirming the absence of undesired side reactions (mutation, deletion, insertion, depurination, etc.) in the DNA manipulation.
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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, 153-8904 Tokyo, Japan
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Nakatsukasa T, Shiraishi Y, Negi S, Imanishi M, Futaki S, Sugiura Y. Site-specific DNA cleavage by artificial zinc finger-type nuclease with cerium-binding peptide. Biochem Biophys Res Commun 2005; 330:247-52. [PMID: 15781257 DOI: 10.1016/j.bbrc.2005.02.164] [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: 02/16/2005] [Indexed: 11/18/2022]
Abstract
The addition of a new function to native proteins is one of the most attractive protein-based designs. In this study, we have converted a C(2)H(2)-type zinc finger as a DNA-binding motif into a novel zinc finger-type nuclease by connecting two distinct zinc finger proteins (Sp1 and GLI) with a functional linker possessing DNA cleavage activity. As a DNA cleavage domain, we chose an analogue of the metal-binding loop (12 amino acid residues), peptide P1, which has been reported to exhibit a strong binding affinity for a lanthanide ion and DNA cleavage ability in the presence of Ce(IV). Our newly designed nucleases, Sp1(P1)GLI and Sp1(P1G)GLI, can strongly bind to a lanthanide ion and show a unique DNA cleavage pattern, in which certain positions between the two DNA-binding sites are specifically cleaved. The present result provides useful information for expanding the design strategy for artificial nucleases.
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Affiliation(s)
- Takako Nakatsukasa
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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Abstract
The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is a fascinating challenge that will show the way to obtaining artificial nucleases able to compete with the natural enzymes. This Feature Article highlights the progress reported toward the realization of synthetic nucleases with particular attention to the strategies that can be pursued to improve efficiency and sequence selectivity.
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Affiliation(s)
- Fabrizio Mancin
- Dipartimento di Scienze Chimiche and Istituto CNR di Tecnologia delle Membrane - Sezione di Padova, Università di Padova, via Marzolo 1, I-35131 Padova, Italy.
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