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Jin GQ, Chau CV, Arambula JF, Gao S, Sessler JL, Zhang JL. Lanthanide porphyrinoids as molecular theranostics. Chem Soc Rev 2022; 51:6177-6209. [PMID: 35792133 DOI: 10.1039/d2cs00275b] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In recent years, lanthanide (Ln) porphyrinoids have received increasing attention as theranostics. Broadly speaking, the term 'theranostics' refers to agents designed to allow both disease diagnosis and therapeutic intervention. This Review summarises the history and the 'state-of-the-art' development of Ln porphyrinoids as theranostic agents. The emphasis is on the progress made within the past decade. Applications of Ln porphyrinoids in near-infrared (NIR, 650-1700 nm) fluorescence imaging (FL), magnetic resonance imaging (MRI), radiotherapy, and chemotherapy will be discussed. The use of Ln porphyrinoids as photo-activated agents ('phototheranostics') will also be highlighted in the context of three promising strategies for regulation of porphyrinic triplet energy dissipation pathways, namely: regioisomeric effects, metal regulation, and the use of expanded porphyrinoids. The goal of this Review is to showcase some of the ongoing efforts being made to optimise Ln porphyrinoids as theranostics and as phototheranostics, in order to provide a platform for understanding likely future developments in the area, including those associated with structure-based innovations, functional improvements, and emerging biological activation strategies.
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Affiliation(s)
- Guo-Qing Jin
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China.
| | - Calvin V Chau
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, USA.
| | - Jonathan F Arambula
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, USA. .,InnovoTEX, Inc. 3800 N. Lamar Blvd, Austin, Texas 78756, USA.
| | - Song Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China. .,Chemistry and Chemical Engineering Guangdong Laboratory, Shantou 515031, P. R. China.,Guangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional Materials, Spin-X Institute, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510641, P. R. China
| | - Jonathan L Sessler
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, USA.
| | - Jun-Long Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China. .,Chemistry and Chemical Engineering Guangdong Laboratory, Shantou 515031, P. R. China
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2
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Putnam WC, Bashkin JK. Oligonucleotides containing abasic threoninol-terpyridine residues as potential artificial ribonucleases. J Inorg Biochem 2022; 232:111831. [DOI: 10.1016/j.jinorgbio.2022.111831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/24/2022]
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3
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Site-Selective Artificial Ribonucleases: Renaissance of Oligonucleotide Conjugates for Irreversible Cleavage of RNA Sequences. Molecules 2021; 26:molecules26061732. [PMID: 33808835 PMCID: PMC8003597 DOI: 10.3390/molecules26061732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
RNA-targeting therapeutics require highly efficient sequence-specific devices capable of RNA irreversible degradation in vivo. The most developed methods of sequence-specific RNA cleavage, such as siRNA or antisense oligonucleotides (ASO), are currently based on recruitment of either intracellular multi-protein complexes or enzymes, leaving alternative approaches (e.g., ribozymes and DNAzymes) far behind. Recently, site-selective artificial ribonucleases combining the oligonucleotide recognition motifs (or their structural analogues) and catalytically active groups in a single molecular scaffold have been proven to be a great competitor to siRNA and ASO. Using the most efficient catalytic groups, utilising both metal ion-dependent (Cu(II)-2,9-dimethylphenanthroline) and metal ion-free (Tris(2-aminobenzimidazole)) on the one hand and PNA as an RNA recognising oligonucleotide on the other, allowed site-selective artificial RNases to be created with half-lives of 0.5-1 h. Artificial RNases based on the catalytic peptide [(ArgLeu)2Gly]2 were able to take progress a step further by demonstrating an ability to cleave miRNA-21 in tumour cells and provide a significant reduction of tumour growth in mice.
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Zellmann F, Göbel MW. A Trisbenzimidazole Phosphoramidite Building Block Enables High-Yielding Syntheses of RNA-Cleaving Oligonucleotide Conjugates. Molecules 2020; 25:molecules25081842. [PMID: 32316292 PMCID: PMC7221912 DOI: 10.3390/molecules25081842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 12/03/2022] Open
Abstract
The RNA cleaving catalyst tris(2-aminobenzimidazole) when attached to the 5’ terminus of oligonucleotides cuts complementary RNA strands in a highly site-specific manner. Conjugation was previously achieved by the acylation of an amino linker by an active ester of the catalyst. However, this procedure was low yielding and not reliable. Here, a phosphoramidite building block is described that can be coupled to oligonucleotides by manual solid phase synthesis in total yields around 85%. Based on this chemistry, we have now studied the impact of LNA (locked nucleic acids) nucleotides on the rates and the site-specificities of RNA cleaving conjugates. The highest reaction rates and the most precise cuts can be expected when the catalyst is attached to a strong 5’ closing base pair and when the oligonucleotide contains several LNA units that are equally distributed in the strand. However, when placed in the 5’ position, LNA building blocks tend to diminish the specificity of RNA cleavage.
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Park S, Matsui H, Fukumoto K, Yum JH, Sugiyama H. Histidine-conjugated DNA as a biomolecular depot for metal ions. RSC Adv 2020; 10:9717-9722. [PMID: 35497221 PMCID: PMC9050151 DOI: 10.1039/d0ra01267j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 12/18/2022] Open
Abstract
Histidine is a versatile amino acid residue that plays a critical role in the active sites of many metalloenzymes. DNA is an attractive biomolecular scaffold owing to its chemical and thermal stability and easy accessibility. Herein, we report histidine-conjugated DNA oligonucleotides, which were synthesized by combining DNA alphabets and natural metal-binding amino acids, as novel biohybrid materials and demonstrate their use as molecular depots for various metal ions. Moreover, histidine-conjugated DNA oligonucleotides could be successfully used in asymmetric catalysis (up to 90% conversion and 95% ee) as DNA metalloenzymes and in 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) oxidation reactions as horseradish-peroxidase (HRP)-mimicking DNAzymes with suitable metal cofactors. Nature-inspired histidine-DNA hybrids will become an attractive strategy to construct fine-tuned coordination environments as an alternative to bioremediation and the development of multimetal enzymes. Histidine is a versatile amino acid residue that plays a critical role in the active sites of many metalloenzymes.![]()
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Affiliation(s)
- Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Haruka Matsui
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Koyuki Fukumoto
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Ji Hye Yum
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
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Brewster JT, Zafar H, Root HD, Thiabaud GD, Sessler JL. Porphyrinoid f-Element Complexes. Inorg Chem 2019; 59:32-47. [DOI: 10.1021/acs.inorgchem.9b00884] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- James T. Brewster
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Hadiqa Zafar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Harrison D. Root
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Gregory D. Thiabaud
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Jonathan L. Sessler
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
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Site-Specific Cleavage of RNAs Derived from the PIM1 3'-UTR by a Metal-Free Artificial Ribonuclease. Molecules 2019; 24:molecules24040807. [PMID: 30813393 PMCID: PMC6412833 DOI: 10.3390/molecules24040807] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 02/19/2019] [Indexed: 11/16/2022] Open
Abstract
Oligonucleotide conjugates of tris(2-aminobenzimidazole) have been reported previously to cleave complementary RNA strands with high levels of sequence and site specificity. The RNA substrates used in these studies were oligonucleotides not longer than 29-mers. Here we show that ~150⁻400-mer model transcripts derived from the 3'-untranslated region of the PIM1 mRNA reacted with rates and specificities comparable to those of short oligonucleotide substrates. The replacement of DNA by DNA/LNA mixmers further increased the cleavage rate. Tris(2-aminobenzimidazoles) were designed to interact with phosphates and phosphate esters. A cell, however, contains large amounts of phosphorylated species that may cause competitive inhibition of RNA cleavage. It is thus important to note that no loss in reaction rates was observed in phosphate buffer. This opens the way to in-cell applications for this type of artificial nuclease. Furthermore, we disclose a new synthetic method giving access to tris(2-aminobenzimidazoles) in multigram amounts.
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Chang CA, Lee HY, Lin SL, Meng CN, Wu TT. Dinuclear Lanthanide(III)-m-ODO2A-dimer Macrocyclic Complexes: Solution Speciation, DFT Calculations, Luminescence Properties, and Promoted Nitrophenyl-Phosphate Hydrolysis Rates. Chemistry 2018; 24:6442-6457. [PMID: 29479746 DOI: 10.1002/chem.201800037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Indexed: 12/24/2022]
Abstract
Potentiometric speciation studies, mass spectrometry, and DFT calculations helped to predict the various structural possibilities of the dinuclear trivalent lanthanide ion (LnIII , Ln=La, Eu, Tb, Yb, Y) complexes of a novel macrocyclic ligand, m-ODO2A-dimer (H4 L), to correlate with their luminescence properties and the promoted BNPP and HPNP phosphodiester bond hydrolysis reaction rates. The stability constants of the dinuclear Ln2 (m-ODO2A-dimer) complexes and various hydrolytic species confirmed by mass spectrometry were determined. DFT calculations revealed that the Y2 LH-1 and the Y2 LH-2 species tended to form structures with the respective closed- and open-form conformations. Luminescence lifetime data for the heterodimetallic TbEuL system confirmed the fluorescence resonance energy transfer from the TbIII to EuIII ion. The internuclear distance RTbEu values were estimated to be in the range of 9.4-11.3 Å (pH 6.7-10.6), which were comparable to those of the DFT calculated open-form conformations. Multiple linear regression analysis of the kobs data was performed using the equation: kobs,corr. =kobs -kobs,OH =kLn2LHM->1 [Ln2 LH-1 ]+kLn2LH-2 [Ln2 LH-2 ] for the observed Ln2 L-promoted BNPP/HPNP hydrolysis reactions in solution pH from 7 to 10.5 (Ln=Eu, Yb). The results showed that the second-order rate constants for the Eu2 LH-2 and Yb2 LH-2 species were about 50-400 times more reactive than the structural analogous Zn2 (m-12 N3 O-dimer) system.
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Affiliation(s)
- C Allen Chang
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, No. 155, Sec. 2, Li-Nong St., Beitou, Taipei, Taiwan), 112, Republic of China.,Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan, Republic of China.,Molecular Imaging Research Center (MIRC), National Yang-Ming University, Taipei, 112, Taiwan, Republic of China.,Department of Biological Science and Technology, National Chiao Tung University, No. 75 Po-Ai Street, Hsinchu, Taiwan, 30039, Republic of China
| | - Hwa-Yu Lee
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, No. 155, Sec. 2, Li-Nong St., Beitou, Taipei, Taiwan), 112, Republic of China
| | - Syue-Liang Lin
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, No. 155, Sec. 2, Li-Nong Street, Taipei, 112, Taiwan, Republic of China
| | - Ching-Ning Meng
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, No. 155, Sec. 2, Li-Nong St., Beitou, Taipei, Taiwan), 112, Republic of China
| | - Tsung-Ta Wu
- Department of Biological Science and Technology, National Chiao Tung University, No. 75 Po-Ai Street, Hsinchu, Taiwan, 30039, Republic of China
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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: 209] [Impact Index Per Article: 26.1] [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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10
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Williams A, Staroseletz Y, Zenkova MA, Jeannin L, Aojula H, Bichenkova EV. Peptidyl-oligonucleotide conjugates demonstrate efficient cleavage of RNA in a sequence-specific manner. Bioconjug Chem 2015; 26:1129-43. [PMID: 25955796 DOI: 10.1021/acs.bioconjchem.5b00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Described here is a new class of peptidyl-oligonucleotide conjugates (POCs) which show efficient cleavage of a target RNA in a sequence-specific manner. Through phosphoramidate attachment of a 17-mer TΨC-targeting oligonucleotide to amphiphilic peptide sequences containing leucine, arginine, and glycine, zero-linker conjugates are created which exhibit targeted phosphodiester cleavage under physiological conditions. tRNA(Phe) from brewer's yeast was used as a model target sequence in order to probe different structural variants of POCs in terms of selective TΨC-arm directed cleavage. Almost quantitative (97-100%) sequence-specific tRNA cleavage is observed for several POCs over a 24 h period with a reaction half-life of less than 1 h. Nontargeted cleavage of tRNA(Phe) or HIV-1 RNA is absent. Structure-activity relationships reveal that removal of the peptide's central glycine residue significantly decreases tRNA cleavage activity; however, this can be entirely restored through replacement of the peptide's C-terminal carboxylic acid group with the carboxamide functionality. Truncation of the catalytic peptide also has a detrimental effect on POC activity. Based on the encouraging results presented, POCs could be further developed with the aim of creating useful tools for molecular biology or novel therapeutics targeting specific messenger, miRNA, and genomic viral RNA sequences.
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Affiliation(s)
- Aled Williams
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
| | - Yaroslav Staroseletz
- ‡Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Marina A Zenkova
- ‡Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Laurent Jeannin
- §Peptisyntha S.A., 310 Rue de Ransbeek, 1120 Brussels, Belgium
| | - Harmesh Aojula
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
| | - Elena V Bichenkova
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
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11
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Kozłowski M, Kierzek R, Kubicki M, Radecka-Paryzek W. Metal-promoted synthesis, characterization, crystal structure and RNA cleavage ability of 2,6-diacetylpyridine bis(2-aminobenzoylhydrazone) lanthanide complexes. J Inorg Biochem 2013; 126:38-45. [PMID: 23770667 DOI: 10.1016/j.jinorgbio.2013.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 05/15/2013] [Accepted: 05/15/2013] [Indexed: 01/21/2023]
Abstract
New 2,6-diacetylpyridine bis(2-aminobenzoylhydrazone) lanthanide complexes were formed in the metal-induced one-step [1+2] condensation reaction between 2,6-diacetylpyridine and 2-aminobenzoylhydrazide in the presence of lanthanide (La(3+), Pr(3+), Nd(3+), Sm(3+), Eu(3+), Gd(3+), Tb(3+), Dy(3+), Ho(3+), Er(3+), Tm(3+) or Yb(3+)) nitrates as template agents. The analytical and spectral characterizations of all the compounds were correlated with the single crystal X-ray structural determination of Eu(3+), Gd(3+), Tb(3+), Dy(3+) and Er(3+) nitrate complexes. The Eu(3+), Gd(3+), Tb(3+)and Dy(3+) complexes of pentadentate 2,6-diacetylpyridine bis(2-aminobenzoylhydrazone) with the N3O2 set of donor atoms display a high and relatively rare coordination number of 11, whereas the Er(3+) ion complex is 9-coordinated, which is consistent with the lanthanide contraction phenomenon. The scission of 21-mer RNA was assessed for Eu(3+), Gd(3+) and Tb(3+) nitrate complexes. Lanthanide complexes not covalently attached to the oligonucleotide are able to cleave RNA at the target site in a sequence-selective or non-selective manner depending on the presence of protecting 12-mer 2'OMe RNA.
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Affiliation(s)
- Michał Kozłowski
- Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland
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12
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Copper(II) complexes of terpyridine derivatives: A footstep towards development of antiproliferative agent for breast cancer. J Inorg Biochem 2012; 117:48-59. [DOI: 10.1016/j.jinorgbio.2012.08.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 08/14/2012] [Accepted: 08/14/2012] [Indexed: 11/17/2022]
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13
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Jiang B, Wang M, Li C, Xie J. DNA-binding and hydrolytic cleavage promoted by tetraazamacycle La(III) and Ce(III) complexes. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0357-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Ballico M, Rapozzi V, Xodo LE, Comuzzi C. Metallation of pentaphyrin with Lu(III) dramatically increases reactive-oxygen species production and cell phototoxicity. Eur J Med Chem 2011; 46:712-20. [DOI: 10.1016/j.ejmech.2010.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 11/24/2010] [Accepted: 12/07/2010] [Indexed: 10/18/2022]
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16
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Hirva P, Nielsen A, Bond AD, McKenzie CJ. Potential cross-linking transition metal complexes (M = Ni, Cu, Zn) in the ligand-modified LNA duplexes. J Phys Chem B 2011; 114:11942-8. [PMID: 20726539 DOI: 10.1021/jp105528y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Options for interstrand DNA duplex linkages have been studied by incorporating transition metal ions in the ligand-functionalized LNA (locked nucleic acid) duplexes. The effect of first-row transition metal ions (M = Ni(2+), Cu(2+), and Zn(2+)) on the geometries and formation energies of mono- and dimetallic model complexes was calculated by DFT methods, and the results were compared with available experimental data. The results showed a clear preference for the formation of copper complexes over the corresponding nickel and zinc complexes, in agreement with the trends observed in the denaturation temperatures of the ligand-functionalized LNA duplexes. In addition, dichloride bridged dimeric complex, [L(LNA)Cu(μ-Cl)(2)CuL(LNA)](2+), in which L(LNA) is N,N-bis(2-pyridylmethyl)-β-alanyl functionalized LNA, was found energetically very stable, providing a potential structural option for an interstrand duplex linkage. The model complex and its simpler structural analogues were synthesized and structurally characterized. Comparison of the dimeric linker introduced into duplex tetramer strands, which provided a computational model for a double helix with two closely located LNA units, with a similar model for mononuclear Cu(L(LNA))(2)(2+) linker also showed a clear preference of the dichloride-bridged option, suggesting that the [L(LNA)Cu(μ-Cl)(2)CuL(LNA)](2+) complex produced a chemically realistic model to explain duplex stabilization in the presence of Cu(2+) and excess Cl(-).
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Affiliation(s)
- Pipsa Hirva
- Department of Chemistry, University of Eastern Finland, Joensuu Campus P.O. Box 111, FI-80101, Joensuu, Finland.
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Affiliation(s)
- Kentaro Tanaka
- a Department of Chemistry, Graduate School of Science , The University of Tokyo , Hongo, Bunkyo-ku, Tokyo , 113-0033 , Japan
| | - Motoyuki Tasaka
- b The Graduate University for Advanced Studies , Myodaiji, Okazaki , 444-8585 , Japan
| | - Honghua Cao
- b The Graduate University for Advanced Studies , Myodaiji, Okazaki , 444-8585 , Japan
| | - Mitsuhiko Shionoya
- a Department of Chemistry, Graduate School of Science , The University of Tokyo , Hongo, Bunkyo-ku, Tokyo , 113-0033 , Japan
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18
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Murtola M, Wenska M, Strömberg R. PNAzymes that are artificial RNA restriction enzymes. J Am Chem Soc 2010; 132:8984-90. [PMID: 20545354 DOI: 10.1021/ja1008739] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
DNA-cleaving restriction enzymes are well-known tools in biomedical and biotechnological research. There are, however, no corresponding enzymes known for RNA cleavage. There has been an ongoing development of artificial ribonucleases, including some attempts at sequence selectivity. However, so far these systems have displayed modest rates of cleavage, and in most cases, the cleaver has been used in excess or in stoichiometric amounts. In the current work, we present PNA-based systems (PNAzymes) that carry a Cu(II)-2,9-dimethylphenanthroline group and that act as site and sequence specific RNases. The general basis for the systems is that the target is cleaved at a nonbase paired region (RNA bulge) which is formed in the substrate upon binding of the PNAzyme. With this copper based system, cleavage takes place at virtually only one site and with a half-life of down to 30 min under stoichiometric conditions. Efficient turnover of RNA-substrate is shown with a 100-fold excess of substrate, thus, demonstrating true enzyme behavior. In addition, alteration of the sequence in the RNA bulge or a mismatch in the base-pairing region leads to substantial decreases in rate showing both kinetic resolution and binding discrimination in the substrate selectivity. The selectivity is further demonstrated by the substrates, with two potential cleavage sites differing in only one base, are cleaved only at the site that either does not have a mismatch or is kinetically preferred. We suggest that these systems can serve as a basis for construction of RNA restriction enzymes for in vitro manipulations.
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Affiliation(s)
- Merita Murtola
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, S-14183, Huddinge, Sweden
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19
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Rui R, Pin Y. Studies of copper (II) complexes as catalysts for the hydrolysis of DNA. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.19990170610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Nwe K, Andolina CM, Morrow JR. Tethered Dinuclear Europium(III) Macrocyclic Catalysts for the Cleavage of RNA. J Am Chem Soc 2008; 130:14861-71. [DOI: 10.1021/ja8037799] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Kido Nwe
- Department of Chemistry, University at Buffalo, State University of New York, Amherst, New York 14260-3000
| | - Christopher M. Andolina
- Department of Chemistry, University at Buffalo, State University of New York, Amherst, New York 14260-3000
| | - Janet R. Morrow
- Department of Chemistry, University at Buffalo, State University of New York, Amherst, New York 14260-3000
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22
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Synthesis, characterization, DNA binding and nuclease activity of binuclear copper(II) complexes of cuminaldehyde thiosemicarbazones. TRANSIT METAL CHEM 2008. [DOI: 10.1007/s11243-008-9094-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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24
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Chaudhary A, Singh R. Review: Metal Complexes of Polyaza and Polyoxaaza Macrocyclic Ligands: A Look into the Past and Present Work. REV INORG CHEM 2008. [DOI: 10.1515/revic.2008.28.1.35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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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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26
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Niittymäki T, Virta P, Ketomäki K, Lönnberg H. Di(azacrown) conjugates of 2'-O-methyl oligoribonucleotides as sequence-selective artificial ribonucleases. Bioconjug Chem 2007; 18:1583-92. [PMID: 17711318 DOI: 10.1021/bc070071o] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functionalized 2'-O-methyl oligoribonucleotides bearing two 3-(3-hydroxypropyl)-1,5,9-triazacyclododecane ligands attached via a phosphodiester linkage to a single non-nucleosidic building block have been prepared on a solid-support by conventional phosphoramidite chemistry. The branching units employed for the purpose include 2,2-bis(3-hydroxypropylaminocarbonyl)propane-1,3-diol, 2-hydroxyethyl 3'-O-(2-hydroxyethyl)-beta-D-ribofuranoside, and 2-hydroxyethyl 2'-O-(2-hydroxyethyl)-beta-D-ribofuranoside. Each of these has been introduced as a phosphoramidite reagent either into the penultimate 3'-terminal site or in the middle of the oligonucleotide chain. The dinuclear Zn2+ complexes of these conjugates have been shown to exhibit enhanced catalytic activity over their monofunctionalized counterpart, the 3'-terminal conjugate derived from 2-hydroxyethyl 3'-O-(2-hydroxyethyl)-beta-D-ribofuranoside being the most efficient cleaving agent. This conjugate cleaves an oligoribonucleotide target at a single phosphodiester bond and shows turnover and 1000-fold cleaving activity compared to the free monomeric Zn2+ chelate of 1,5,9-triazacyclododecane.
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Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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27
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Venkatesan N, Kim BH. Peptide conjugates of oligonucleotides: synthesis and applications. Chem Rev 2007; 106:3712-61. [PMID: 16967918 DOI: 10.1021/cr0502448] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Natarajan Venkatesan
- Laboratory for Modified Nucleic Acid Systems, Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
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28
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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29
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Farquhar ER, Richard JP, Morrow JR. Formation and Stability of Mononuclear and Dinuclear Eu(III) Complexes and Their Catalytic Reactivity Toward Cleavage of an RNA Analog. Inorg Chem 2007; 46:7169-77. [PMID: 17655292 DOI: 10.1021/ic7005666] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The complex between Eu(III) and 1,7-diaza-4,10,13-trioxacyclopentadecane-N,N'-diacetic acid (L4) was characterized by pH potentiometric titration and 1H NMR spectroscopy. The conversion of the monomer to a dimeric complex is observed as the pH is increased from 7 to 10 in a reaction that releases one mol/HO- per dimer formed. The dimeric complex undergoes a further ionization with a pKa of 10.7. Kinetic parameters are reported for the cleavage of the simple phosphodiester 2-hydroxypropyl-4-nitrophenyl phosphate catalyzed by both the monomeric and the dimeric Eu(III) complexes. These data show that the monomer and dimer stabilize their bound reaction transition states with similar free energies of 7.1 and 7.6 kcal/mol, respectively. Clearly, a bridging hydroxide is not an optimal linker to promote cooperative catalysis between Eu(III) centers in macrocycles with multiple polyaminocarboxylate pendent groups.
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Affiliation(s)
- Erik R Farquhar
- Department of Chemistry, University at Buffalo, State University of New York, Amherst, NY 14260-3000, USA
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30
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Kalek M, Madsen AS, Wengel J. Effective modulation of DNA duplex stability by reversible transition metal complex formation in the minor groove. J Am Chem Soc 2007; 129:9392-400. [PMID: 17616191 DOI: 10.1021/ja071076z] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein we describe the reversible changing of DNA duplex thermal stability by exploiting transition metal complexation phenomena. A terpyridine ligand was conjugated to the N2'-atoms of 2'-amino-2'-deoxyuridine and its locked counterpart 2'-amino-LNA, and these metal-complexing monomers were incorporated into oligodeoxyribonucleotides. Upon addition of varying amounts of transition metal ions, the thermal stability of DNA duplexes containing these terpyridine-functionalized units in different constitutions was affected to different degrees (DeltaTm values = -15.5 to +49.0 degrees C, relative to the unmodified duplex). The most pronounced effects were observed when two complexing monomers were positioned in opposite strands. Addition of 1 equiv of Ni2+ to such a system induced extraordinary duplex stabilization. Molecular modeling studies suggest, as an explanation for this phenomenon, formation of nickel-mediated interstrand linkages in the minor groove. Addition of an excess of metal ions resulted in largely decreased Tm values. Alternating addition of metal ions and EDTA demonstrated reversibility of metal ion-induced changes in hybridization strength, proving that the described approach provides an efficient method for duplex stability modulation.
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Affiliation(s)
- Marcin Kalek
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense M, Denmark
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31
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Rossiter CS, Mathews RA, Morrow JR. Cleavage of an RNA analog by Zn(II) macrocyclic catalysts appended with a methyl or an acridine group. J Inorg Biochem 2007; 101:925-34. [PMID: 17462740 DOI: 10.1016/j.jinorgbio.2007.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 02/18/2007] [Accepted: 03/11/2007] [Indexed: 11/25/2022]
Abstract
Two macrocycles (1 and 2) are prepared that incorporate pendent groups in macrocycle 3 (3=1-oxa-4,7,10-triazacyclododecane) with the goal of studying the effect of these pendent groups on metal ion complexation, solution chemistry and catalysis. Zn(1) contains a macrocyclic ligand with a pendent acridine group and Zn(2) has an appended methyl group. Water ligand pK(a) values for Zn(1) (6.7) and Zn(2) (7.3) are lower than that of Zn(3) (7.7). Zn(II) complexes of 1 and 2 are studied as catalysts for the cleavage of 2-hydroxypropyl 4-nitrophenylphosphate (HpPNP), an RNA analog. Zn(2) has a lower catalytic activity over the pH range 7-10 for cleavage of HpPNP compared to the parent macrocyclic complex, Zn(3). In contrast, Zn(1) has a threefold larger rate constant at pH 7.0 compared to Zn(2), attributed to the presence of a catalytic species which has a protonated acridine amino group. The binding constant of 1.5mM at pH 8.0 for formation of the Zn(2)-uridine adduct is similar to that for Zn(3), suggesting that N-alkylation of the macrocyclic ligand does not interfere with binding of the Zn(II) complex to uridine groups. Binding of cytidine to Zn(2) was not detectable under similar conditions up to 25mM nucleoside. Binding experiments under similar conditions could not be carried out for adenosine or guanosine due to their low solubility.
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Affiliation(s)
- Clifford S Rossiter
- Department of Chemistry, University at Buffalo, State University of New York, Amherst, NY 14260, United States
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32
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Juan D, Xiangguang M, Wei H, Xiancheng Z. Phosphate Monoester Cleavage with Dinuclear Zinc(II) and Copper(II) Macrocyclic Complexes in Micellar Solution. J DISPER SCI TECHNOL 2007. [DOI: 10.1080/01932690601057606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Du Juan
- a Faculty of Chemistry , Sichuan University , Chengdu , P. R. China
| | - Meng Xiangguang
- a Faculty of Chemistry , Sichuan University , Chengdu , P. R. China
| | - Hu Wei
- a Faculty of Chemistry , Sichuan University , Chengdu , P. R. China
| | - Zeng Xiancheng
- a Faculty of Chemistry , Sichuan University , Chengdu , P. R. China
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33
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Nwe K, Richard JP, Morrow JR. Direct excitation luminescence spectroscopy of Eu(iii) complexes of 1,4,7-tris(carbamoylmethyl)-1,4,7,10- tetraazacyclododecane derivatives and kinetic studies of their catalytic cleavage of an RNA analog. Dalton Trans 2007:5171-8. [DOI: 10.1039/b710072h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Beilstein AE, Tierney MT, Grinstaff MW. Site-Specifically Labeled Metallo-Oligodeoxynucleotides. COMMENT INORG CHEM 2006. [DOI: 10.1080/02603590008050865] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Mironova NL, Pyshnyi DV, Stadler DV, Prokudin IV, Boutorine YI, Ivanova EM, Zenkova MA, Gross HJ, Vlassov VV. G-specific RNA-cleaving conjugates of short peptides and oligodeoxyribonucleotides. J Biomol Struct Dyn 2006; 23:591-602. [PMID: 16615805 DOI: 10.1080/07391102.2006.10507084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Artificial ribonucleases, conjugates of short oligodeoxyribonucleotides and peptides built of arginine, leucine, proline, and serine, were synthesized and assessed in terms of ribonuclease activity and specificity of RNA cleavage. A specific group of the conjugates was identified that display T1-ribonuclease-like activity and cleave RNA predominantly at G-X sequences. Circular dichroism study of the structures of the most active conjugates, free peptide (LR)4G, and oligonucleotides revealed that conjugation of oligonucleotide to the peptide results in a specific peptide folding that possibly provides ribonuclease activity to the conjugate.
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Affiliation(s)
- Nadezhda L Mironova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Russian Federation, Novosibirsk, 630090
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36
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Alemdaroglu FE, Ding K, Berger R, Herrmann A. DNA-gestützte Synthese in drei Dimensionen: Einführung eines micellaren Templats für organische Reaktionen. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600524] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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Alemdaroglu FE, Ding K, Berger R, Herrmann A. DNA-Templated Synthesis in Three Dimensions: Introducing a Micellar Scaffold for Organic Reactions. Angew Chem Int Ed Engl 2006; 45:4206-10. [PMID: 16705747 DOI: 10.1002/anie.200600524] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Fikri E Alemdaroglu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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38
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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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39
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Transesterification of Phosphodiester by a Zinc-Containing Cyclen Derivative: Identification of the Active Species. European J Org Chem 2006. [DOI: 10.1002/jlac.199619960611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Putnam WC, Bashkin JK. Synthesis and evaluation of RNA transesterification efficiency using stereospecific serinol-terpyridine conjugates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:1309-23. [PMID: 16252668 DOI: 10.1080/15257770500230426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Six novel artificial ribonucleases were synthesized employing a stereochemically pure abasic serinol backbone residue for attachment of the RNA transesterification agent copper(II) terpyridine. These stereochemically pure abasic residues were synthesized as phosphoramidite building blocks from the parent L-serine and D-serine starting building blocks and incorporated into oligonucleotides via solid-phase DNA synthesis. These artificial ribonucleases were constructed to determine if the stereochemistry of the alpha carbon of an abasic serinol residue has influence over RNA transesterification through selective placement of a pendant transesterification agent in either the major or minor groove. The novel artificial ribonucleases and previously synthesized artificial ribonucleases were challenged with a 28-mer and 159-mer RNA substrate. It was determined that the stereochemistry of the carbon atom derived from the alpha-carbon of serine did not influence the extent of cleavage in these studies using copper(II) terpyridine conjugated artificial ribonucleases.
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Affiliation(s)
- William C Putnam
- Department of Chemistry, Washington University, St. Louis, Missouri, USA.
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41
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42
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Radecka-Paryzek W, Patroniak V, Lisowski J. Metal complexes of polyaza and polyoxaaza Schiff base macrocycles. Coord Chem Rev 2005. [DOI: 10.1016/j.ccr.2005.02.021] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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43
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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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44
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Chang CA, Wu BH, Kuan BY. Macrocyclic Lanthanide Complexes as Artificial Nucleases and Ribonucleases: Effects of pH, Metal Ionic Radii, Number of Coordinated Water Molecules, Charge, and Concentrations of the Metal Complexes. Inorg Chem 2005; 44:6646-54. [PMID: 16156622 DOI: 10.1021/ic0485458] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have been interested in the design, synthesis, and characterization of artificial nucleases and ribonucleases by employing macrocyclic lanthanide complexes because their high thermodynamic stability, low kinetic lability, high coordination number, and charge density (Lewis acidity) allow more design flexibility and stability. In this paper, we report the study of the use of the europium(III) complex, EuDO2A+ (DO2A is 1,7-dicarboxymethyl-1,4,7,10-tetraazacyclododecane) and other lanthanide complexes (i.e., LaDO2A+, YbDO2A+, EuK21DA+, EuEDDA+, and EuHEDTA where K21DA is 1,7-diaza-4,10,13-trioxacyclopentadecane-N,N'-diacetic acid, EDDA is ethylenediamine-N,N'-diacetic acid, and HEDTA is N-hydroxyethyl-ethylenediamine-N,N',N'-triacetic acid), as potential catalysts for the hydrolysis of the phosphodiester bond of BNPP (sodium bis(4-nitrophenyl)-phosphate). For the pH range 7.0-11.0 studied, EuDO2A+ promotes BNPP hydrolysis with the quickest rates among LaDO2A+, EuDO2A+, and YbDO2A+. This indicates that charge density is not the only factor affecting the reaction rates. Among the four complexes, EuDO2A+, EuK21DA+, EuEDDA+, and EuHEDTA, with their respective number of inner-sphere coordinated water molecules three, two, five, and three, EuEDDA+, with the greatest number of inner-sphere coordinated water molecules and a positive charge, promotes BNPP hydrolysis more efficiently at pH below 8.4, and the observed rate trend is EuEDDA+ > EuDO2A+ > EuK21DA+ > EuHEDTA. At pH > 8.4, the EuEDDA+ solution becomes misty and precipitates form. At pH 11.0, the hydrolysis rate of BNPP in the presence of EuDO2A+ is 100 times faster than that of EuHEDTA, presumably because the positively charged EuDO2A+ is more favorable for binding with the negatively charged phosphodiester compounds. The logarithmic hydrolysis constants (pKh) were determined, and are reported in the parentheses, by fitting the kinetic k(obs) data vs pH for EuDO2A+ (8.4), LaDO2A+ (8.4), YbDO2A+ (9.4), EuK21DA+ (7.8), EuEDDA+ (9.0), and EuHEDTA (10.1). The preliminary rate constant-[EuDO2A+] data at pH 9.35 were fitted to a monomer-dimer reaction model, and the dimer rate constant is 400 times greater than that of the monomer. The fact that YbDO2A+ catalyzes BNPP less effectively than EuDO2A+ is tentatively explained by the formation of an inactive dimer, [Yb(DO2A)(OH)]2, with no coordination unsaturation for BNPP substrate binding.
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Affiliation(s)
- C Allen Chang
- Dept. of Biological Science and Technology, National Chiao Tung University, 75 Po-Ai Street, Hsinchu, Taiwan 30039, R.O.C
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45
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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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46
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Gunnlaugsson T, Leonard JP. Responsive lanthanide luminescent cyclen complexes: from switching/sensing to supramolecular architectures. Chem Commun (Camb) 2005:3114-31. [PMID: 15968347 DOI: 10.1039/b418196d] [Citation(s) in RCA: 271] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article highlights some of the recent developments in the use of responsive cyclen based lanthanide luminescent devices, focusing on Eu(III), Tb(III), Nd(III) and Yb(III) complexes, where the photophysical properties, such as the excited state lifetimes, quantum yield/intensity and emission polarisation are modulated by the local chemical environment, e.g. ions and molecules, or through self-assembly of either f-f or mixed f-d cyclen complexes.
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47
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Niittymäki T, Lönnberg H. Sequence-selective cleavage of oligoribonucleotides by 3d transition metal complexes of 1,5,9-triazacyclododecane-functionalized 2'-O-methyl oligoribonucleotides. Bioconjug Chem 2005; 15:1275-80. [PMID: 15546193 DOI: 10.1021/bc0498323] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
2'-O-Methyl oligoribonucleotides bearing a 3'-[2,6-dioxo-3,7-diaza-10-(1,5,9-triazacyclododec-3-yl)decyl phospate conjugate group have been shown to cleave in slight excess of Zn(2+) ions complementary oligoribonucleotides at the 5'-side of the last base-paired nucleotide. The cleavage obeys first-order kinetics and exhibits turnover. The acceleration compared to the monomeric Zn(2+) 1,5,9-triazacyclododecane chelate is more than 100-fold. In addition, 2'-O-methyl oligoribonucleotides having the 1,5,9-triazacyclododec-3-yl group tethered to the anomeric carbon of an intrachain 2-deoxy-beta-d-erythro-pentofuranosyl group via a 2-oxo-3-azahexyl, 2,6-dioxo-3,7-diazadecyl, or 2,9-dioxo-3,10-diazatridecyl linker have been studied as cleaving agents. These cleave as zinc chelates a tri- and pentaadenyl bulge opposite to the conjugate group approximately 50 times as fast as the monomeric chelate and show turnover. The cleavage rate is rather insensitive to the length of linker. Interestingly, a triuridyl bulge remains virtually intact in striking contrast to a triadenyl bulge. Evidently binding of the zinc chelate to a uracil base prevents its catalytic action. Replacement of Zn(2+) with Cu(2+) or Ni(2+) retards the cleaving activity of all the cleaving agents tested.
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Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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48
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Kurz K, Göbel MW. Hydrolytical Cleavage of TAR-RNA, thetrans-Activation Responsive Region of HIV-1, by a Bis(guanidinium) Catalyst Attached to Arginine. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19960790719] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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49
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Kurz K. Hydrolytische Spaltung von Nucleinsäuren-vom Enzymmechanismus zum Enzymmodell. CHEM UNSERER ZEIT 2004. [DOI: 10.1002/ciuz.19980320206] [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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50
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Coordination chemistry mimics of nuclease-activity in the hydrolytic cleavage of phosphodiester bond. CHINESE SCIENCE BULLETIN-CHINESE 2004. [DOI: 10.1007/bf03184297] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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