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Li A, Zhang Y, Wan L, Peng R, Zhang X, Guo Q, Xu S, Qiao D, Zheng P, Li N, Zhu W, Pan Q. Coordination-Driven Self-Assembly of Metal Ion-Antisense Oligonucleotide Nanohybrids for Chronic Bacterial Infection Therapy. ACS APPLIED MATERIALS & INTERFACES 2024; 16:28041-28055. [PMID: 38767982 DOI: 10.1021/acsami.4c01453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Bacterial infection poses a significant challenge to wound healing and skin regeneration, leading to substantial economic burdens on patients and society. Therefore, it is crucial to promptly explore and develop effective methodologies for bacterial infections. Herein, we propose a novel approach for synthesizing nanostructures based on antisense oligonucleotides (ASOs) through the coordination-driven self-assembly of Zn2+ with ASO molecules. This approach aims to provide effective synergistic therapy for chronic wound infections caused by Staphylococcus aureus (S. aureus). The resulting hybrid nanoparticles successfully preserve the structural integrity and biological functionalities of ASOs, demonstrating excellent ASO encapsulation efficiency and bioaccessibility. In vitro antibacterial experiments reveal that Zn-ASO NPs exhibit antimicrobial properties against Escherichia coli, Staphylococcus aureus, and Bacillus subtilis. This antibacterial ability is attributed to the high concentration of metal zinc ions and the generation of high levels of reactive oxygen species. Additionally, the ftsZ-ASO effectively inhibits the expression of the ftsZ gene, further enhancing the antimicrobial effect. In vivo antibacterial assays demonstrate that the Zn-ASO NPs promote optimal skin wound healing and exhibit favorable biocompatibility against S. aureus infections, resulting in a residual infected area of less than 8%. This combined antibacterial strategy, which integrates antisense gene therapy and metal-coordination-directed self-assembly, not only achieves synergistic and augmented antibacterial outcomes but also expands the horizons of ASO coordination chemistry. Moreover, it addresses the gap in the antimicrobial application of metal-coordination ASO self-assembly, thereby advancing the field of ASO-based therapeutic approaches.
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Affiliation(s)
- Anqi Li
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Yan Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Li Wan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Rujue Peng
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Xuan Zhang
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Qiuyan Guo
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Shan Xu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Dan Qiao
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Pengwu Zheng
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Na Li
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, College of Biological and Agricultural Sciences, Honghe University, Mengzi 661199, China
| | - Wufu Zhu
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
| | - Qingshan Pan
- Jiangxi Provincial Key Laboratory of Drug Design and Evaluation, School of Pharmacy, Jiangxi Science & Technology Normal University, Nanchang 330013, Jiangxi, China
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Amirloo B, Staroseletz Y, Yousaf S, Clarke DJ, Brown T, Aojula H, Zenkova MA, Bichenkova EV. "Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates. Nucleic Acids Res 2021; 50:651-673. [PMID: 34967410 PMCID: PMC8789077 DOI: 10.1093/nar/gkab1273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
Antisense sequence-specific knockdown of pathogenic RNA offers opportunities to find new solutions for therapeutic treatments. However, to gain a desired therapeutic effect, the multiple turnover catalysis is critical to inactivate many copies of emerging RNA sequences, which is difficult to achieve without sacrificing the sequence-specificity of cleavage. Here, engineering two or three catalytic peptides into the bulge-loop inducing molecular framework of antisense oligonucleotides achieved catalytic turnover of targeted RNA. Different supramolecular configurations revealed that cleavage of the RNA backbone upon sequence-specific hybridization with the catalyst accelerated with increase in the number of catalytic guanidinium groups, with almost complete demolition of target RNA in 24 h. Multiple sequence-specific cuts at different locations within and around the bulge-loop facilitated release of the catalyst for subsequent attacks of at least 10 further RNA substrate copies, such that delivery of only a few catalytic molecules could be sufficient to maintain knockdown of typical RNA copy numbers. We have developed fluorescent assay and kinetic simulation tools to characterise how the limited availability of different targets and catalysts had restrained catalytic reaction progress considerably, and to inform how to accelerate the catalytic destruction of shorter linear and larger RNAs even further.
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Affiliation(s)
- Bahareh Amirloo
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Sameen Yousaf
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Harmesh Aojula
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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Staroseletz Y, Amirloo B, Williams A, Lomzov A, Burusco KK, Clarke DJ, Brown T, Zenkova MA, Bichenkova EV. Strict conformational demands of RNA cleavage in bulge-loops created by peptidyl-oligonucleotide conjugates. Nucleic Acids Res 2020; 48:10662-10679. [PMID: 33010175 PMCID: PMC7641753 DOI: 10.1093/nar/gkaa780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/04/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Potent knockdown of pathogenic RNA in vivo is an urgent health need unmet by both small-molecule and biologic drugs. ‘Smart’ supramolecular assembly of catalysts offers precise recognition and potent destruction of targeted RNA, hitherto not found in nature. Peptidyl-oligonucleotide ribonucleases are here chemically engineered to create and attack bulge-loop regions upon hybridization to target RNA. Catalytic peptide was incorporated either via a centrally modified nucleotide (Type 1) or through an abasic sugar residue (Type 2) within the RNA-recognition motif to reveal striking differences in biological performance and strict structural demands of ribonuclease activity. None of the Type 1 conjugates were catalytically active, whereas all Type 2 conjugates cleaved RNA target in a sequence-specific manner, with up to 90% cleavage from 5-nt bulge-loops (BC5-α and BC5L-β anomers) through multiple cuts, including in folds nearby. Molecular dynamics simulations provided structural explanation of accessibility of the RNA cleavage sites to the peptide with adoption of an ‘in-line’ attack conformation for catalysis. Hybridization assays and enzymatic probing with RNases illuminated how RNA binding specificity and dissociation after cleavage can be balanced to permit turnover of the catalytic reaction. This is an essential requirement for inactivation of multiple copies of disease-associated RNA and therapeutic efficacy.
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Affiliation(s)
- Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russia
| | - Bahareh Amirloo
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Aled Williams
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Alexander Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russia
| | - Kepa K Burusco
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russia
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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Wang R, Ranganathan SV, Haruehanroengra P, Mao S, Scalabrin M, Fabris D, Chen A, Liu H, Hassan AEA, Gan J, Sheng J. Construction and structure studies of DNA-bipyridine complexes as versatile scaffolds for site-specific incorporation of metal ions into DNA. J Biomol Struct Dyn 2018; 37:551-561. [PMID: 29447072 DOI: 10.1080/07391102.2018.1441071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The facile construction of metal-DNA complexes using 'Click' reactions is reported here. A series of 2'-propargyl-modified DNA oligonucleotides were initially synthesized as structure scaffolds and were then modified through 'Click' reaction to incorporate a bipyridine ligand equipped with an azido group. These metal chelating ligands can be placed in the DNA context in site-specific fashion to provide versatile templates for binding various metal ions, which are exchangeable using a simple EDTA washing-and-filtration step. The constructed metal-DNA complexes were found to be thermally stable. Their structures were explored by solving a crystal structure of a propargyl-modified DNA duplex and installing the bipyridine ligands by molecular modeling and simulation. These metal-DNA complexes could have wide applications as novel organometallic catalysts, artificial ribonucleases, and potential metal delivery systems.
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Affiliation(s)
- Rui Wang
- a Department of Chemistry , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA.,b The RNA Institute , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA
| | - Srivathsan V Ranganathan
- b The RNA Institute , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA
| | - Phensinee Haruehanroengra
- a Department of Chemistry , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA.,b The RNA Institute , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA
| | - Song Mao
- a Department of Chemistry , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA.,b The RNA Institute , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA
| | - Matteo Scalabrin
- a Department of Chemistry , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA.,b The RNA Institute , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA
| | - Daniele Fabris
- a Department of Chemistry , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA.,b The RNA Institute , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA
| | - Alan Chen
- a Department of Chemistry , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA.,b The RNA Institute , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA
| | - Hehua Liu
- c State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences , Fudan University , Shanghai 200433 , China
| | - Abdalla E A Hassan
- d Applied Nucleic Acids Research Center, Faculty of Science , Zagazig University , Zagazig , Egypt
| | - Jianhua Gan
- c State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences , Fudan University , Shanghai 200433 , China
| | - Jia Sheng
- a Department of Chemistry , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA.,b The RNA Institute , University at Albany, State University of New York , 1400 Washington Ave., Albany , NY 12222 , USA
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5
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Desbouis D, Troitsky IP, Belousoff MJ, Spiccia L, Graham B. Copper(II), zinc(II) and nickel(II) complexes as nuclease mimetics. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.12.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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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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7
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Tang SP, Chen S, Wu GF, Chen HY, Mao ZW, Ji LN. Ester catalytic hydrolysis by a tridentate N,N′,N″-copper bridged cyclodextrin dimer. INORG CHEM COMMUN 2011. [DOI: 10.1016/j.inoche.2010.10.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Sanada H, Nakanishi T, Inoue H, Kitamura M. Cloning and expression of the MutM gene from obligate anaerobic bacterium Desulfovibrio vulgaris (Miyazaki F). J Biochem 2009; 145:525-32. [PMID: 19151100 DOI: 10.1093/jb/mvp005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The gene encoding a MutM from Desulfovibrio vulgaris (Miyazaki F) was cloned and expressed in Escherichia coli. A 5.9-kb DNA fragment, isolated from D. vulgaris (Miyazaki F) by XhoI and PvuII, contained a MutM gene and other open reading frames. The nucleotide sequence of the MutM gene indicated that the protein was composed of 336 amino acids. The amino-acid sequence deduced from the MutM gene was highly homologous with the MutM of other bacteria; however an additional insert consisted of 64 amino acids. An expression system for the MutM gene under the control of the T7 promoter was constructed in E. coli. From the kinetic analysis results, the purified His-tagged MutM showed 8-oxoguanine-DNA glycosylase activity comparable with that of MutM from E. coli. In this study, the amounts of mRNA and protein for MutM were scant in the D. vulgaris (Miyazaki F). MutM activity may be induced by oxidative stress. However, its induction may not be frequently generated because sulfate-reducing bacteria generally grow in anaerobic conditions. MutM might play a role in the protection against the mutagenicity of oxygen when oxygen stress exceeded the capacity of the defense systems against oxygen toxicity.
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Affiliation(s)
- Hideaki Sanada
- Department of Applied and Bioapplied Chemistry, Graduate School of Engineering, Osaka City University, Sugimoto 3-3-138, Sumiyoshi-ku, Osaka 558-8585, Japan
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9
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Chan YT, Moorefield CN, Newkome GR. Synthesis, characterization, and self-assembled nanofibers of carbohydrate-functionalized mono- and di(2,2′:6′,2″-terpyridinyl)arenes. Chem Commun (Camb) 2009:6928-30. [DOI: 10.1039/b914743h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Beves JE, Constable EC, Housecroft CE, Neuburger M, Schaffner S, Zampese JA. 4′-Chloro-2,2′:6′,2″-terpyridine (L): ethyl sulfate salts of [H2L]2+ and the single crystal structures of [H2L][EtOSO3]Cl·H2O and [ML2][PF6]2 with M=Fe and Ru. INORG CHEM COMMUN 2008. [DOI: 10.1016/j.inoche.2008.04.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Chacko AM, Qu W, Kung HF. Synthesis of 5-fluoroalkylated pyrimidine nucleosides via Negishi cross-coupling. J Org Chem 2008; 73:4874-81. [PMID: 18522415 PMCID: PMC4122541 DOI: 10.1021/jo800444y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Fluoroalkylated pyrimidine nucleosides (1) have potential as therapeutic agents and molecular imaging agents targeting HSV1-tk suicide gene therapy. Thus, straightforward preparation of 5-fluoroalkylated nucleoside derivatives has been developed. Reported herein are the first examples of Pd-catalyzed Negishi cross-coupling of 3-N-benzoyl-3',5'-di-O-benzoyl-5-iodo-2'-deoxyuridine (2a) and 3-N-benzoyl-3',5'-di-O-benzoyl-5-iodo-2'-deoxy-2'-fluoroarabinouridine (2b) with unactivated Csp(3) fluoroalkylzinc bromides. This paper demonstrates the first synthesis of six 5-fluoroalkyl-2'-deoxypyrimidine nucleoside derivatives with three to five methylene chain lengths (5). Furthermore, this methodology has been extended to create a series of 13 5-alkyl-substituted nucleosides, including the target nucleosides 5 and 5-silyloxypropyl and 5-cyanobutyl derivatives.
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Affiliation(s)
- Ann-Marie Chacko
- Department of Pharmacology, University of Pennsylvania, 3700 Market Street, Suite 305, Philadelphia, PA 19104, USA
| | - Wenchao Qu
- Department of Radiology, University of Pennsylvania, 3700 Market Street, Suite 305, Philadelphia, PA 19104, USA
| | - Hank F. Kung
- Department of Pharmacology, University of Pennsylvania, 3700 Market Street, Suite 305, Philadelphia, PA 19104, USA
- Department of Radiology, University of Pennsylvania, 3700 Market Street, Suite 305, Philadelphia, PA 19104, USA
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Kalek M, Benediktson P, Vester B, Wengel J. Identification of efficient and sequence specific bimolecular artificial ribonucleases by a combinatorial approach. Chem Commun (Camb) 2008:762-4. [DOI: 10.1039/b712532a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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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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15
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Cacciapaglia R, Casnati A, Mandolini L, Peracchi A, Reinhoudt DN, Salvio R, Sartori A, Ungaro R. Efficient and selective cleavage of RNA oligonucleotides by calix[4]arene-based synthetic metallonucleases. J Am Chem Soc 2007; 129:12512-20. [PMID: 17880217 DOI: 10.1021/ja0737366] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Di- and trinuclear copper(II) complexes of [12]aneN3 macrocycles anchored at the upper rim of cone calix[4]arenes in 1,2-, 1,3-, and 1,2,3-positions were investigated as cleaving agents of 6-, 7-, and 17-meric oligoribonucleotides. A kinetic investigation of the cleavage reactions was carried out using gel electrophoresis to separate and analyze reactants and products having a radioactive phosphate label in the terminal 5'-position. The degree of cooperation was assessed on the basis of a comparison with rates of cleavage by mononuclear controls. A remarkable selectivity of cleavage of the CpA phosphodiester bond was observed for all metal complexes, in sharp contrast with the UpU and UpG selectivity previously observed in the cleavage of diribonucleoside monophosphates by the same metal complexes. The highest rate acceleration, brought about in the cleavage of the 5'-pCpA bond in hexanucleotide 9 by 50 muM trinuclear complex 5-Cu3 (water solution, pH 7.4, 50 degrees C), amounts to 5 x 105-fold, as based on the estimated background reactivity of the CpA dimer. Selectivity in the cleavage of oligoribonucleotides by copper(II) complexes closely resembles that experienced by ribonuclease A and by a number of metal-independent RNase A mimicks. The possible role of the dianionic phosphate at the 5'-terminal positions as a primary anchoring site for the metal catalyst is discussed.
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Affiliation(s)
- Roberta Cacciapaglia
- Dipartimento di Chimica and IMC - CNR Sezione Meccanismi di Reazione, Università La Sapienza, Box 34 - Roma 62, 00185 Roma, Italy
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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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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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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19
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Metal ion-directed cooperative DNA binding of small molecules. J Inorg Biochem 2006; 100:1744-54. [DOI: 10.1016/j.jinorgbio.2006.06.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Revised: 05/23/2006] [Accepted: 06/25/2006] [Indexed: 11/19/2022]
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Ossipov DA, Strömberg R. Studies in oligonucleotide-based artificial nuclease systems. intramolecular copper (II) complex formation in an oligonucleotide bis-phenanthroline conjugate. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:901-5. [PMID: 16248058 DOI: 10.1081/ncn-200059261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We have recently developed oligonucleotide based artificial nuclease (OBAN) systems based on 2'-O-methyloligoribonucleotides carrying a 2,9-dimethylphenanthroline x Zn(II) complex. These hybridize to an RNA molecule with bulge formation in the central region of the target and cleave the RNA target in a catalytic manner. When studying an 11-mer 2'-O-methyloligoribonucleotide carrying two 2,9-dimethylphenanthroline moieties, located 5 base pairs apart from each other, we found that this forms a cyclic structure in the presence of Cu2+ ions. This is due to intramolecular Cu(2,9-dimethylphenanthroline)2 complex formation, i.e., with the two ligands conjugated to the same oligonucleotide.
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Affiliation(s)
- Dmitri A Ossipov
- Division of Organic and Bioorganic Chemistry, MBB, Scheele Laboratory, Karolinska Intitutet, S-17177, Sweden
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21
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Chen W, Komiyama M. Site-selective DNA hydrolysis by Ce(IV)-EDTA with the use of one oligonucleotide additive bearing two monophosphates. Chembiochem 2005; 6:1825-30. [PMID: 16196014 DOI: 10.1002/cbic.200500119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two deoxyuridine derivatives each bearing a monophosphate group at the 5-position with a C3 linker, were incorporated into an oligonucleotide. By using this modified oligonucleotide, a bulge was formed at a predetermined position in a DNA substrate, and two monophosphate groups were placed at both junctions of the bulge. Upon treatment of the mixture with Ce(IV)-EDTA at pH 7.0, the phosphodiester linkages at the bulge site were selectively and efficiently hydrolyzed. The monophosphate groups introduced into the bulge site greatly accelerated site-selective DNA scission. Compared with the previously reported two-additive system, which combines two oligonucleotide additives each with a monophosphate at their termini, the present one-additive system is simpler and more convenient. Furthermore, site-selective DNA hydrolysis by using this one-additive system is successful even at high reaction temperatures (e.g., 55 degrees C). This reflects the thermodynamic stability of the duplexes formed between the substrate and the additive DNA.
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Affiliation(s)
- Wen Chen
- Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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22
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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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Schiller A, Scopelliti R, Benmelouka M, Severin K. Highly Cross-linked Polymers Containing N,N‘,N‘ ‘-Chelate Ligands for the Cu(II)-Mediated Hydrolysis of Phosphoesters. Inorg Chem 2005; 44:6482-92. [PMID: 16124831 DOI: 10.1021/ic0504588] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three immobilized Cu(II) complexes were generated by the following: (a) homopolymerization of the N,N',N' '-chelate ligand tris[2-(1-vinylimidazolyl)]phosphine (1) and subsequent metalation with CuCl2; (b) copolymerization of 1 with ethyleneglycol dimethacrylate (EGDMA) und subsequent metalation with CuCl2; or (c) molecular imprinting with the organometallic Mo-complex [Mo(eta3-C4H7)(CO)2(1)](TsO) (5) and EGDMA and subsequent replacement of Mo(II) by Cu(II). All three polymeric Cu complexes were found to efficiently promote the hydrolysis of activated phosphoesters with the relative activity being dependent on the nature of the polymer and the substrate.
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Affiliation(s)
- Alexander Schiller
- Institut des Sciences et Ingénieries Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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24
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Cyclen based lanthanide ion ribonuclease mimics: the effect of pyridine cofactors upon phosphodiester HPNP hydrolysis. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.03.150] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Abstract
Synthetic metallonucleases are versatile metal ion catalysts that use multiple catalytic strategies for the cleavage of RNA. Recent work in the design of more active metallonucleases combines a single metal ion with functional groups that interact with RNA, including amino acid fragments or additional metal ions. Rate enhancements by multifunctional catalysts for cleavage of simple model substrates with good leaving groups are as high as 10(6) but somewhat lower (10(5)) for real RNA. However, cleavage of RNA substrates is complicated by different binding modes and steric interactions that can interfere with catalysis. Antisense oligonucleotides, peptides and small molecules that act as RNA recognition agents increase the strength of substrate binding, but not necessarily the catalytic rate constant. In general, catalytic strategies used by synthetic metallonucleases are probably not optimized. A better grasp of the mechanism of RNA cleavage by metal ions and more effort on positioning the metal ion complex with respect to the cleavage site may lead to improved catalysts.
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Affiliation(s)
- Janet R Morrow
- Department of Chemistry, University at Buffalo, State University of New York, Amherst, NY 14260-3000, USA.
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26
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Shi Y, Niikura F, Kuzuya A, Komiyama M. Noncovalent Combination of Oligoamine and Oligonucleotide as Totally Organic Site-selective RNA Cutter. CHEM LETT 2004. [DOI: 10.1246/cl.2004.1012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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27
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Kuzuya A, Mizoguchi R, Sasayama T, Zhou JM, Komiyama M. Selective activation of two sites in RNA by acridine-bearing oligonucleotides for clipping of designated RNA fragments. J Am Chem Soc 2004; 126:1430-6. [PMID: 14759201 DOI: 10.1021/ja0389568] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Artificial enzymes for selective scission of RNA at two designated sites, which are valuable for advanced RNA science, have been prepared by combining lanthanide(III) ion with an oligonucleotide bearing two acridine groups. When these modified oligonucleotides form heteroduplexes with substrate RNA, the two phosphodiester linkages in front of the acridines are selectively activated and preferentially hydrolyzed by lanthanide ion. This two-site RNA scission does not require any specific RNA sequence at the scission sites, and the length of clipped RNA fragment is easily and precisely controllable by changing the distance between two acridine groups in the modified oligonucleotide. The two-site scission is also successful even when the substrate RNA has higher-order structures. By using these two-site RNA cutters, RNA fragments of predetermined length were obtained from long RNA substrates and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Single nucleotide polymorphisms in homozygous and heterozygous samples were accurately and easily detected in terms of the difference in mass number. Multiplex analyses of in vitro transcripts from human genome were also successful.
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Affiliation(s)
- Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan
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29
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Czlapinski JL, Sheppard TL. Site-specific oxidative cleavage of DNA by metallosalen–DNA conjugates. Chem Commun (Camb) 2004:2468-9. [PMID: 15514819 DOI: 10.1039/b410493e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ni-salen-DNA conjugates, prepared by template-directed synthesis, targeted oxidative adduct formation and strand scission at deoxyguanosine sites in complementary DNA strands of Watson-Crick duplexes.
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Affiliation(s)
- Jennifer L Czlapinski
- Northwestern University, Department of Chemistry, 2145 Sheridan Road, Evanston, Illinois 60208-3113, USA
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