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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: 6] [Impact Index Per Article: 2.0] [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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2
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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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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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Chen Y, Wang X, Zhang K, Bao Y. Intercalation of cytosine into Eu3+-doped hydrocalumite and their fluorescent responses. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2017. [DOI: 10.1007/s13738-017-1176-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Reverte M, Barvik I, Vasseur JJ, Smietana M. RNA-directed off/on switch of RNase H activity using boronic ester formation. Org Biomol Chem 2017; 15:8204-8210. [DOI: 10.1039/c7ob02145c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new concept to modulate RNase H activity is presented based on the boronic acid/boronate switch.
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Affiliation(s)
- Maëva Reverte
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Ivan Barvik
- Institute of Physics
- Faculty of Mathematics and Physics
- Charles University
- 121 16 Prague 2
- Czech Republic
| | - Jean-Jacques Vasseur
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
| | - Michael Smietana
- Institut des Biomolecules Max Mousseron
- IBMM UMR 5247 CNRS
- Université de Montpellier
- ENSCM
- 34095 Montpellier
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6
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Dogandzhiyski P, Ghidini A, Danneberg F, Strömberg R, Göbel MW. Studies on Tris(2-aminobenzimidazole)-PNA Based Artificial Nucleases: A Comparison of Two Analytical Techniques. Bioconjug Chem 2015; 26:2514-9. [PMID: 26544527 DOI: 10.1021/acs.bioconjchem.5b00534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new peptide nucleic acid (PNA) construct carrying a tris(2-aminobenzimidazole) phosphodiester cleaver is presented. This non-metal-based artificial nuclease hydrolyzes RNA substrates that form a bulge upon binding to the PNA. Reaction rates depend on the bulge sequence. For conjugates of tris(2-aminobenzimidazole), substrate turnover is shown for the first time. Two methods of analysis for the kinetics are compared: IE-HPLC separation of oligonucleotide fragments and analysis of Cy5-labeled oligonucleotide fragments by denaturating PAGE on a DNA sequencer, respectively. The different methods give rates that are in the same range where, in general, the substrates for the sequencer method give slightly lower rates.
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Affiliation(s)
- Plamena Dogandzhiyski
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Friederike Danneberg
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
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Ma X, Yin Y, Geng Z, Yang Z, Wen J, Wang Z. The first example of a model compound of RNase U2 and its intermediate with CPP directly monitored by ESI-MS. RSC Adv 2014. [DOI: 10.1039/c4ra07950g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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8
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Göbel MW, Roussev CD, Scheffer U. RNA Cleavage Catalyzed by Amphoteric Bis(acyl)guanidinium Derivatives. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201300308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Lanthanide-mediated dephosphorylation used for peptide cleavage during solid phase peptide synthesis. Molecules 2013; 18:3894-905. [PMID: 23549296 PMCID: PMC3955260 DOI: 10.3390/molecules18043894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 02/27/2013] [Accepted: 03/27/2013] [Indexed: 12/01/2022] Open
Abstract
Lanthanide(III) ions can accelerate the hydrolysis of phosphomonoesters and phosphodiesters in neutral aqueous solution. In this paper, lanthanide-mediated dephosphorylation has been applied in aqueous media as an orthogonal cleavage condition that can be employed in conventional solid phase peptide synthesis (SPPS). A phosphorylated polymeric support for SPPS was developed using Boc chemistry. The cleavage of resin-bound phosphates was investigated with the addition of Eu(III), Yb(III), acid or base, a mixture of solvents or different temperatures. To demonstrate the utility of this approach for SPPS, a peptide sequence was synthesized on a phosphorylated polymeric support and quantitatively cleaved with lanthanide ions in neutral aqueous media. The protecting groups for side chains were retained during peptide cleavage using lanthanide ions. This new methodology provides a mild orthogonal cleavage condition of phosphoester as a linker during SPPS.
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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: 52] [Impact Index Per Article: 3.7] [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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Belousoff MJ, Ung P, Forsyth CM, Tor Y, Spiccia L, Graham B. New macrocyclic terbium(III) complex for use in RNA footprinting experiments. J Am Chem Soc 2009; 131:1106-14. [PMID: 19119812 PMCID: PMC2633772 DOI: 10.1021/ja807301r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Reaction of terbium triflate with a heptadentate ligand derivative of cyclen, L1 = 2-[7-ethyl-4,10-bis(isopropylcarbamoylmethyl)-1,4,7,10-tetraazacyclododec-1-yl]-N-isopropyl-acetamide, produced a new synthetic ribonuclease, [Tb(L1)(OTf)(OH(2))](OTf)(2).MeCN (C1). X-ray crystal structure analysis indicates that the terbium(III) center in C1 is 9-coordinate, with a capped square-antiprism geometry. While the terbium(III) center is tightly bound by the L1 ligand, two of the coordination sites are occupied by labile water and triflate ligands. In water, the triflate ligand is likely to be displaced, forming [Tb(L1)(OH(2))(2)](3+), which is able to effectively promote RNA cleavage. This complex greatly accelerates the rate of intramolecular transesterification of an activated model RNA phosphodiester, uridine-3'-p-nitrophenylphosphate (UpNP), with k(obs) = 5.5(1) x 10(-2) s(-1) at 21 degrees C and pH 7.5, corresponding to an apparent second-order rate constant of 277(5) M(-1) s(-1). By contrast, the analogous complex of an octadentate derivative of cyclen featuring only a single labile coordination site, [Tb(L2)(OH(2))](OTf)(3) (C2), where L2 = 2-[4,7,10-tris(isopropylcarbamoylmethyl)-1,4,7,10-tetraazacyclododec-1-yl]-N-isopropyl-acetamide, is inactive. [Tb(L1)(OH(2))(2)](3+) is also capable of hydrolyzing short transcripts of the HIV-1 transactivation response (TAR) element, HIV-1 dimerization initiation site (DIS) and ribosomal A-site, as well as formyl methionine tRNA (tRNA(fMet)), albeit at a considerably slower rate than UpNP transesterification (k(obs) = 2.78(8) x 10(-5) s(-1) for TAR cleavage at 37 degrees C, pH 6.5, corresponding to an apparent second-order rate constant of 0.56(2) M(-1)s(-1)). Cleavage is concentrated at the single-stranded "bulge" regions of these RNA motifs. Exploiting this selectivity, [Tb(L1)(OH(2))(2)](3+) was successfully employed in footprinting experiments, in which binding of the Tat peptide and neomycin B to the bulge region of the TAR stem-loop was confirmed.
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Affiliation(s)
- Matthew J. Belousoff
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
| | - Phuc Ung
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
| | - Craig M. Forsyth
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
| | - Leone Spiccia
- School of Chemistry, Monash University, Clayton, Vic 3800, Australia
| | - Bim Graham
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Vic 3052, Australia
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14
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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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15
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Wang P, Miller JE, Henling LM, Stern CL, Frank NL, Eckermann AL, Meade TJ. Synthesis and Characterization of Ruthenium and Rhenium Nucleosides. Inorg Chem 2007; 46:9853-62. [DOI: 10.1021/ic701250r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peijiao Wang
- Departments of Chemistry, Biochemistry and Molecular and Cell Biology, Neurobiology and Physiology and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, University of Washington, School of Law, William H. Gates Hall, Box 353020 Seattle, Washington 98195, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, P.O. Box 3065, STN CSC, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Jeremiah E. Miller
- Departments of Chemistry, Biochemistry and Molecular and Cell Biology, Neurobiology and Physiology and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, University of Washington, School of Law, William H. Gates Hall, Box 353020 Seattle, Washington 98195, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, P.O. Box 3065, STN CSC, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Lawrence M. Henling
- Departments of Chemistry, Biochemistry and Molecular and Cell Biology, Neurobiology and Physiology and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, University of Washington, School of Law, William H. Gates Hall, Box 353020 Seattle, Washington 98195, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, P.O. Box 3065, STN CSC, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Charlotte L. Stern
- Departments of Chemistry, Biochemistry and Molecular and Cell Biology, Neurobiology and Physiology and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, University of Washington, School of Law, William H. Gates Hall, Box 353020 Seattle, Washington 98195, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, P.O. Box 3065, STN CSC, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Natia L. Frank
- Departments of Chemistry, Biochemistry and Molecular and Cell Biology, Neurobiology and Physiology and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, University of Washington, School of Law, William H. Gates Hall, Box 353020 Seattle, Washington 98195, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, P.O. Box 3065, STN CSC, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Amanda L. Eckermann
- Departments of Chemistry, Biochemistry and Molecular and Cell Biology, Neurobiology and Physiology and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, University of Washington, School of Law, William H. Gates Hall, Box 353020 Seattle, Washington 98195, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, P.O. Box 3065, STN CSC, University of Victoria, Victoria, BC, V8W 3V6, Canada
| | - Thomas J. Meade
- Departments of Chemistry, Biochemistry and Molecular and Cell Biology, Neurobiology and Physiology and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, University of Washington, School of Law, William H. Gates Hall, Box 353020 Seattle, Washington 98195, Beckman Institute, California Institute of Technology, Pasadena, California 91125, and Department of Chemistry, P.O. Box 3065, STN CSC, University of Victoria, Victoria, BC, V8W 3V6, Canada
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Gnaccarini C, Peter S, Scheffer U, Vonhoff S, Klussmann S, Göbel MW. Site-specific cleavage of RNA by a metal-free artificial nuclease attached to antisense oligonucleotides. J Am Chem Soc 2007; 128:8063-7. [PMID: 16771522 DOI: 10.1021/ja061036f] [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: 11/30/2022]
Abstract
RNA cleaving tris(2-aminobenzimidazoles) have been attached to DNA oligonucleotides via disulfide or amide bonds. The resulting conjugates are effective organocatalytic nucleases showing substrate and site selectivity as well as saturation kinetics. The benzimidazole conjugates also degrade enantiomeric RNA. This observation rules out contamination effects as an alternative explanation of RNA degradation. The pH dependency shows that the catalyst is most active in the deprotonated state. Typical half-lifes of RNA substrates are in the range of 12-17 h. Thus, conjugates of tris(2-aminobenzimidazoles) can compete with the majority of metal-dependent artificial nucleases.
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Affiliation(s)
- Claudio Gnaccarini
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Marie-Curie-Str. 11, D-60439 Frankfurt am Main, Germany
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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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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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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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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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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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Scheffer U, Strick A, Ludwig V, Peter S, Kalden E, Göbel MW. Metal-free catalysts for the hydrolysis of RNA derived from guanidines, 2-aminopyridines, and 2-aminobenzimidazoles. J Am Chem Soc 2005; 127:2211-7. [PMID: 15713099 DOI: 10.1021/ja0443934] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
2-aminopyridine and 2-aminobenzimidazole were chosen as structural analogues to substitute guanidinium groups in receptor molecules designed as phosphoryl transfer catalysts. Shifting the pKa of the guanidinium analogues toward 7 was expected to raise catalytic activities in aqueous buffer. Although the pKa's of both heterocycles are similar (6.2 and 7.0), only 2-aminobenzimidazole led to active RNA cleavers. All cleavage assays were run with fluorescently labeled substrates and a DNA sequencer. RNase contaminations would degrade RNA enantioselectively. In contrast, achiral catalysts such as 9b and 10b necessarily induce identical cleavage patterns in RNA and its mirror image. This principle allowed us to safely rule out contamination effects in this study. The most active catalysts, tris(2-aminobenzimidazoles) 9b and 10b, were shown by fluorescence correlation spectroscopy (FCS) to aggregate with oligonucleotides. However, at very low concentrations the compounds are still active in the nonaggregated state. Conjugates of 10b with antisense oligonucleotides or RNA binding peptides, therefore, will be promising candidates as site specific artificial ribonucleases.
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Affiliation(s)
- Ute Scheffer
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Marie-Curie-Str. 11, 60439 Frankfurt am Main, Germany
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23
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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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24
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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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25
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Whitney A, Gavory G, Balasubramanian S. Site-specific cleavage of human telomerase RNA using PNA-neocuproine.Zn(II) derivatives. Chem Commun (Camb) 2003:36-7. [PMID: 12610953 DOI: 10.1039/b210135a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we report the synthesis of a novel PNA based neocuproine.Zn RNA cleaving agent; we demonstrate that such agents sequence specifically cleave a synthetic RNA target and in particular the RNA component of human telomerase.
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Affiliation(s)
- Andrew Whitney
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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26
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Bünzli JCG, Piguet C. Lanthanide-containing molecular and supramolecular polymetallic functional assemblies. Chem Rev 2002; 102:1897-928. [PMID: 12059257 DOI: 10.1021/cr010299j] [Citation(s) in RCA: 753] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jean-Claude G Bünzli
- Institute of Molecular and Biological Chemistry, Swiss Federal Institute of Technology, BCH 1402, CH-1015 Lausanne, Switzerland.
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27
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Scarso A, Scheffer U, Göbel M, Broxterman QB, Kaptein B, Formaggio F, Toniolo C, Scrimin P. A peptide template as an allosteric supramolecular catalyst for the cleavage of phosphate esters. Proc Natl Acad Sci U S A 2002; 99:5144-9. [PMID: 11943857 PMCID: PMC122736 DOI: 10.1073/pnas.072642699] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2001] [Indexed: 11/18/2022] Open
Abstract
The heptapeptide H-Iva-Api-Iva-ATANP-Iva-Api-Iva-NHCH(3) (P1a), where Iva is (S)-isovaline, Api is 4-amino-4-carboxypiperidine, and ATANP is (S)-2-amino-3-[1-(1,4,7-triazacyclononane)]propanoic acid, has been synthesized. Its conformation in aqueous solution is essentially that of a 3(10)-helix. By connecting three copies of P1a to a functionalized Tris(2-aminoethyl)amine (Tren) platform a new peptide template, [T(P1)(3)], was obtained. This molecule is able to bind up to four metal ions (Cu(II) or Zn(II)): one in the Tren subsite and three in the azacyclononane subunits. The binding of the metals to the Tren platform induces a change from an open to a closed conformation in which the three short, helical peptides are aligned in a parallel manner with the azacyclonane units pointing inward within the pseudocavity they define. T(P1)(3) shows a peculiar behavior in the transphosphorylation of phosphate esters; the tetrazinc complex is a catalyst of the cleavage of 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP), whereas the free ligand is a catalyst of the cleavage of an oligomeric RNA sequence with selectivity for pyrimidine bases. In the case of HPNP, Zn(II) acts as a positive allosteric effector by enhancing the catalytic efficiency of the system. In the case of the polyanionic RNA substrate, Zn(II) switches off the activity, thus behaving as a negative allosteric regulator. It is suggested that the opposite behavior of the catalyst induced by Zn(II) is associated with the change of conformation of the Tren platform, and consequently of the relative spatial disposition of the three linked peptides, that occurs after binding of the metal ion.
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Affiliation(s)
- Alessandro Scarso
- University of Padova, Department of Organic Chemistry and Consiglio Nazionale delle Ricerche-Centro Meccanismi Reazioni Organiche, 35131 Padova, Italy
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28
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Manoharan M. Oligonucleotide conjugates as potential antisense drugs with improved uptake, biodistribution, targeted delivery, and mechanism of action. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2002; 12:103-28. [PMID: 12074364 DOI: 10.1089/108729002760070849] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
This review summarizes the effect of conjugating small molecules and large biomacromolecules to antisense oligonucleotides to improve their therapeutic potential. In many cases, favorable changes in pharmacokinetic and pharmacodynamic properties were observed. Opportunities exist to change the terminating mechanism of antisense action or to enhance the RNase H mode of action via conjugate formation.
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Affiliation(s)
- Muthiah Manoharan
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc, Carlsbad, CA 92008, USA.
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29
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Putnam WC, Daniher AT, Trawick BN, Bashkin JK. Efficient new ribozyme mimics: direct mapping of molecular design principles from small molecules to macromolecular, biomimetic catalysts. Nucleic Acids Res 2001; 29:2199-204. [PMID: 11353090 PMCID: PMC55460 DOI: 10.1093/nar/29.10.2199] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2000] [Revised: 01/29/2001] [Accepted: 03/10/2001] [Indexed: 11/13/2022] Open
Abstract
Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specific RNA cleavage when compared with analogous o-phenanthroline- and terpyridine-derived reagents. The suppression of hydroxide-bridged dimers and the greater activation of coordinated water by Cu(II) neocuproine (compared with the o-phenanthroline and terpyridine complexes) better allow Cu(II) to reach its catalytic potential as a biomimetic RNA cleavage agent. This work demonstrates the direct mapping of molecular design principles from small-molecule cleavage to macromolecular cleavage events, generating enhanced biomimetic, sequence-specific RNA cleavage agents.
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Affiliation(s)
- W C Putnam
- Department of Chemistry, Washington University, St Louis, MO 63130-4899, USA
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30
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Giegé R, Felden B, Zenkova MA, Sil'nikov VN, Vlassov VV. Cleavage of RNA with synthetic ribonuclease mimics. Methods Enzymol 2001; 318:147-65. [PMID: 10889986 DOI: 10.1016/s0076-6879(00)18050-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- R Giegé
- UPR 9002 Structure de Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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31
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Mikkola S, Oivanen M, Neuvonen K, Piitari S, Ketomäki K, Lönnberg H. Cleavage of the phosphodiester bond of uridylyl-(3',5')-8-carboxymethylaminoadenosine by hydronium, hydroxide and zinc(II) ions: a model study aimed at elucidating the potential of a carboxylate function as an intramolecular catalyst. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1675-92. [PMID: 11200265 DOI: 10.1080/15257770008045452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Uridylyl-(3',5')-8-carboxymethylaminoadenosine has been synthesised, and its transesterification to uridine 2',3'-cyclic phosphate in the presence and absence of Zn2+ ion has been studied. The results show that a carboxylate function in the vicinity of the phosphodiester bond accelerates the metal ion promoted cleavage but not the metal ion independent reaction. Under acidic conditions, the predominant reaction is the cleavage of the side chain, giving the 8-amino derivative.
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Affiliation(s)
- S Mikkola
- Department of Chemistry, University of Turku, Finland.
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32
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Beloglazova NG, Sil'nikov VN, Zenkova MA, Vlassov VV. Cleavage of yeast tRNAPhe with complementary oligonucleotide conjugated to a small ribonuclease mimic. FEBS Lett 2000; 481:277-80. [PMID: 11007978 DOI: 10.1016/s0014-5793(00)02029-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An oligonucleotide conjugate bearing a chemical construct mimicking the catalytic center of ribonuclease A has been designed and studied. The conjugate efficiently cleaves yeast tRNAPhe at a single site adjacent to the target complementary sequence.
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Affiliation(s)
- N G Beloglazova
- Institute of Bioorganic Chemistry, Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Avenue, 630090, Novosibirsk, Russia
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33
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Synthesis, structural characterization and potentiometric studies of divalent metal complexes with an octadentate tetraazamacrocyclic ligand and their DNA cleavage ability. Polyhedron 2000. [DOI: 10.1016/s0277-5387(00)00420-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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34
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Affiliation(s)
- S T Crooke
- ISIS Pharmaceuticals, Inc., Carlsbad, California 92008, USA
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35
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36
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Zagórowska I, Kuusela S, Lönnberg H. Metal ion-dependent hydrolysis of RNA phosphodiester bonds within hairpin loops. A comparative kinetic study on chimeric ribo/2'-O-methylribo oligonucleotides. Nucleic Acids Res 1998; 26:3392-6. [PMID: 9649624 PMCID: PMC147710 DOI: 10.1093/nar/26.14.3392] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Several chimeric ribo/2'- O -methylribo oligonucleotides were synthesized and their hydrolytic cleavage studied in the presence of Mg2+, Zn2+, Pb2+and the 1,4,9-triaza-cyclododecane chelate of Zn2+(Zn2+[12]aneN3) to evaluate the importance of RNA secondary structure as a factor determining the reactivity of phosphodiester bonds. In all the cases studied, a phosphodiester bond within a 4-7 nt loop was hydrolytically more stable than a similar bond within a linear single strand, but markedly less stable than that in a double helix. With Zn2+and Zn2+[12]aneN3, the hydrolytic stability of a phosphodiester bond within a hairpin loop gradually decreased on increasing the distance from the stem. A similar but less systematic trend was observed with Pb2+. Zn2+- and Pb2+-promoted cleavage was observed to be considerably more sensitive to the secondary structure of the chain than that induced by Zn2+[12]aneN3. This difference in behaviour may be attributed to bidentate binding of uncomplexed aquo ions to two different phosphodiester bonds. Mg2+was observed to be catalytically virtually inactive compared with the other cleaving agents studied.
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Affiliation(s)
- I Zagórowska
- University of Turku, Department of Chemistry, FIN-20500 Turku, Finland
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37
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Molenveld P, Engbersen JFJ, Kooijman H, Spek AL, Reinhoudt DN. Efficient Catalytic Phosphate Diester Cleavage by the Synergetic Action of Two Cu(II) Centers in a Dinuclear Cis-Diaqua Cu(II) Calix[4]arene Enzyme Model. J Am Chem Soc 1998. [DOI: 10.1021/ja9805324] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Molenveld
- Contribution from the Laboratory of Supramolecular Chemistry and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and the Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Johan F. J. Engbersen
- Contribution from the Laboratory of Supramolecular Chemistry and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and the Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Huub Kooijman
- Contribution from the Laboratory of Supramolecular Chemistry and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and the Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Anthony L. Spek
- Contribution from the Laboratory of Supramolecular Chemistry and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and the Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - David N. Reinhoudt
- Contribution from the Laboratory of Supramolecular Chemistry and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands, and the Bijvoet Center for Biomolecular Research, Crystal and Structural Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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38
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Toward the development of metal-based synthetic nucleases and peptidases: a rationale and progress report in applying the principles of coordination chemistry. Coord Chem Rev 1998. [DOI: 10.1016/s0010-8545(98)00157-x] [Citation(s) in RCA: 487] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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40
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Abstract
Many elegant dinuclear transition metal and lanthanide complexes that efficiently hydrolyze phosphate esters including RNA and DNA have been reported recently. In most cases, the dinuclear complexes are much more reactive than the corresponding mononuclear metal complexes. Furthermore, structural and kinetic data indicate that substantial rate acceleration for phosphate diester cleavage is obtained by bridging the dinuclear metal centers with the two phosphoryl oxygens. Interestingly, such bridging structures have recently been implicated in several metalloenzyme catalyzed phosphate hydrolyses.
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Affiliation(s)
- J Chin
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 2K5, Canada.
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41
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Renaud F, Piguet C, Bernardinelli G, Bünzli JCG, Hopfgartner G. In Search for Mononuclear Helical Lanthanide Building Blocks with Predetermined Properties: Triple-stranded Helical Complexes withN,N,N',N'-tetraethylpyridine-2,6-dicarboxamide. Chemistry 1997. [DOI: 10.1002/chem.19970031014] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Baker BF, Khalili H, Wei N, Morrow JR. Cleavage of the 5‘ Cap Structure of mRNA by a Europium(III) Macrocyclic Complex with Pendant Alcohol Groups. J Am Chem Soc 1997. [DOI: 10.1021/ja971050f] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Häner R, Hall J. The sequence-specific cleavage of RNA by artificial chemical ribonucleases. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:423-30. [PMID: 9303194 DOI: 10.1089/oli.1.1997.7.423] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Based on work spanning 50 years, several groups have recently achieved the specific cleavage of RNA by attaching RNA-cleaving chemical moieties to antisense oligonucleotides. Such artificial chemical ribonucleases have potential as a possible next generation of antisense compounds and also as probes for structural and functional investigations of RNA. Different chemical moieties, such as polyamines, imidazoles, and metal complexes, have been used as the catalytic part of the artificial nucleases. To be of practical use as therapeutics, however, the conjugates must fulfil a number of strict requirements, such as ease of preparation, chemical stability, selectivity, nontoxicity, and, for metal complexes, inertness to loss of cation from the ligand. In addition, high cleavage efficiency is essential to overcome short lifetimes of cellular mRNA targets, and the reaction should not depend on additional cofactors. Based on these criteria, we believe that metal complexes, in particular macrocyclic lanthanide complexes, have the best chance of success for said purpose.
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Affiliation(s)
- R Häner
- Novartis Pharma AG, Basel, Switzerland
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44
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Magda D, Wright M, Crofts S, Lin A, Sessler JL. Metal Complex Conjugates of Antisense DNA Which Display Ribozyme-Like Activity. J Am Chem Soc 1997. [DOI: 10.1021/ja9711223] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Hall J, Hüsken D, Häner R. Sequence-Specific Cleavage of RNA Using Macrocyclic Lanthanide Complexes Conjugated to Oligonucleotides: A Structure Activity Study. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708006187] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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46
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Daniher AT, Xie J, Mathur S, Bashkin JK. Modulation of RNase H activity by modified DNA probes: major groove vs minor groove effects. Bioorg Med Chem 1997; 5:1037-42. [PMID: 9222496 DOI: 10.1016/s0968-0896(97)00040-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have previously prepared ribozyme mimics and chemical nucleases from modified DNA containing pendant bipyridine and terpyridine groups. The ability of these modified DNA probes to support RNase H cleavage of complementary RNA is described. DNA/RNA duplexes were formed using DNA probes designed to deliver metal complexes via either the major groove or the minor groove of the duplex. The duplexes were treated with Escherichia coli RNase H. Modifications in the major groove produced the same RNA cleavage pattern as unmodified DNA probes. However, minor groove substituents inhibited RNA cleavage over a four-base region. Comparison was made with a DNA probe containing a 2'-OMe modification. Our results support enzyme binding in the minor groove of a DNA/RNA duplex. We do not observe cleavage directly across from the modified nucleoside. The RNA cleavage efficiency effected by RNase H and a DNA probe decreases as follows: unmodified DNA > or = C-5 modified DNA >> c2'-modified DNA > C1'-modified DNA. Results with 28-mer RNA substrates roughly parallel those obtained with a 159-mer RNA target. The differences observed between low and high MW RNA substrates can be explained by a much higher enzyme-substrate binding constant for the high MW target.
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Affiliation(s)
- A T Daniher
- Department of Chemistry, Washington University, St Louis, MO 63130, USA
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47
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Hegg EL, Deal KA, Kiessling LL, Burstyn JN. Hydrolysis of Double-Stranded and Single-Stranded RNA in Hairpin Structures by the Copper(II) Macrocycle Cu([9]aneN(3))Cl(2). Inorg Chem 1997; 36:1715-1718. [PMID: 11669765 DOI: 10.1021/ic960955b] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Eric L. Hegg
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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48
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Haner R, Hall J, Rihs G. Synthesis and Structure of a Macrocyclic Europium Complex and its possible role as a catalyst for phosphodiester transesterification. Helv Chim Acta 1997. [DOI: 10.1002/hlca.19970800213] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Magda D, Crofts S, Lin A, Miles D, Wright M, Sessler JL. Synthesis and Kinetic Properties of Ribozyme Analogues Prepared Using Phosphoramidite Derivatives of Dysprosium(III) Texaphyrin. J Am Chem Soc 1997. [DOI: 10.1021/ja9627149] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Darren Magda
- Pharmacyclics, Inc., 995 E. Arques Avenue Sunnyvale, California 94086 Department of Chemistry and Biochemistry University of Texas at Austin, Austin, Texas 78712
| | - Shaun Crofts
- Pharmacyclics, Inc., 995 E. Arques Avenue Sunnyvale, California 94086 Department of Chemistry and Biochemistry University of Texas at Austin, Austin, Texas 78712
| | - Alice Lin
- Pharmacyclics, Inc., 995 E. Arques Avenue Sunnyvale, California 94086 Department of Chemistry and Biochemistry University of Texas at Austin, Austin, Texas 78712
| | - Dale Miles
- Pharmacyclics, Inc., 995 E. Arques Avenue Sunnyvale, California 94086 Department of Chemistry and Biochemistry University of Texas at Austin, Austin, Texas 78712
| | - Meredith Wright
- Pharmacyclics, Inc., 995 E. Arques Avenue Sunnyvale, California 94086 Department of Chemistry and Biochemistry University of Texas at Austin, Austin, Texas 78712
| | - Jonathan L. Sessler
- Pharmacyclics, Inc., 995 E. Arques Avenue Sunnyvale, California 94086 Department of Chemistry and Biochemistry University of Texas at Austin, Austin, Texas 78712
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50
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Perreault DM, Anslyn EV. Der Mechanismus der RNA-Spaltung durch Umesterung – eine vereinheitlichende Analyse des aktuellen Diskussionsstandes. Angew Chem Int Ed Engl 1997. [DOI: 10.1002/ange.19971090505] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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