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Ortmeyer J, Vukadinovic Y, Neuba A, Flörke U, Henkel G. Combining a Phenanthroline Moiety with Peralkylated Guanidine Residues: Homometallic Cu
II
, Ni
II
and Zn
II
Halide Complexes with Site‐Differentiating Janus Head Ligands. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201800905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jochen Ortmeyer
- Fakultät für Naturwissenschaften Department Chemie Universität Paderborn Warburger Strasse 100 33098 Paderborn Germany
| | - Yannik Vukadinovic
- Fakultät für Naturwissenschaften Department Chemie Universität Paderborn Warburger Strasse 100 33098 Paderborn Germany
| | - Adam Neuba
- Fakultät für Naturwissenschaften Department Chemie Universität Paderborn Warburger Strasse 100 33098 Paderborn Germany
| | - Ulrich Flörke
- Fakultät für Naturwissenschaften Department Chemie Universität Paderborn Warburger Strasse 100 33098 Paderborn Germany
| | - Gerald Henkel
- Fakultät für Naturwissenschaften Department Chemie Universität Paderborn Warburger Strasse 100 33098 Paderborn Germany
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2
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Ortmeyer J, Vukadinovic Y, Neuba A, Egold H, Flörke U, Henkel G. Combining a Phenanthroline Moiety with Two Peralkylated Guanidine Residues: Janus Head Pro-Ligands. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jochen Ortmeyer
- Fakultät für Naturwissenschaften, Department Chemie; Universität Paderborn; Warburger Strasse 100 33098 Paderborn Germany
| | - Yannik Vukadinovic
- Fakultät für Naturwissenschaften, Department Chemie; Universität Paderborn; Warburger Strasse 100 33098 Paderborn Germany
| | - Adam Neuba
- Fakultät für Naturwissenschaften, Department Chemie; Universität Paderborn; Warburger Strasse 100 33098 Paderborn Germany
| | - Hans Egold
- Fakultät für Naturwissenschaften, Department Chemie; Universität Paderborn; Warburger Strasse 100 33098 Paderborn Germany
| | - Ulrich Flörke
- Fakultät für Naturwissenschaften, Department Chemie; Universität Paderborn; Warburger Strasse 100 33098 Paderborn Germany
| | - Gerald Henkel
- Fakultät für Naturwissenschaften, Department Chemie; Universität Paderborn; Warburger Strasse 100 33098 Paderborn Germany
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3
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Yu Z, Cowan JA. Catalytic Metallodrugs: Substrate-Selective Metal Catalysts as Therapeutics. Chemistry 2017; 23:14113-14127. [PMID: 28688119 DOI: 10.1002/chem.201701714] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Zhen Yu
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
| | - James A. Cowan
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
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4
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Synthesis of acridine-1,8-dione substituted (E)-5-(3-aminoallyl)-uridine-5′-triphosphate: a new potential fluorogenic molecular probe. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.03.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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5
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Liu C, Zhu Y, Tang M. Theoretical studies on binding modes of copper-based nucleases with DNA. J Mol Graph Model 2015; 64:11-29. [PMID: 26766349 DOI: 10.1016/j.jmgm.2015.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 01/06/2023]
Abstract
In the present work, molecular simulations were performed for the purpose of predicting the binding modes of four types of copper nucleases (a total 33 compounds) with DNA. Our docking results accurately predicted the groove binding and electrostatic interaction for some copper nucleases with B-DNA. The intercalation modes were also reproduced by "gap DNA". The obtained results demonstrated that the ligand size, length, functional groups and chelate ring size bound to the copper center could influence the binding affinities of copper nucleases. The binding affinities obtained from the docking calculations herein also replicated results found using MM-PBSA approach. The predicted DNA binding modes of copper nucleases with DNA will ultimately help us to better understand the interaction of copper compounds with DNA.
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Affiliation(s)
- Chunmei Liu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China
| | - Yanyan Zhu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China.
| | - Mingsheng Tang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China.
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6
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Bencini A, Lippolis V. 1,10-Phenanthroline: A versatile building block for the construction of ligands for various purposes. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2010.04.008] [Citation(s) in RCA: 288] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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DNA oxidative cleavage induced by the novel peptide derivatives of 3-(quinoxalin-6-yl)alanine in combination with Cu(II) or Fe(II) ions. Bioinorg Chem Appl 2010:906836. [PMID: 20224817 PMCID: PMC2834960 DOI: 10.1155/2009/906836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 12/17/2009] [Indexed: 11/17/2022] Open
Abstract
Three model dipeptides containing 3-(2,3-di(pyridin-2-yl)quinoxalin-6-yl)alanine, 3-(dipyrido[3,2-a:2,3-c]phenazin-11-yl)alanine, and 3-(2,3-diphenylquinoxalin-6-yl)alanine were studied with respect to their ability to bind selected transition metal ions, such as Cu(II), Fe(II), Ni(II), Co(II), Mn(II), and Cr(III). It was found that only Cu(II) and Fe(II) ions could form stable complex species with the studied compounds. The ability to form the complexes correlated well with DNA damage experiments. Only the ferrous and cupric complexes are capable of generating both single- and double-strand scissions. However, double-strand breakages appear to be dominating lesions in the presence of hydrogen peroxide, especially for copper(II) containing systems. The quantity of breakage products in the presence of N-(3-(dipyrido[3,2-a:2,3-c]phenazine-11-yl)alanyl)glycine complexes was the highest as compared to the complexes of the remaining compounds. Moreover, this ligand was the only one that cleaved DNA in the absence of either Cu(II) or Fe(II) ions.
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8
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Noestheden M, Hu Q, Tonary AM, Tay LL, Pezacki JP. Evaluation of chemical labeling strategies for monitoring HCV RNA using vibrational microscopy. Org Biomol Chem 2007; 5:2380-9. [PMID: 17637957 DOI: 10.1039/b704812b] [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: 02/05/2023]
Abstract
Raman and coherent anti-Stokes Raman scattering (CARS) microscopies have the potential to aid in detailed longitudinal studies of RNA localization. Here, we evaluate the use of carbon-deuterium and benzonitrile functional group labels as contrast agents for vibrational imaging of hepatitis C virus (HCV) replicon RNA. Dynamic light scattering and atomic force microscopy were used to evaluate the structural consequences of altering HCV subgenomic replicon RNA. Modification with benzonitrile labels caused the replicon RNA tertiary structure to partially unfold. Conversely, deuterium-modified replicon RNA was structurally similar to unmodified replicon RNA. Furthermore, the deuterated replicon RNA provided promising vibrational contrast in Raman imaging experiments. The functional effect of modifying subgenomic HCV replicon RNA was evaluated using the luciferase gene as a genetic reporter of translation. Benzonitrile labeling of the replicon RNA prevented translation in cell-based luciferase assays, while the deuterated replicon RNA retained both translation and replication competency. Thus, while the scattering cross-section for benzonitrile labels was higher, only carbon-deuterium labels proved to be non-perturbative to the function of HCV replicon RNA.
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Affiliation(s)
- Matthew Noestheden
- Steacie Institute for Molecular Sciences, The National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, Canada
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9
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Niranjanakumari S, Day-Storms JJ, Ahmed M, Hsieh J, Zahler NH, Venters RA, Fierke CA. Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage. RNA (NEW YORK, N.Y.) 2007; 13:521-35. [PMID: 17299131 PMCID: PMC1831860 DOI: 10.1261/rna.308707] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 12/21/2006] [Indexed: 05/03/2023]
Abstract
Bacterial ribonuclease P (RNase P) is a ribonucleoprotein complex composed of one catalytic RNA (PRNA) and one protein subunit (P protein) that together catalyze the 5' maturation of precursor tRNA. High-resolution X-ray crystal structures of the individual P protein and PRNA components from several species have been determined, and structural models of the RNase P holoenzyme have been proposed. However, holoenzyme models have been limited by a lack of distance constraints between P protein and PRNA in the holoenzyme-substrate complex. Here, we report the results of extensive cross-linking and affinity cleavage experiments using single-cysteine P protein variants derivatized with either azidophenacyl bromide or 5-iodoacetamido-1,10-o-phenanthroline to determine distance constraints and to model the Bacillus subtilis holoenzyme-substrate complex. These data indicate that the evolutionarily conserved RNR motif of P protein is located near (<15 Angstroms) the pre-tRNA cleavage site, the base of the pre-tRNA acceptor stem and helix P4 of PRNA, the putative active site of the enzyme. In addition, the metal binding loop and N-terminal region of the P protein are proximal to the P3 stem-loop of PRNA. Studies using heterologous holoenzymes composed of covalently modified B. subtilis P protein and Escherichia coli M1 RNA indicate that P protein binds similarly to both RNAs. Together, these data indicate that P protein is positioned close to the RNase P active site and may play a role in organizing the RNase P active site.
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10
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Ramiro P, García-Fresnadillo D, Orellana G. Synthesis and characterisation of N-1,10-phenanthrolin-5-ylalkylamides and their photosensitising heteroleptic Ru(II) complexes. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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DNA and RNA Cleavage Mediated by Phenanthroline-Cuprous Oligonucleotides: From Properties to Applications. ARTIFICIAL NUCLEASES 2004. [DOI: 10.1007/978-3-642-18510-6_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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12
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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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13
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Marzi S, Knight W, Brandi L, Caserta E, Soboleva N, Hill WE, Gualerzi CO, Lodmell JS. Ribosomal localization of translation initiation factor IF2. RNA (NEW YORK, N.Y.) 2003; 9:958-69. [PMID: 12869707 PMCID: PMC1370462 DOI: 10.1261/rna.2116303] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2002] [Accepted: 05/15/2003] [Indexed: 05/22/2023]
Abstract
Bacterial translation initiation factor IF2 is a GTP-binding protein that catalyzes binding of initiator fMet-tRNA in the ribosomal P site. The topographical localization of IF2 on the ribosomal subunits, a prerequisite for understanding the mechanism of initiation complex formation, has remained elusive. Here, we present a model for the positioning of IF2 in the 70S initiation complex as determined by cleavage of rRNA by the chemical nucleases Cu(II):1,10-orthophenanthroline and Fe(II):EDTA tethered to cysteine residues introduced into IF2. Two specific amino acids in the GII domain of IF2 are in proximity to helices H3, H4, H17, and H18 of 16S rRNA. Furthermore, the junction of the C-1 and C-2 domains is in proximity to H89 and the thiostrepton region of 23S rRNA. The docking is further constrained by the requisite proximity of the C-2 domain with P-site-bound tRNA and by the conserved GI domain of the IF2 with the large subunit's factor-binding center. Comparison of our present findings with previous data further suggests that the IF2 orientation on the 30S subunit changes during the transition from the 30S to 70S initiation complex.
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Affiliation(s)
- Stefano Marzi
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, 62032 Camerino (MC) Italy
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14
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García-Raso A, Fiol JJ, Adrover B, Moreno V, Mata I, Espinosa E, Molins E. Synthesis, structure and nuclease properties of several ternary copper(II) peptide complexes with 1,10-phenanthroline. J Inorg Biochem 2003; 95:77-86. [PMID: 12763651 DOI: 10.1016/s0162-0134(03)00121-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Three new ternary peptide-Cu(II)-1,10-phenanthroline (phen) complexes, [Cu(L-ala-gly)(phen)].3.5H(2)O 1, [Cu(L-val-gly)(phen)] 2 and [Cu(gly-L-trp)(phen)].2H(2)O 3, have been prepared and structurally characterised. These compounds exist as distorted square pyramidal complexes with the five co-ordination sites occupied by the tridentate peptide dianion and the two heterocyclic nitrogens of the phenanthroline ligand. The bulk of the lateral chain in the peptide moiety determines the relative disposition of the phen ligand. Thus, in [Cu(L-val-gly)(phen)] 2, the phenanthroline plane is deviated towards the opposite side of the isopropyl group of the L-valine moiety. On the other hand, in [Cu(gly-L-trp)(phen)].2H(2)O 3 the absence of stacking interactions between phen and indole rings and the presence of an intramolecular CH...pi interaction should be pointed out. These complexes exhibit significant differences in their nuclease activity which depends on the nature of the peptidic moiety, the complex [Cu(gly-L-trp) (phen)].2H(2)O 3 being the most active.
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Affiliation(s)
- Angel García-Raso
- Departament de Quĭmica, Universitat de les Illes Balears, Cra. Valldemossa Km 7.5, 07122, Palma de Mallorca, Spain.
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15
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Copper-dioxygen complexes and their roles in biomimetic oxidation reactions. ADVANCES IN CATALYTIC ACTIVATION OF DIOXYGEN BY METAL COMPLEXES 2003. [DOI: 10.1007/0-306-47816-1_2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Abstract
Chemical cleavage is developing into a powerful tool for analysis and characterization of nucleic acids. Phenanthroline-Cu(II) cleavage has been used extensively for studies of DNA for the last two decades, but recently has been applied to structural studies of RNA as well. This approach has been used to study the structure and structural changes occurring in ribosomal RNA within the ribosomes. In this article we discuss the mechanism by which phenanthroline cleaves, the applications possible using this approach, and the results that can be obtained. Protocols for use of phenanthroline are outlined as well.
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Affiliation(s)
- G W Muth
- Division of Biological Sciences and Department of Chemistry, University of Montana, Missoula, Montana 59812, USA
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17
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Wan R, Zhao G, Chen J, Zhao Y. Research progresses of artificial nucleic acid cleavage agents. ACTA ACUST UNITED AC 2000. [DOI: 10.1007/bf03183520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Milne L, Xu Y, Perrin DM, Sigman DS. An approach to gene-specific transcription inhibition using oligonucleotides complementary to the template strand of the open complex. Proc Natl Acad Sci U S A 2000; 97:3136-41. [PMID: 10716709 PMCID: PMC16205 DOI: 10.1073/pnas.97.7.3136] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The single-stranded region of DNA within the open complex of transcriptionally active genes provides a unique target for the design of gene-specific transcription inhibitors. Using the Escherichia coli lac UV5 and trp EDCBA promoters as in vitro models of open complex formation, we have identified the sites inside these transcription bubbles that are accessible for hybridization by short, nuclease-resistant, non-extendable oligoribonucleotides (ORNs). Binding of ORNs inside the open complex was determined by linking the chemical nuclease bis(1,10-phenanthroline) cuprous chelate [(OP)(2)Cu(+)] to the ORN and demonstrating template-specific DNA scission. In addition, these experiments were supported by in vitro transcription inhibition. We find that the most effective inhibitors are 5 nt long and have sequences that are complementary to the DNA template strand in the region near the transcription start site. The ORNs bind to the DNA template strand, forming an antiparallel heteroduplex inside the open complex. In this system, RNA polymerase is essential not only to melt the duplex DNA but also to facilitate hybridization of the incoming ORN. This paradigm for gene-specific inactivation relies on the base complementarity of the ORN and the catalytic activity and sequence specificity of RNA polymerase for the site- and sequence-specific recognition and inhibition of transcriptionally active DNA.
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Affiliation(s)
- L Milne
- Department of Biological Chemistry, School of Medicine, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1570, USA
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19
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An approach to gene-specific transcription inhibition using oligonucleotides complementary to the template strand of the open complex. Proc Natl Acad Sci U S A 2000. [PMID: 10716709 PMCID: PMC16205 DOI: 10.1073/pnas.050544597] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The single-stranded region of DNA within the open complex of transcriptionally active genes provides a unique target for the design of gene-specific transcription inhibitors. Using the Escherichia coli lac UV5 and trp EDCBA promoters as in vitro models of open complex formation, we have identified the sites inside these transcription bubbles that are accessible for hybridization by short, nuclease-resistant, non-extendable oligoribonucleotides (ORNs). Binding of ORNs inside the open complex was determined by linking the chemical nuclease bis(1,10-phenanthroline) cuprous chelate [(OP)(2)Cu(+)] to the ORN and demonstrating template-specific DNA scission. In addition, these experiments were supported by in vitro transcription inhibition. We find that the most effective inhibitors are 5 nt long and have sequences that are complementary to the DNA template strand in the region near the transcription start site. The ORNs bind to the DNA template strand, forming an antiparallel heteroduplex inside the open complex. In this system, RNA polymerase is essential not only to melt the duplex DNA but also to facilitate hybridization of the incoming ORN. This paradigm for gene-specific inactivation relies on the base complementarity of the ORN and the catalytic activity and sequence specificity of RNA polymerase for the site- and sequence-specific recognition and inhibition of transcriptionally active DNA.
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20
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Watnick RS, Gottesman ME. Binding of transcription termination protein nun to nascent RNA and template DNA. Science 1999; 286:2337-9. [PMID: 10600743 DOI: 10.1126/science.286.5448.2337] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The amino-terminal arginine-rich motif of coliphage HK022 Nun binds phage lambda nascent transcript, whereas the carboxyl-terminal domain interacts with RNA polymerase (RNAP) and blocks transcription elongation. RNA binding is inhibited by zinc (Zn2+) and stimulated by Escherichia coli NusA. To study these interactions, the Nun carboxyl terminus was extended by a cysteine residue conjugated to a photochemical cross-linker. The carboxyl terminus contacted NusA and made Zn2+-dependent intramolecular contacts. When Nun was added to a paused transcription elongation complex, it cross-linked to the DNA template. Nun may arrest transcription by anchoring RNAP to DNA.
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Affiliation(s)
- R S Watnick
- Department of Biochemistry and Molecular Biophysics and Institute of Cancer Research, Columbia University, New York, NY 10032, USA
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21
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Perrin DM, Garestier T, Hélène C. Expanding the catalytic repertoire of nucleic acid catalysts: simultaneous incorporation of two modified deoxyribonucleoside triphosphates bearing ammonium and imidazolyl functionalities. NUCLEOSIDES & NUCLEOTIDES 1999; 18:377-91. [PMID: 10358942 DOI: 10.1080/15257779908043083] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Two nucleoside triphosphates, a pyrimidine modified with an ammonium functionality and a purine modified with an imidazolyl functionality are compatible with all conditions for a combinatorial selection of nucleic-acid catalysts. We believe that this work is the first to demonstrate the potential for using not one but two modified nucleotides in tandem. The potential for an enriched catalytic repertoire is envisioned.
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Affiliation(s)
- D M Perrin
- Laboratoire de Biophysique, Museum National d'Histoire Naturelle, Paris, France
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22
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23
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24
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Bucklin DJ, van Waes MA, Bullard JM, Hill WE. Cleavage of 16S rRNA within the ribosome by mRNA modified in the A-site codon with phenanthroline-Cu(II). Biochemistry 1997; 36:7951-7. [PMID: 9201941 DOI: 10.1021/bi9624954] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cleavage of 16S rRNA was obtained through mRNA modified at position +5 with the chemical cleavage agent 1,10-o-phenanthroline. In the presence of Cu2+, and after addition of reducing agent to the modified mRNA-70S complex, cleavage of proximal nucleotides within the 16S rRNA occurred. Primer extension analysis of 16S rRNA fragments revealed that nucleotides 528-532, 1196, and 1396-1397 were cleaved. Nucleotides 1053-1055 were also cleaved but did not show the same level of specificity as the former. These results provide evidence that at some point in the translation process these regions are all within 15 A of position +5, the A-site codon, on the mRNA.
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Affiliation(s)
- D J Bucklin
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
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25
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Landgraf R, Ramamurthi KS, Sigman DS. Kinetics of spontaneous displacement of RNA from heteroduplexes by DNA. Nucleic Acids Res 1996; 24:3246-52. [PMID: 8774908 PMCID: PMC146063 DOI: 10.1093/nar/24.16.3246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have used R-loop formation and direct hybridization techniques to analyze the kinetics by which RNA is displaced from a heteroduplex by DNA of identical sequence. Using random walk simulations we were able to calculate the step times for a single displacement reaction. For RNA with a GC content of 57-60% the data indicate an RNA exchange probability of 50.06%, which is indicative of a modest destabilization of the heteroduplex compared with a DNA duplex in the presence of magnesium. The average step time for the reversible exchange of a single nucleotide is 345.0 (+/- 1.3) ms/step. An acceleration of the displacement reaction was observed in the absence of magnesium. A comparison with step times for elongation shows that RNA displacement would not be rate limiting to transcription elongation under two conditions: (i) if magnesium is eliminated from the newly synthesized heteroduplex; (ii) if displacement is kept in a forward only exchange mode through binding of the emerging RNA. Distamycin, a minor groove binding drug, is very effective as a 'catalyst' of RNA displacement. This effect is likely to be due to preferential binding of distamycin to the minor groove of the DNA duplex as opposed to the heteroduplex. This kinetic assay could therefore serve as a convenient assay for the determination of binding preferences of nucleic acid ligands.
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Affiliation(s)
- R Landgraf
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles 90024-1570, USA
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26
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Huang B, Schaeffer CJ, Li Q, Tsai MD. Splase: a new class IIS zinc-finger restriction endonuclease with specificity for Sp1 binding sites. JOURNAL OF PROTEIN CHEMISTRY 1996; 15:481-9. [PMID: 8895094 DOI: 10.1007/bf01886856] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A new restriction endonuclease, named Splase, was constructed by genetically fusing the DNA-cleavage domain of the restriction endonuclease Fok1 with the zinc-finger DNA-binding domain of the transcription factor Sp1. The resulting protein was expressed in Escherichia coli., partially purified, and shown to selectively digest plasmid DNA harboring consensus Sp1 sites. Splase was also shown to selectively digest the long terminal repeat of the HIV-1 DNA at Sp1 sites. Splase recognizes a 10-bp DNA sequence and hydrolyzes phosphodiester bonds upstream of the binding sequence. The binding specificity of Splase makes this a "rare cutter" restriction enzyme which could be valuable in creating large DNA fragments for genome sequencing projects. The result also presents the opportunity to create other restriction enzymes by altering the binding specificity of the zinc-finger recognition helix.
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Affiliation(s)
- B Huang
- Ohio State Biochemistry Program, Ohio State University, Columbus 43210, USA
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27
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Lin PS, Ho KC. New cytotoxic mechanism of the bioreductive agent Tirapazamine (SR 4233) mediated by forming complex with copper. ACTA ACUST UNITED AC 1996. [DOI: 10.1002/(sici)1520-6823(1996)4:5<211::aid-roi3>3.0.co;2-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Perrin DM, Mazumder A, Sigman DS. Oxidative chemical nucleases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 52:123-51. [PMID: 8821260 DOI: 10.1016/s0079-6603(08)60966-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- D M Perrin
- Department of Biological Chemistry, University of California, Los Angeles 90024, USA
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29
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Landgraf R, Chen CH, Sigman DS. Double stranded scission of DNA directed through sequence-specific R-loop formation. Nucleic Acids Res 1995; 23:3524-30. [PMID: 7567465 PMCID: PMC307233 DOI: 10.1093/nar/23.17.3524] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
R-loop formation with short (100 nt) RNAs provides a highly flexible and stringent method to achieve sequence-specific separation of target DNA at any given sequence. After stabilization of R-loops with glyoxal and removal of the RNA through RNase treatment the remaining single-stranded DNA bubble provides a highly favorable substrate for attenuated micrococcal nuclease. We investigated this method for sequence-specific scission of double-stranded DNA and achieved quantitative scission of 3-5 kb plasmids. The applicability to larger size DNA is demonstrated through specific excision of the intervening segment between two R-loops from a P1 plasmid of approximately 120 kb.
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Affiliation(s)
- R Landgraf
- Department of Biological Chemistry, School of Medicine, University of California-Los Angeles 90024-1570, USA
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30
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Landgraf R, Chen CH, Sigman DS. R-loop stability as a function of RNA structure and size. Nucleic Acids Res 1995; 23:3516-23. [PMID: 7567464 PMCID: PMC307232 DOI: 10.1093/nar/23.17.3516] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The sequence-specific formation of R-loops can be assayed using RNAs which overlap a HindIII cleavage site in a 3.5 kb plasmid. Chemical modification of the displaced DNA strand has permitted stabilization of these R-loops and allowed a systematic investigation of the dependence of these triple-stranded structures on the chain length and structure of the input RNA. RNAs as short as 50 nt form stable R-loops if 5-allylamine uridines (Uaa-RNA) are used in place of normal uridines; normal RNAs must be 100 nt long to form R-loops quantitatively. Since acetic anhydride decreases the hybridization efficiency of Uaa-RNAs, the positive charge of the RNAs must diminish the electrostatic repulsion of the three negatively charged phosphodiester backbones. The dependence of R-loop stability on the length of RNA can be stimulated with a random walk model, which also applies to strand migration within Holiday junctions. R-loop hybridization provides a versatile method to generate single-stranded DNA in a sequence-selective manner.
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Affiliation(s)
- R Landgraf
- Department of Biological Chemistry, School of Medicine, University of California-Los Angeles 90024-1570, USA
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31
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Pratviel G, Bernadou J, Meunier B. Die CH-Bindungen der Zuckerbausteine von DNA als Angriffspunkte für chemische Nucleasen und Wirkstoffe. Angew Chem Int Ed Engl 1995. [DOI: 10.1002/ange.19951070705] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Pendergrast PS, Ebright YW, Ebright RH. High-specificity DNA cleavage agent: design and application to kilobase and megabase DNA substrates. Science 1994; 265:959-62. [PMID: 8052855 DOI: 10.1126/science.8052855] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Strategies to cleave double-stranded DNA at specific DNA sites longer than those of restriction endonucleases (longer than 8 base pairs) have applications in chromosome mapping, chromosome cloning, and chromosome sequencing--provided that the strategies yield high DNA-cleavage efficiency and high DNA-cleavage specificity. In this report, the DNA-cleaving moiety copper:o-phenanthroline was attached to the sequence-specific DNA binding protein catabolite activator protein (CAP) at an amino acid that, because of a difference in DNA bending, is close to DNA in the specific CAP-DNA complex but is not close to DNA in the nonspecific CAP-DNA complex. The resulting CAP derivative, OP26CAP, cleaved kilobase and megabase DNA substrates at a 22-base pair consensus DNA site with high efficiency and exhibited no detectable nonspecific DNA-cleavage activity.
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Affiliation(s)
- P S Pendergrast
- Department of Chemistry, Rutgers University, New Brunswick, NJ 08855
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33
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Sigman DS, Chen CH, Gorin MB. Sequence-specific scission of DNA by RNAs linked to a chemical nuclease. Nature 1993; 363:474-5. [PMID: 7684825 DOI: 10.1038/363474a0] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
RNAs linked to the chemical nuclease 1,10-phenanthroline-copper cut double-stranded DNA of complementary sequence. This cleavage reaction is applicable to all sequences and can be used to measure the distance between marker genes in base pairs, map the size of a transcription unit and define positions of chromosomal breakpoints.
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Affiliation(s)
- D S Sigman
- Department of Biological Chemistry, School of Medicine, University of California, Los Angeles 90024-1570
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