1
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Sur S, Pujari S, Ranjan N, Azankia Temgoua L, Wicks SL, Conner A, Arya DP. Enhanced Sequence-Specific DNA Recognition Using Oligodeoxynucleotide-Benzimidazole Conjugates. ACS BIO & MED CHEM AU 2024; 4:154-164. [PMID: 38911908 PMCID: PMC11191566 DOI: 10.1021/acsbiomedchemau.3c00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 06/25/2024]
Abstract
Synthetic modification of oligodeoxynucleotides (ODNs) via conjugation to nucleic acid binding small molecules can improve hybridization and pharmacokinetic properties. In the present study, five Hoechst 33258 derived benzimidazoles were conjugated to T rich ODNs and their hybridization effectiveness was tested. Thermal denaturation studies revealed significant stabilization of complementary duplexes by ODN-benzimidazole conjugates, with the extent of stabilization being highly dependent on the length of the linker between DNA and benzimidazole. The increases in thermal stability were determined to be due to the binding of the benzimidazole moiety to the duplex. Circular dichroism and molecular modeling studies provided insights toward the influence of conjugation on duplex structure and how linker length impacts placement of the benzimidazole moiety in the minor groove. Furthermore, thermal denaturation studies with the complementary strand containing a single base mismatch or being RNA revealed that covalent conjugation of benzimidazoles to an ODN also enhances the sequence specificity. The fundamental studies reported herein provide a strategy to improve the stability and specificity properties of the ODN probes, which can be of use for targeting and diagnostics applications.
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Affiliation(s)
- Souvik Sur
- Laboratory of Medicinal Chemistry,
Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Suresh Pujari
- Laboratory of Medicinal Chemistry,
Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Nihar Ranjan
- Laboratory of Medicinal Chemistry,
Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Lidivine Azankia Temgoua
- Laboratory of Medicinal Chemistry,
Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Sarah L. Wicks
- Laboratory of Medicinal Chemistry,
Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Andrea Conner
- Laboratory of Medicinal Chemistry,
Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry,
Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
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2
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Hussein MK, Papež M, Dhiman H, Baumann M, Galosy S, Borth N. In silico design of CMV promoter binding oligonucleotides and their impact on inhibition of gene expression in Chinese hamster ovary cells. J Biotechnol 2022; 359:185-193. [DOI: 10.1016/j.jbiotec.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 10/31/2022]
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3
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Montazersaheb S, Avci ÇB, Bagca BG, Ay NPO, Tarhriz V, Nielsen PE, Charoudeh HN, Hejazi MS. Targeting TdT gene expression in Molt-4 cells by PNA-octaarginine conjugates. Int J Biol Macromol 2020; 164:4583-4590. [PMID: 32941907 DOI: 10.1016/j.ijbiomac.2020.09.081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acid (PNA) is an amide based structural nucleic acid mimic with potential applications in gene therapeutic drug discovery. In the present study, we evaluated and compared the effects on gene expression, cell viability and apoptosis of two antisense PNA-d-octaarginine conjugates, targeting sequences at the AUG translation start site or the 5'-UTR of the TdT (terminal deoxynucleotidyl transferase) gene, as well as a sense oligomer corresponding to the 5'-UTR-antisense, in Molt-4 cells. The protein level of TdT was determined by flow cytometry, and qPCR was used for mRNA expression analysis. Mismatch PNAs were used as control to address the sequence/target spcifity of the biological effects. The results showed that treatment with the AUG- and to slightly lesser extent with the 5'-UTR-antisense PNAs reduced the TdT mRNA as wel as the protein level, whereas only very low effect was observed for the 5'-UTR-sense PNA. A parallel effect was observed on reduced cell survival and increased rate of apoptosis. Our findings suggest that antisense PNAs can inhibit expression of the TdT gene and induce apoptosis in Molt-4 cells.
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Affiliation(s)
- Soheila Montazersaheb
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Çığır Biray Avci
- Faculty of Medicine, Department of Medical Biology, Ege University, Izmir, Turkey
| | - Bakiye Goker Bagca
- Faculty of Medicine, Department of Medical Biology, Ege University, Izmir, Turkey
| | | | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Peter E Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | | | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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4
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Cao S, Cheng R, Wang D, Zhao Y, Tang R, Yang X, Chen J. Dinuclear copper(II) complexes of “end-off” bicompartmental ligands: Alteration of the chelating arms on ligands to regulate the reactivity of the complexes towards DNA. J Inorg Biochem 2019; 192:126-139. [DOI: 10.1016/j.jinorgbio.2018.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/23/2018] [Accepted: 12/24/2018] [Indexed: 01/08/2023]
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5
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Corey DR. RNA-Mediated Gene Activation: Identifying a Candidate RNA for Preclinical Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [DOI: 10.1007/978-981-10-4310-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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6
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Karmakar S, Madsen AS, Guenther DC, Gibbons BC, Hrdlicka PJ. Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2'-alkylated RNA monomers. Org Biomol Chem 2014; 12:7758-73. [PMID: 25144705 PMCID: PMC4167914 DOI: 10.1039/c4ob01183j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite advances with triplex-forming oligonucleotides, peptide nucleic acids, polyamides and--more recently--engineered proteins, there remains an urgent need for synthetic ligands that enable specific recognition of double-stranded (ds) DNA to accelerate studies aiming at detecting, regulating and modifying genes. Invaders, i.e., energetically activated DNA duplexes with interstrand zipper arrangements of intercalator-functionalized nucleotides, are emerging as an attractive approach toward this goal. Here, we characterize and compare Invaders based on 1-, 2- and 4-pyrenyl-functionalized O2'-alkylated uridine monomers X-Z by means of thermal denaturation experiments, optical spectroscopy, force-field simulations and recognition experiments using DNA hairpins as model targets. We demonstrate that Invaders with +1 interstrand zippers of X or Y monomers efficiently recognize mixed-sequence DNA hairpins with single nucleotide fidelity. Intercalator-mediated unwinding and activation of the double-stranded probe, coupled with extraordinary stabilization of probe-target duplexes (ΔT(m)/modification up to +14.0 °C), provides the driving force for dsDNA recognition. In contrast, Z-modified Invaders show much lower dsDNA recognition efficiency. Thus, even very conservative changes in the chemical makeup of the intercalator-functionalized nucleotides used to activate Invader duplexes, affects dsDNA-recognition efficiency of the probes, which highlights the importance of systematic structure-property studies. The insight from this study will guide future design of Invaders for applications in molecular biology and nucleic acid diagnostics.
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Affiliation(s)
- Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID 83844, USA.
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7
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Hernández-Gil J, Ferrer S, Castiñeiras A, Liu-González M, Lloret F, Ribes Á, Čoga L, Bernecker A, Mareque-Rivas JC. Two Novel Ternary Dicopper(II) μ-Guanazole Complexes with Aromatic Amines Strongly Activated by Quantum Dots for DNA Cleavage. Inorg Chem 2013; 53:578-93. [DOI: 10.1021/ic4027249] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Javier Hernández-Gil
- Departament
de Química Inorgànica, Universitat de València, Vicent Andrés
Estellés s/n, 46100 Burjassot,
Valencia, Spain
| | - Sacramento Ferrer
- Departament
de Química Inorgànica, Universitat de València, Vicent Andrés
Estellés s/n, 46100 Burjassot,
Valencia, Spain
| | - Alfonso Castiñeiras
- Departamento
de Química Inorgánica, Universidad de Santiago de Compostela, Campus Universitario
Sur, E-15782 Santiago de Compostela, Spain
| | - Malva Liu-González
- S.C.S.I.E., Universitat de València, Dr.
Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Francesc Lloret
- Institut
de Ciència Molecular, Universitat de València, Catedràtic
José Beltrán n° 2, 46980 Paterna, Valencia, Spain
| | - Ángela Ribes
- Departament
de Química Inorgànica, Universitat de València, Vicent Andrés
Estellés s/n, 46100 Burjassot,
Valencia, Spain
| | - Lucija Čoga
- Departament
de Química Inorgànica, Universitat de València, Vicent Andrés
Estellés s/n, 46100 Burjassot,
Valencia, Spain
| | - Anja Bernecker
- Cooperative Centre for Research in Biomaterials (CIC biomaGUNE), 20009 San Sebastián, Spain
| | - Juan C. Mareque-Rivas
- Cooperative Centre for Research in Biomaterials (CIC biomaGUNE), 20009 San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
- Departmento
de Bioquimica y Biologia Molecular, Universidad del Pais Vasco, 48940 Leioa, Spain
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8
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Xie Z. PROG BIOCHEM BIOPHYS 2013; 39:1174-1177. [DOI: 10.3724/sp.j.1206.2012.00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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9
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Green VA, Weinberg MS. Small RNA-induced transcriptional gene regulation in mammals mechanisms, therapeutic applications, and scope within the genome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 102:11-46. [PMID: 21846568 DOI: 10.1016/b978-0-12-415795-8.00005-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Argonaute-bound small RNAs, derived from RNA interference and related pathways, are well-known effectors of posttranscriptional gene silencing (PTGS). Yet, these complexes also play an important role in affecting gene expression at the transcriptional level, either by transcriptional gene silencing (TGS) or activation (TGA). Our current understanding of how small RNAs are able to both activate and suppress transcription is unclear. In this review, we briefly outline the biogenesis of small RNAs and explore the mechanisms behind the various phenomena attributed to AGO-bound small RNA-mediated transcriptional regulation. The therapeutic potential of TGS and TGA is examined, emphasizing the distinct advantages over PTGS approaches with examples of application to cancer and diseases associated with viruses, aberrant splicing, and dysregulated heterochromatin. Finally, the influence of promoter architecture on gene susceptibility to transcriptional regulation is discussed in the light of how this impacts the scope of small RNA-induced transcriptional regulation within the genome.
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Affiliation(s)
- Victoria A Green
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
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10
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Hansen ME, Bentin T, Nielsen PE. High-affinity triplex targeting of double stranded DNA using chemically modified peptide nucleic acid oligomers. Nucleic Acids Res 2009; 37:4498-507. [PMID: 19474349 PMCID: PMC2715256 DOI: 10.1093/nar/gkp437] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
While sequence-selective dsDNA targeting by triplex forming oligonucleotides has been studied extensively, only very little is known about the properties of PNA–dsDNA triplexes—mainly due to the competing invasion process. Here we show that when appropriately modified using pseudoisocytosine substitution, in combination with (oligo)lysine or 9-aminoacridine conjugation, homopyrimidine PNA oligomers bind complementary dsDNA targets via triplex formation with (sub)nanomolar affinities (at pH 7.2, 150 mM Na+). Binding affinity can be modulated more than 1000-fold by changes in pH, PNA oligomer length, PNA net charge and/or by substitution of pseudoisocytosine for cytosine, and conjugation of the DNA intercalator 9-aminoacridine. Furthermore, 9-aminoacridine conjugation also strongly enhanced triplex invasion. Specificity for the fully matched target versus one containing single centrally located mismatches was more than 150-fold. Together the data support the use of homopyrimidine PNAs as efficient and sequence selective tools in triplex targeting strategies under physiological relevant conditions.
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Affiliation(s)
- Mads E Hansen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200-N, Denmark
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11
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Beane R, Gabillet S, Montaillier C, Arar K, Corey DR. Recognition of chromosomal DNA inside cells by locked nucleic acids. Biochemistry 2009; 47:13147-9. [PMID: 19053275 DOI: 10.1021/bi801930p] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sequence-selective recognition of DNA inside cells by oligonucleotides would provide valuable insights into cellular processes and new leads for therapeutics. Recent work, however, has shown that noncoding RNA transcripts overlap chromosomal DNA. These RNAs provide alternate targets for oligonucleotides designed to bind promoter DNA, potentially overturning previous assumptions about mechanism. Here, we show that antigene locked nucleic acids (agLNAs) reduce RNA levels of targeted genes, block RNA polymerase and transcription factor association at gene promoters, and bind to chromosomal DNA. These data suggest that the mechanism of LNAs involves recognition of chromosomal DNA and that LNAs are bona fide antigene molecules.
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Affiliation(s)
- Randall Beane
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, Texas 75390-9041, USA
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12
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Chen J, Wang X, Shao Y, Zhu J, Zhu Y, Li Y, Xu Q, Guo Z. A Trinuclear Copper(II) Complex of 2,4,6-Tris(di-2-pyridylamine)-1,3,5-triazine Shows Prominent DNA Cleavage Activity. Inorg Chem 2007; 46:3306-12. [PMID: 17355128 DOI: 10.1021/ic0614162] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A highly water soluble 3:2 complex of copper(II) and 2,4,6-tris(di-2-pyridylamine)-1,3,5-triazine (TDAT) has been synthesized and structurally characterized. The complex crystallized in a triclinic P1 space group with a molecular formula of [Cu3(TDAT)2Cl3]Cl3.2H2O (1), where each copper ion is coordinated by four pyridine nitrogen atoms and an apical chloride. The trinuclear complex is stable at physiological relevant conditions. It can bind to DNA through electrostatic attraction and cleave efficiently the supercoiled pBR322 DNA into its nicked and linear forms at micromolar concentrations. Active oxygen intermediates such as hydroxyl radicals and singlet oxygen generated in the presence of 1 may act as active species for the DNA scission.
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Affiliation(s)
- Jingwen Chen
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
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13
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14
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Janowski BA, Kaihatsu K, Huffman KE, Schwartz JC, Ram R, Hardy D, Mendelson CR, Corey DR. Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids. Nat Chem Biol 2005; 1:210-5. [PMID: 16408037 DOI: 10.1038/nchembio724] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 07/12/2005] [Indexed: 12/27/2022]
Abstract
Synthetic molecules that recognize specific sequences within cellular DNA are potentially powerful tools for investigating chromosome structure and function. Here, we designed antigene peptide nucleic acids (agPNAs) to target the transcriptional start sites for the human progesterone receptor B (hPR-B) and A (hPR-A) isoforms at sequences predicted to be single-stranded within the open complex of chromosomal DNA. We found that the agPNAs were potent inhibitors of transcription, showing for the first time that synthetic molecules can recognize transcription start sites inside cells. Breast cancer cells treated with agPNAs showed marked changes in morphology and an unexpected relationship between the strictly regulated levels of hPR-B and hPR-A. We confirmed these phenotypes using siRNAs and antisense PNAs, demonstrating the power of combining antigene and antisense strategies for gene silencing. agPNAs provide a general approach for controlling transcription initiation and a distinct option for target validation and therapeutic development.
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Affiliation(s)
- Bethany A Janowski
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
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15
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Abstract
The recognition of cellular nucleic acids by synthetic oligonucleotides is a versatile strategy for regulating biological processes. The vast majority of published studies have focused on antisense oligonucleotides that target mRNA, but it is also possible to design antigene oligonucleotides that are complementary to chromosomal DNA. Antigene oligomers could be used to inhibit the expression of any gene or analyze promoter structure and the mechanisms governing gene regulation. Other potential applications of antigene oligomers include activation of expression of chosen genes or the introduction of mutations to correct genetic disease. Peptide nucleic acid (PNA) is a nonionic DNA/RNA mimic that possesses outstanding potential for recognition of duplex DNA. Here we describe properties of PNAs and the challenges for their development as robust antigene agents.
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Affiliation(s)
- Kunihiro Kaihatsu
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 USA
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16
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Tu C, Shao Y, Gan N, Xu Q, Guo Z. Oxidative DNA Strand Scission Induced by a Trinuclear Copper(II) Complex. Inorg Chem 2004; 43:4761-6. [PMID: 15257606 DOI: 10.1021/ic049731g] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel trinuclear copper(II) complex, Cu3-L (L = N,N,N',N',N' ',N' '-hexakis(2-pyridyl)-1,3,5-tris(aminomethyl)benzene), exhibited efficient oxidative strand scission of plasmid DNA. The solution behavior of the complex has been studied by potentiometric titration, UV spectroscopy, and cyclic voltammetry. The data showed that there are three redox-active copper ions in the complex with three types of bound water. The complex demonstrated a moderate binding ability for DNA. Cu3-L readily cleaves plasmid DNA in the presence of ascorbate to give nicked (form II) and then linear (form III) products, while the cleavage efficiency using H2O2 is less than by ascorbate, suggesting that the cleavage mode of the trinuclear complex is somewhat different from the traditional Fenton-like catalysis. Meanwhile, Cu3-L is far more efficient than its mononuclear analogue Cu-DPA (DPA = 2,2'-dipyridylamine) at the same [Cu2+] concentration, which suggests a possible synergy between the three or at least two Cu(II) centers in Cu3-L that contributes to its relatively high nucleolytic efficiency. Furthermore, the presence of standard radical scavengers does not have clear effect on the cleavage efficiency, suggesting the reactive intermediates leading to DNA cleavage are not freely diffusible radicals.
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Affiliation(s)
- Chao Tu
- State Key Laboratory of Coordination Chemistry, Coordination Chemistry Institute, Nanjing University, 210093 Nanjing, P. R. China
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17
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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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18
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Connors WH, Narayanan S, Kryatova OP, Richert C. Synthesis of oligonucleotides with a 2'-cap at the 3'-terminus via reversed phosphoramidites. Org Lett 2003; 5:247-50. [PMID: 12556163 DOI: 10.1021/ol020212w] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] A method is presented for the synthesis of single compounds or small combinatorial libraries of oligonucleotides with 2'-acylamido-2'-deoxyuridine residues at the 3'-terminus. Selection experiments identified the residue of anthraquinone-2-carboxylic acid as a "molecular cap" that increases the UV melting point of the duplex (5'-ACGCGU-3')(2) by up to 28 degrees C compared to the unmodified control duplex.
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Affiliation(s)
- William H Connors
- Department of Chemistry, University of Constance, 78457 Konstanz, Germany
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19
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Kryatova OP, Connors WH, Bleczinski CF, Mokhir AA, Richert C. A 2‘-Acylamido Cap That Increases the Stability of Oligonucleotide Duplexes. Org Lett 2001. [DOI: 10.1021/ol0003782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Olga P. Kryatova
- Departments of Chemistry, Tufts University, Medford, Massachusetts 02155, and University of Constance, D-78457 Konstanz, Germany
| | - William H. Connors
- Departments of Chemistry, Tufts University, Medford, Massachusetts 02155, and University of Constance, D-78457 Konstanz, Germany
| | - Colleen F. Bleczinski
- Departments of Chemistry, Tufts University, Medford, Massachusetts 02155, and University of Constance, D-78457 Konstanz, Germany
| | - Andriy A. Mokhir
- Departments of Chemistry, Tufts University, Medford, Massachusetts 02155, and University of Constance, D-78457 Konstanz, Germany
| | - Clemens Richert
- Departments of Chemistry, Tufts University, Medford, Massachusetts 02155, and University of Constance, D-78457 Konstanz, Germany
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20
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Milne L, Perrin DM, Sigman DS. Oligoribonucleotide-based gene-specific transcription inhibitors that target the open complex. Methods 2001; 23:160-8. [PMID: 11181035 DOI: 10.1006/meth.2000.1117] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We have demonstrated that oligoribonucleotides that lack a 3'-OH group and cannot be extended by RNA polymerase can hybridize to the single-stranded DNA formed inside the transcription initiation bubble (or open complex) and inhibit transcription. Using the lacUV5/Escherichia coli RNA polymerase or trpEDCBA/E. coli RNA polymerase transcription system as a model, we have found that effective inhibitors are five nucleotides in length and must be complementary to the DNA template strand in the region from -5 to +2 about the transcription start site (designated +1). We have used the DNA cleavage activity of 1,10-phenanthroline-copper to confirm that the mechanism of inhibition is via oligoribonucleotide hybridization to the open complex and have used this cleavage chemistry to demonstrate that these oligonucleotide inhibitors hybridize in an antiparallel orientation to their DNA target. Systematic modification of the parent phosphodiester oligoribonucleotide pentamer revealed that the phosphorothioate backbone-containing analogs have increased open complex binding affinity and are more effective transcription inhibitors than their phosphodiester counterparts.
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Affiliation(s)
- L Milne
- Department of Biological Chemistry, School of Medicine, and Molecular Biology Institute, UCLA, Los Angeles, California 90095-1570, USA
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