1
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Hennessy J, McGorman B, Molphy Z, Farrell NP, Singleton D, Brown T, Kellett A. A Click Chemistry Approach to Targeted DNA Crosslinking with
cis
‐Platinum(II)‐Modified Triplex‐Forming Oligonucleotides. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202110455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Joseph Hennessy
- School of Chemical Sciences and National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin 9 Ireland
| | - Bríonna McGorman
- School of Chemical Sciences and National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin 9 Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin 9 Ireland
- Synthesis and Solid-State Pharmaceutical Centre School of Chemical Sciences Dublin City University, Glasnevin Dublin 9 Ireland
| | - Nicholas P. Farrell
- Department of Chemistry Virginia Commonwealth University Richmond VA 23284-2006 USA
| | - Daniel Singleton
- ATDBio Ltd. School of Chemistry University of Southampton Southampton SO17 1BJ UK
| | - Tom Brown
- ATDBio Ltd. School of Chemistry University of Southampton Southampton SO17 1BJ UK
- Chemistry Research Laboratory University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology Dublin City University, Glasnevin Dublin 9 Ireland
- Synthesis and Solid-State Pharmaceutical Centre School of Chemical Sciences Dublin City University, Glasnevin Dublin 9 Ireland
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2
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Aro-Heinilä A, Lepistö A, Äärelä A, Lönnberg TA, Virta P. 2-Trifluoromethyl-6-mercurianiline Nucleotide, a Sensitive 19F NMR Probe for Hg(II)-mediated Base Pairing. J Org Chem 2022; 87:137-146. [PMID: 34905374 PMCID: PMC8749955 DOI: 10.1021/acs.joc.1c02056] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 01/02/2023]
Abstract
A 2-trifluoromethylaniline C-nucleoside was synthesized, incorporated in the middle of an oligonucleotide, and mercurated. The affinity of the mercurated oligonucleotide toward complementary strands placing each of the canonical nucleobases opposite to the organomercury nucleobase analogue was examined by ultraviolet (UV), circular dichroism (CD), and 19F NMR spectroscopy analyses. According to the UV melting profile analysis, the organomercury nucleobase analogue showed increased affinities in the order T > G > C > A. The CD profiles indicated the typical B-type helix in each case. The 19F resonance signal proved sensitive for the local environmental changes, showing clearly distinct signals for the duplexes with different opposing nucleobases. Furthermore, valuable information on the mercurated oligonucleotide and its binding to complementary strands at varying temperature could be obtained by 19F NMR spectroscopy.
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Affiliation(s)
- Asmo Aro-Heinilä
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Assi Lepistö
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Antti Äärelä
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
| | | | - Pasi Virta
- Department of Chemistry, University
of Turku, Henrikinkatu 2, 20500 Turku, Finland
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3
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Hennessy J, McGorman B, Molphy Z, Farrell NP, Singleton D, Brown T, Kellett A. A Click Chemistry Approach to Targeted DNA Crosslinking with cis-Platinum(II)-Modified Triplex-Forming Oligonucleotides. Angew Chem Int Ed Engl 2021; 61:e202110455. [PMID: 34652881 PMCID: PMC9299770 DOI: 10.1002/anie.202110455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/11/2021] [Indexed: 01/05/2023]
Abstract
Limitations of clinical platinum(II) therapeutics include systemic toxicity and inherent resistance. Modern approaches, therefore, seek new ways to deliver active platinum(II) to discrete nucleic acid targets. In the field of antigene therapy, triplex‐forming oligonucleotides (TFOs) have attracted interest for their ability to specifically recognise extended duplex DNA targets. Here, we report a click chemistry based approach that combines alkyne‐modified TFOs with azide‐bearing cis‐platinum(II) complexes—based on cisplatin, oxaliplatin, and carboplatin motifs—to generate a library of PtII‐TFO hybrids. These constructs can be assembled modularly and enable directed platinum(II) crosslinking to purine nucleobases on the target sequence under the guidance of the TFO. By covalently incorporating modifications of thiazole orange—a known DNA‐intercalating fluorophore—into PtII‐TFOs constructs, enhanced target binding and discrimination between target and off‐target sequences was achieved.
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Affiliation(s)
- Joseph Hennessy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Bríonna McGorman
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA, 23284-2006, USA
| | - Daniel Singleton
- ATDBio Ltd., School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- ATDBio Ltd., School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK.,Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, 9, Ireland.,Synthesis and Solid-State Pharmaceutical Centre, School of Chemical Sciences, Dublin City University, Glasnevin, Dublin, 9, Ireland
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4
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Kishimoto T, Yoshikawa Y, Yoshikawa K, Komeda S. Different Effects of Cisplatin and Transplatin on the Higher-Order Structure of DNA and Gene Expression. Int J Mol Sci 2019; 21:E34. [PMID: 31861648 PMCID: PMC6981875 DOI: 10.3390/ijms21010034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
Despite the effectiveness of cisplatin as an anticancer agent, its trans-isomer, transplatin, is clinically ineffective. Although both isomers target nuclear DNA, there is a large difference in the magnitude of their biological effects. Here, we compared their effects on gene expression in an in vitro luciferase assay and quantified their effects on the higher-order structure of DNA using fluorescence microscopy (FM) and atomic force microscopy (AFM). The inhibitory effect of cisplatin on gene expression was about 7 times that of transplatin. Analysis of the fluctuation autocorrelation function of the intrachain Brownian motion of individual DNA molecules showed that cisplatin increases the spring and damping constants of DNA by one order of magnitude and these visco-elastic characteristics tend to increase gradually over several hours. Transplatin had a weaker effect, which tended to decrease with time. These results agree with a stronger inhibitory effect of cisplatin on gene expression. We discussed the characteristic effects of the two compounds on the higher-order DNA structure and gene expression in terms of the differences in their binding to DNA.
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Affiliation(s)
- Toshifumi Kishimoto
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan; (T.K.); (Y.Y.); (K.Y.)
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan; (T.K.); (Y.Y.); (K.Y.)
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto 610-0394, Japan; (T.K.); (Y.Y.); (K.Y.)
| | - Seiji Komeda
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka, Mie 513-8670, Japan
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5
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Naskar S, Guha R, Müller J. Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads. Angew Chem Int Ed Engl 2019; 59:1397-1406. [PMID: 31259475 DOI: 10.1002/anie.201905913] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 01/02/2023]
Abstract
The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of AgI -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.
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Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 30, 48149, Münster, Germany
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6
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Naskar S, Guha R, Müller J. Metallmodifizierte Nukleinsäuren: Metallvermittelte Basenpaare, ‐tripel und ‐tetraden. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shuvankar Naskar
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Rweetuparna Guha
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie Westfälische Wilhelms-Universität Münster Corrensstraße 30 48149 Münster Deutschland
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7
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Aro-Heinilä A, Lönnberg T, Virta P. 3-Fluoro-2-mercuri-6-methylaniline Nucleotide as a High-Affinity Nucleobase-Specific Hybridization Probe. Bioconjug Chem 2019; 30:2183-2190. [PMID: 31246432 DOI: 10.1021/acs.bioconjchem.9b00405] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A 3-fluoro-6-methylaniline nucleoside was synthesized and incorporated into an oligonucleotide, and its ability to form mercury-mediated base pairs was studied. UV melting experiments revealed increased duplex stability with thymine, guanine, and cytosine opposite to the probe and a clear nucleobase-specific binding preference (T > G > C > A). Moreover, the 3-fluoro group was utilized as a spin label that showed distinct 19F NMR resonance shifts depending on the complementary nucleobase, providing more detailed information on Hg(II)-mediated base pairing.
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Affiliation(s)
- Asmo Aro-Heinilä
- Department of Chemistry , University of Turku , Vatselankatu 2 , 20014 Turku , Finland
| | - Tuomas Lönnberg
- Department of Chemistry , University of Turku , Vatselankatu 2 , 20014 Turku , Finland
| | - Pasi Virta
- Department of Chemistry , University of Turku , Vatselankatu 2 , 20014 Turku , Finland
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8
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Hande M, Saher O, Lundin KE, Smith CIE, Zain R, Lönnberg T. Oligonucleotide⁻Palladacycle Conjugates as Splice-Correcting Agents. Molecules 2019; 24:E1180. [PMID: 30917503 PMCID: PMC6470670 DOI: 10.3390/molecules24061180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/14/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
2'-O-Methylribo phosphorothioate oligonucleotides incorporating cyclopalladated benzylamine conjugate groups at their 5'-termini have been prepared and their ability to hybridize with a designated target sequence was assessed by conventional UV melting experiments. The oligonucleotides were further examined in splice-switching experiments in human cervical cancer (HeLa Luc/705), human liver (HuH7_705), and human osteosarcoma (U-2 OS_705) reporter cell lines. Melting temperatures of duplexes formed by the modified oligonucleotides were approximately 5 °C lower than melting temperatures of the respective unmodified duplexes. The cyclopalladated oligonucleotides functioned as splice-correcting agents in the HeLa Luc/705 cell line somewhat more efficiently than their unmodified counterparts. Furthermore, the introduction of this chemical modification did not induce toxicity in cells. These results demonstrate the feasibility of using covalently metalated oligonucleotides as therapeutic agents.
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Affiliation(s)
- Madhuri Hande
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - Osama Saher
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
- Department of Pharmaceutics and Industrial Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Karin E Lundin
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Huddinge, Sweden.
- Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, FIN-20014 Turku, Finland.
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9
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Ukale DU, Lönnberg T. 2,6‐Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809398] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Tuomas Lönnberg
- Department of ChemistryUniversity of Turku Vatselankatu 2 20014 Turku Finland
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10
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Ukale DU, Lönnberg T. 2,6-Dimercuriphenol as a Bifacial Dinuclear Organometallic Nucleobase. Angew Chem Int Ed Engl 2018; 57:16171-16175. [PMID: 30358071 DOI: 10.1002/anie.201809398] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/11/2018] [Indexed: 11/07/2022]
Abstract
A C-nucleoside having 2,6-dimercuriphenol as the base moiety has been synthesized and incorporated into an oligonucleotide. NMR and UV melting experiments revealed the ability of this bifacial organometallic nucleobase surrogate to form stable dinuclear HgII -mediated base triples with adenine, cytosine, and thymine (or uracil) in solution as well as within a triple-helical oligonucleotide. A single HgII -mediated base triple between 2,6-dimercuriphenol and two thymines increased both Hoogsteen and Watson-Crick melting temperatures of a 15-mer pyrimidine⋅purine*pyrimidine triple helix by more than 10 °C relative to an unmodified triple helix of the same length. This novel binding mode could be exploited in targeting certain pathogenic nucleic acids as well as in DNA nanotechnology.
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Affiliation(s)
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland
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11
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Hande M, Maity S, Lönnberg T. Palladacyclic Conjugate Group Promotes Hybridization of Short Oligonucleotides. Int J Mol Sci 2018; 19:ijms19061588. [PMID: 29843368 PMCID: PMC6032164 DOI: 10.3390/ijms19061588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 11/16/2022] Open
Abstract
Short oligonucleotides with cyclopalladated benzylamine moieties at their 5'-termini have been prepared to test the possibility of conferring palladacyclic anticancer agents sequence-selectivity by conjugation with a guiding oligonucleotide. Hybridization of these oligonucleotides with natural counterparts was studied by UV and CD (circular dichroism) melting experiments in the absence and presence of a competing ligand (2-mercaptoethanol). Cyclopalladated benzylamine proved to be strongly stabilizing relative to unmetalated benzylamine and modestly stabilizing relative to an extra A•T base pair. The stabilization was largely abolished in the presence of 2-mercaptoethanol, suggesting direct coordination of Pd(II) to a nucleobase of the complementary strand. In all cases, fidelity of Watson-Crick base pairing between the two strands was retained. Hybridization of the cyclopalladated oligonucleotides was characterized by relatively large negative enthalpy and entropy, consistent with stabilizing Pd(II) coordination partially offset by the entropic penalty of imposing conformational constraints on the flexible diethylene glycol linker between the oligonucleotide and the palladacyclic moiety.
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Affiliation(s)
- Madhuri Hande
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
| | - Sajal Maity
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland.
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12
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Ukale DU, Lönnberg T. Triplex Formation by Oligonucleotides Containing Organomercurated Base Moieties. Chembiochem 2018; 19:1096-1101. [PMID: 29575511 DOI: 10.1002/cbic.201800112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Indexed: 12/26/2022]
Abstract
Homothymine oligonucleotides with a single 5-mercuricytosine or 5-mercuriuracil residue at their termini have been synthesized and their capacity to form triplexes has been examined with an extensive array of double-helical targets. UV and circular dichroism (CD) melting experiments revealed the formation and thermal denaturation of pyrimidine⋅purine*pyrimidine-type triple helices with all oligonucleotide combinations studied. Nearly all triplexes were destabilized upon mercuration of the 3'-terminal residue of the triplex-forming oligonucleotide, in all likelihood due to competing intramolecular HgII -mediated base pairing. Two exceptions from this general pattern were, however, observed: 5-mercuricytosine was stabilizing when placed opposite to a T⋅A or A⋅T base pair. The stabilization was further amplified in the presence of 2-mercaptoethanol (but not hexanethiol, thiophenol or cysteine), suggesting a stabilizing interaction other than HgII -mediated base pairing.
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Affiliation(s)
| | - Tuomas Lönnberg
- University of Turku, Department of Chemistry, Vatselankatu 2, 20014, Turku, Finland
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13
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Maity SK, Lönnberg T. Oligonucleotides Incorporating Palladacyclic Nucleobase Surrogates. Chemistry 2018; 24:1274-1277. [DOI: 10.1002/chem.201705797] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Sajal Kumar Maity
- Department of Chemistry; University of Turku; Vatselankatu 2 20014 Turku Finland
| | - Tuomas Lönnberg
- Department of Chemistry; University of Turku; Vatselankatu 2 20014 Turku Finland
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14
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Lippert B, Sanz Miguel PJ. Merging Metal–Nucleobase Chemistry With Supramolecular Chemistry. ADVANCES IN INORGANIC CHEMISTRY 2018. [DOI: 10.1016/bs.adioch.2017.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Taherpour S, Golubev O, Lönnberg T. On the feasibility of recognition of nucleic acid sequences by metal-ion-carrying oligonucleotides. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.01.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Ukale D, Shinde VS, Lönnberg T. 5-Mercuricytosine: An Organometallic Janus Nucleobase. Chemistry 2016; 22:7917-23. [PMID: 27113075 DOI: 10.1002/chem.201600851] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/10/2022]
Abstract
The base-pairing properties of 5-mercuricytosine have been explored at the monomer level by NMR titrations and at the oligonucleotide level by melting temperature measurements. The NMR studies revealed a relatively high affinity for guanine, hypoxanthine, and uridine, that is, bases that are deprotonated upon coordination of Hg(II) . Within an oligonucleotide duplex, 5-mercuricytosine formed Hg(II) -mediated base pairs with thymine and guanine. In the former case, the duplex formed was as stable as the respective duplex comprising solely Watson-Crick base pairs. Based on detailed thermodynamic analysis of the melting curves, the stabilization by the Hg(II) -mediated base pairs may be attributed to a comparatively low entropic penalty of hybridization.
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Affiliation(s)
- Dattatraya Ukale
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland.,Department of Chemistry, Savirtibai Phule Pune University, Pune, 411007, India
| | - Vaishali S Shinde
- Department of Chemistry, Savirtibai Phule Pune University, Pune, 411007, India
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Vatselankatu 2, 20014, Turku, Finland.
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17
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Graham MK, Brown TR, Miller PS. Targeting the human androgen receptor gene with platinated triplex-forming oligonucleotides. Biochemistry 2015; 54:2270-82. [PMID: 25768916 DOI: 10.1021/bi501565n] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Platinum-derivatized homopyrimidine triplex-forming oligonucleotides (Pt-TFOs) consisting of 2'-O-methyl-5-methyluridine, 2'-O-methyl-5-methylcytidine, and a single 3'-N7-trans-chlorodiammine platinum(II)-2'-deoxyguanosine were designed to cross-link to the transcribed strand at four different sequences in the human androgen receptor (AR) gene. Fluorescence microscopy showed that a fluorescein-tagged Pt-TFO localizes in both the cytoplasm and nucleus when it is transfected into LAPC-4 cells, a human prostate cancer cell line, using Lipofectamine 2000. A capture assay employing streptavidin-coated magnetic beads followed by polymerase chain reaction (PCR) amplification was used to demonstrate that 5'-biotin-conjugated Pt-TFOs cross-link in vitro to their four designated AR gene targets in genomic DNA extracted from LAPC-4 cells. Similarly, the capture assay was used to examine cross-linking between the 5'-biotin-conjugated Pt-TFOs and the AR gene in LAPC-4 cells in culture. Three of the four Pt-TFOs cross-linked to their designated target, suggesting that different regions of the AR gene are not uniformly accessible to Pt-TFO cross-linking. LAPC-4 cells were transfected with fluorescein-tagged Pt-TFO or a control oligonucleotide that does not bind or cross-link to AR DNA. The levels of AR mRNA in highly fluorescent cells isolated by fluorescence-activated cell sorting were determined by RT-qPCR, and the levels of AR protein were monitored by immunofluorescence microscopy. Decreases in mRNA and protein levels of 40 and 30%, respectively, were observed for fluorescein-tagged Pt-TFO versus control treated cells. Although the levels of knockdown of AR mRNA and protein were modest, the results suggest that Pt-TFOs hold potential as agents for controlling gene expression by cross-linking to DNA and disrupting transcription.
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Affiliation(s)
- Mindy K Graham
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Terry R Brown
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Paul S Miller
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, United States
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18
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Albertí FM, Rodríguez-Santiago L, Sodupe M, Mirats A, Kaitsiotou H, Sanz Miguel PJ, Lippert B. Mixed adenine/guanine quartets with three trans-a2 Pt(II) (a=NH(3) or MeNH(2)) cross-links: linkage and rotational isomerism, base pairing, and loss of NH(3). Chemistry 2014; 20:3394-407. [PMID: 24532472 DOI: 10.1002/chem.201304686] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Indexed: 11/12/2022]
Abstract
Of the numerous ways in which two adenine and two guanines (N9 positions blocked in each) can be cross-linked by three linear metal moieties such as trans-a2 Pt(II) (with a=NH3 or MeNH2 ) to produce open metalated purine quartets with exclusive metal coordination through N1 and N7 sites, one linkage isomer was studied in detail. The isomer trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)}2 ][(ClO4 )6 ]⋅3H2 O (1) (with 9-EtA=9-ethyladenine and 9-MeGH=9-methylguanine) was crystallized from water and found to adopt a flat Z-shape in the solid state as far as the trinuclear cation is concerned. In the presence of excess 9-MeGH, a meander-like construct, trans,trans,trans-[{Pt(NH3 )2 (N7-9-EtA-N1)2 }{Pt(MeNH2 )2 (N7-9-MeGH)2 }][(ClO4 )6 ]⋅[(9-MeGH)2 ]⋅7 H2 O (2) is formed, in which the two extra 9-MeGH nucleobases are hydrogen bonded to the two terminal platinated guanine ligands of 1. Compound 1, and likewise the analogous complex 1 a (with NH3 ligands only), undergo loss of an ammonia ligand and formation of NH4 (+) when dissolved in [D6 ]DMSO. From the analogy between the behavior of 1 and 1 a it is concluded that a NH3 ligand from the central Pt atom is lost. Addition of 1-methylcytosine (1-MeC) to such a DMSO solution reveals coordination of 1-MeC to the central Pt. In an analogous manner, 9-MeGH can coordinate to the central Pt in [D6 ]DMSO. It is proposed that the proton responsible for formation of NH4 (+) is from one of the exocyclic amino groups of the two adenine bases, and furthermore, that this process is accompanied by a conformational change of the cation from Z-form to U-form. DFT calculations confirm the proposed mechanism and shed light on possible pathways of this process. Calculations show that rotational isomerism is not kinetically hindered and that it would preferably occur previous to the displacement of NH3 by DMSO. This displacement is the most energetically costly step, but it is compensated by the proton transfer to NH3 and formation of U(-H(+) ) species, which exhibits an intramolecular hydrogen bond between the deprotonated N6H(-) of one adenine and the N6H2 group of the other adenine. Finally the question is examined, how metal cross-linking patterns in closed metallacyclic quartets containing two adenine and two guanine nucleobases influence the overall shape (square, rectangle, trapezoid) and the planarity of a metalated purine quartet.
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Affiliation(s)
- Francisca M Albertí
- Fakultät Chemie und Chemische Biologie, Technische Universität Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund (Germany), Fax: (+49) 231-755-3797
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19
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Graham MK, Miller PS. Inhibition of transcription by platinated triplex-forming oligonucleotides. J Biol Inorg Chem 2012; 17:1197-208. [PMID: 22965663 DOI: 10.1007/s00775-012-0933-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/20/2012] [Indexed: 12/14/2022]
Abstract
Platinated triplex-forming oligonucleotides (TFOs) consisting of 2'-methoxythymidine and 2'-methoxy-5-methylcytidine and an N-7 platinated deoxyguanosine ((Pt)G) at the 5'-((Pt)G-TFO), 3'-(TFO-G(Pt)), or 3'- and 5'-((Pt)G-TFO-G(Pt)) ends of the TFO form mono-((Pt)G-TFO and TFO-G(Pt)) and interstrand ((Pt)G-TFO-G(Pt)) cross-links with target DNA as a result of reaction of the (Pt)G with guanines adjacent to the homopurine TFO binding site in the target. The extent of cross-linking is greatest when the (Pt)G is located on the 3' end of the TFO and the target guanine is on the same strand as the TFO binding site. Multiple, contiguous deoxyguanosines in the TFO binding site or a cytosine adjacent to the G(Pt) of the TFO significantly reduce cross-linking. DNA reporter plasmids in which platinated TFOs were cross-linked at a site in the transcribed region between a CMV promoter and a luciferase reporter gene were transfected into Chinese hamster ovary cells, and luciferase expression was compared with that for the corresponding non-cross-linked plasmid. Luciferase expression was inhibited 95 % when TFO-G(Pt) was bound and cross-linked to the transcribed strand, demonstrating that the cross-linked TFO was able to block transcription elongation. Further inhibition (99 %) was observed in nucleotide excision repair (NER) deficient cells, suggesting that NER may repair this lesion. The 3'-G(Pt) group of TFO-G(Pt) protects the TFO from degradation by exonucleases found in mammalian serum. Taken together, these results suggest that platinated TFOs of the type TFO-G(Pt) may find applications as agents for suppressing DNA transcription and consequently inhibiting gene expression in mammalian cells.
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Affiliation(s)
- Mindy K Graham
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21212, USA
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20
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Rao L, West TK, Saluta G, Kucera GL, Bierbach U. Probing platinum-adenine-n3 adduct formation with DNA minor-groove binding agents. Chem Res Toxicol 2010; 23:1148-50. [PMID: 20578739 DOI: 10.1021/tx100170p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Me-lex(py/py), an adenine-N3-selective alkylating agent, and the reversible minor-groove binder netropsin were used to probe the formation of unusual minor-groove adducts by the cytotoxic hybrid agent PT-ACRAMTU ([PtCl(en)(ACRAMTU)](NO(3))(2); en = ethane-1,2-diamine, ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea). PT-ACRAMTU was found by chemical footprinting to inhibit specific Me-lex-mediated DNA cleavage at several adenine sites but not at nonspecific guanine, which is consistent with the platination of adenine-N3. In a cell proliferation assay, a significant decrease in cytotoxicity was observed for PT-ACRAMTU, when cancer cells were pretreated with netropsin, suggesting that minor-groove adducts in cellular DNA contribute to the biological activity of the hybrid agent.
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Affiliation(s)
- Lu Rao
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109, USA
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21
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Campbell MA, Miller PS. Transplatin-conjugated triplex-forming oligonucleotides form adducts with both strands of DNA. Bioconjug Chem 2010; 20:2222-30. [PMID: 19950917 DOI: 10.1021/bc900008s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) can bind to polypurine x polypyrimidine tracts in DNA and, as a consequence, perturb the normal functioning of a targeted gene. The effectiveness of such antigene TFOs can potentially be enhanced by covalent attachment of the TFO to its DNA target. Here, we report that attachment of N-7-platinated guanine nucleosides to the 3'- and/or 5'-ends of oligopyrimidine TFOs enables these TFOs to form highly stable adducts with target DNA deoxyguanosines or deoxyadenosines that are adjacent to the TFO binding site. Such adduct formation stably anchors the TFO to its target. Depending on the sequences adjacent to the TFO binding site, adduct formation can occur on either strand of the DNA. Adduct formation by 3',5'-bis-platinated TFOs can result in the formation of an interstrand cross-link between both strands of the DNA duplex. Formation of the adducts, which could be reversed by treatment with sodium cyanide, was dependent upon the ability of the TFO to bind to DNA and appeared to occur at a rate slower than that at which the TFO bound to the DNA duplex. The extent of adduct formation at 37 degrees C by platinated deoxyribo-TFOs diminished as the pH was increased from 6.5 to 7.4. In contrast, high levels (approximately 86%) of adduct formation by platinated 2'-O-methylribo-TFOs were observed at both pH 6.5 and pH 7.4. Platinated 2'-O-methylribo-TFOs were also shown to bind to plasmid DNA and inhibit transcription in vitro, and to inhibit plasmid replication in E. coli cells. These results suggest that platinum-conjugated TFOs may be good candidates for use as antigene agents.
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Affiliation(s)
- Meghan A Campbell
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA
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22
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Campbell MA, Miller PS. Cross-linking to an interrupted polypurine sequence with a platinum-modified triplex-forming oligonucleotide. J Biol Inorg Chem 2009; 14:873-81. [PMID: 19350290 DOI: 10.1007/s00775-009-0499-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
Abstract
Triplex-forming oligonucleotides (TFOs) can bind specifically to polypurine sequences in double-stranded DNA. A single interruption of this polypurine tract can greatly destabilize triplex formation. The stability of triplexes can be significantly enhanced by covalently linking the TFO to its DNA target with reactive functional groups conjugated to the TFO. Covalently cross-linked TFOs are effective inhibitors of transcription of the target DNA sequence. We have designed a TFO with a platinum-modified base that can interact with and cross-link to a cytosine interruption in the polypurine tract of a target DNA duplex. The TFO contains an N(4)-(aminoalkyl)cytosine derivatized with cis-diamminediaquaplatinum(II) or trans-diamminediaquaplatinum(II). When bound to its target, the tethered platinum of the TFO can reach across the major groove and form an adduct with the guanine N7 of the interrupting C.G base pair. The optimal tether length is five methylene groups, and cross-linking is most efficient when the tether is modified with trans-diamminediaquaplatinum(II). Cross-linking requires that the TFO is bound to its designated DNA target. Addition of cyanide to the cross-linked TFO product reversed the cross-link, behavior that is consistent with the presence of a platinum-guanine adduct. The kinetics of the cross-linking reaction were studied and the half-life of the cross-linking reaction was approximately 3 h. Our results demonstrate that platinum-conjugated TFOs can be designed to cross-link with DNA targets that contain a single pyrimidine interruption. Modifications of this type may prove useful for expanding the DNA sequences that can be targeted by TFOs and increasing the stability of the resulting triplexes.
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Affiliation(s)
- Meghan A Campbell
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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23
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Protagonists in chemistry. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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24
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Lippert B. Coordinative Bond Formation Between Metal Ions and Nucleic Acid Bases. NUCLEIC ACID–METAL ION INTERACTIONS 2008. [DOI: 10.1039/9781847558763-00039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Bernhard Lippert
- Fakultät für Chemie, Technische Universität Dortmund Otto-Hahn-Strasse 6 D-44227 Dortmund Germany
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25
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Sharma SK, McLaughlin LW. Triplex mediated delivery of a platinum complex to a specific DNA target site. J Inorg Biochem 2004; 98:1570-7. [PMID: 15458818 DOI: 10.1016/j.jinorgbio.2004.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2004] [Revised: 03/26/2004] [Accepted: 03/27/2004] [Indexed: 11/21/2022]
Abstract
Tethering an ethylene diamine linker to the 5' terminus of an oligothymidine sequence provides a site for complexation with K(2)PtCl(4). Due to the low reactivity of dT toward a platinum source, we chose dT(8) and dT(15) as our initial synthetic targets for platination. Post-synthetic reaction of the platinum reagent with the diamino oligothymidine generates the diamino dichloro platinum-DNA conjugate that can be used for DNA duplex targeting by oligodeoxyncleotide-mediated triplex formation. The dT(8) sequence is not sufficiently long to facilitate triplex formation and Pt-cross-linking, whereas with a dT(15) sequence cross-linking between the third strand and the duplex occurs exclusively with the duplex target strand directly involved in triplex formation. No examples of cross-linking to the complementary target strand, or of cross-linking to both target strands are observed. Most efficient cross-linking occurs when the dinucleotide d(GpG) is present in the target strand and no cross-linking occurs with the corresponding 7-deazaG dinucleotide target. Cross-linking is also observed when dC or dA residues are present in the target strand, or even with a single dG residue, but it is not observed in any cases to dT residues. Triplex formation provides the ability to target specific sequences of double-stranded DNA and the orientational control arising from triplex formation is sufficient to alter the binding preferences of platinum. Conjugates of the type described here offer the potential of delivering a platinum complex to a specific DNA site.
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Affiliation(s)
- Sunil K Sharma
- Department of Chemistry, University of Delhi, Delhi 110 007, India
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26
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Gu J, Wang J, Leszczynski J. H−Bonding Patterns in the Platinated Guanine−Cytosine Base Pair and Guanine−Cytosine−Guanine−Cytosine Base Tetrad: an Electron Density Deformation Analysis and AIM Study. J Am Chem Soc 2004; 126:12651-60. [PMID: 15453799 DOI: 10.1021/ja0492337] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The atoms in molecule theory (AIM) and electronic structure analysis are applied together to investigate H-bonding patterns in metalated nucleobase complexes. The influence of Pt on the intra GC base pair H-bonding has been found to reduce intra base pair H-bonding of N4(C)...O6(G) in the platinated GC pair and GCGC tetrad. The relaxation of geometry constrains in metalated nucleobases is found to be decisively important in the formation of novel molecular architectures from nucleobases and metal entities. The incorporation of the platinum in the GCGC tetrad benefits the formation of the unique CH...N (H5(C)...N1(G)) hydrogen bond pattern in the tetrad by offering improved geometric constraints rather than through changing the electronic properties around the H5(C) and N1(G) sites. Platination at the N7 of guanine reduces the deprotonation energy considerably.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, PR China.
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27
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Abstract
Although most antibiotics do not need metal ions for their biological activities, there are a number of antibiotics that require metal ions to function properly, such as bleomycin (BLM), streptonigrin (SN), and bacitracin. The coordinated metal ions in these antibiotics play an important role in maintaining proper structure and/or function of these antibiotics. Removal of the metal ions from these antibiotics can cause changes in structure and/or function of these antibiotics. Similar to the case of "metalloproteins," these antibiotics are dubbed "metalloantibiotics" which are the title subjects of this review. Metalloantibiotics can interact with several different kinds of biomolecules, including DNA, RNA, proteins, receptors, and lipids, rendering their unique and specific bioactivities. In addition to the microbial-originated metalloantibiotics, many metalloantibiotic derivatives and metal complexes of synthetic ligands also show antibacterial, antiviral, and anti-neoplastic activities which are also briefly discussed to provide a broad sense of the term "metalloantibiotics."
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Affiliation(s)
- Li-June Ming
- Department of Chemistry and Institute for Biomolecular Science, University of South Florida, Tampa, Florida 33620-5250, USA.
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28
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Schmidt KS, Boudvillain M, Schwartz A, van der Marel GA, van Boom JH, Reedijk J, Lippert B. Monofunctionally trans-diammine platinum(II)-modified peptide nucleic acid oligomers: a new generation of potential antisense drugs. Chemistry 2002; 8:5566-70. [PMID: 12458496 DOI: 10.1002/1521-3765(20021216)8:24<5566::aid-chem5566>3.0.co;2-#] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A solid-phase approach is described that provides facile access to monofunctionally trans-PtII-modified PNA oligomers of arbitrary sequence for potential use both in antigene and antisense strategies. The approach includes the synthesis of a platinated building block 1 and its subsequent incorporation into three different PNA oligomers 5-7 by solid-phase synthesis. In a model cross-linking reaction one of the latter is found to recognize sequence-specifically a target oligonucleotide 8 and to cross-link to it. The resulting structure is the trans-PtII-cross-linked PNA/DNA duplex 9 as revealed by mass spectrometry in combination with a Maxam-Gilbert sequencing experiment.
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Affiliation(s)
- Kathrin S Schmidt
- Fachbereich Chemie, Universität Dortmund Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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29
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Erxleben A, Metzger S, Britten JF, Lock CJ, Albinati A, Lippert B. Model of the most abundant DNA interstrand cross-link of Transplatin: X-ray structures of two modifications and H bonding behavior in the solid state and in solution of trans-[Pt(NH3)2(1-MeC-N3)(9-EtGH-N7)](ClO4)2·nH2O (1-MeC=1-methylcytosine; 9-EtGH=9-ethylguanine). Inorganica Chim Acta 2002. [DOI: 10.1016/s0020-1693(02)00955-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Sharma SK, McLaughlin LW. Cross-linking of a DNA conjugate tethering a cis-bifunctional platinated complex to a target DNA duplex. J Am Chem Soc 2002; 124:9658-9. [PMID: 12175195 DOI: 10.1021/ja020500n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tethering an ethylene diamine linker to the 5' terminus of an oligothymidine sequence provides a ligand for complexation with K2PtCl4. Post-synthetic reaction of the platinum reagent with the diamino oligothymidine generates the diamino dichloro platinum-DNA conjugate that can be used for DNA duplex targeting by oligodeoxyncleotide-mediated triplex formation. Cross-linking between the third strand and the duplex occurs exclusively with the duplex target strand directly involved in triplex formation. No examples of cross-linking to the complementary target strand or cases of cross-linking to both target strands are observed. Most efficient cross-linking occurs when the dinucleotide d(GpG) is present in the target strand and no cross-linking occurs with the corresponding 7-deazaG dinucleotide target. Cross-linking is also observed when dC or dA residues are present in the target strand, or even with a single dG residue, but it is not observed in any cases to dT residues. Triplex formation provides the ability to target specific sequences of double-stranded DNA; conjugates of the type described here offer the potential of delivering a platinum complex to a specific DNA site.
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Affiliation(s)
- Sunil K Sharma
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167, USA
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31
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Abstract
A preorganized cationic receptor 2 for cytosine (C) is described which is composed of trans-a2PtII (a= NH3 or CH3NH2) cross-linked modules with adenine (A), guanine (G), and uracil (U) or thymine (T) model nucleobases. The functions of these three modules are as follows: i) Adenine orientates the two other bases at right angles, thus producing the L-shape of the receptor. ii) Guanine is the primary receptor. iii) Uracil or thymine act as coreceptors. Compared with the normal Watson-Crick pair between G and C, the association constant between 2 and C increases by a factor of 3 (in DMSO). As deduced from 1H NMR spectroscopy and confirmed by the X-ray crystal structure of the C adduct 4b, cytosine is fixed through five hydrogen bonds to the receptor, one of which involves the aromatic H(5) of C. A comparison of C binding is made with a structurally related linkage isomer receptor as well as the precursor molecule trans[alpha2PtAG]2+. The potential of modular, cationic receptors is illustrated.
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Affiliation(s)
- M S Lüth
- Fachbereich Chemie der Universität Dortmund, Germany
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32
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Praseuth D, Guieysse AL, Hélène C. Triple helix formation and the antigene strategy for sequence-specific control of gene expression. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1489:181-206. [PMID: 10807007 DOI: 10.1016/s0167-4781(99)00149-9] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Specific gene expression involves the binding of natural ligands to the DNA base pairs. Among the compounds rationally designed for artificial regulation of gene expression, oligonucleotides can bind with a high specificity of recognition to the major groove of double helical DNA by forming Hoogsteen type bonds with purine bases of the Watson-Crick base pairs, resulting in triple helix formation. Although the potential target sequences were originally restricted to polypurine-polypyrimidine sequences, considerable efforts were devoted to the extension of the repertoire by rational conception of appropriate derivatives. Efficient tools based on triple helices were developed for various biochemical applications such as the development of highly specific artificial nucleases. The antigene strategy remains one of the most fascinating fields of triplex application to selectively control gene expression. Targeting of genomic sequences is now proved to be a valuable concept on a still limited number of studies; local mutagenesis is in this respect an interesting application of triplex-forming oligonucleotides on cell cultures. Oligonucleotide penetration and compartmentalization in cells, stability to intracellular nucleases, accessibility of the target sequences in the chromatin context, the residence time on the specific target are all limiting steps that require further optimization. The existence and the role of three-stranded DNA in vivo, its interaction with intracellular proteins is worth investigating, especially relative to the regulation of gene transcription, recombination and repair processes.
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Affiliation(s)
- D Praseuth
- Laboratoire de Biophysique, INSERM U201, CNRS UMR 8646, Muséum National d'Histoire Naturelle, Paris, France
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33
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Sigel RKO, Sabat M, Freisinger E, Mower A, Lippert B. Metal-Modified Base Pairs Involving Different Donor Sites of Purine Nucleobases: trans-[a2Pt(7,9-DimeG-N1)(9-EtGH-N7)]2+andtrans-[a2Pt(7,9-DimeG-N1)(9-EtG-N7)]+(a = NH3or CH3NH2; 9-EtGH = 9-Ethylguanine; 7,9-DimeG = 7,9-Dimethylguanine). Possible Relevance to Metalated DNA Triplex Structures. Inorg Chem 1999. [DOI: 10.1021/ic981005o] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lippert B. Impact of Cisplatin on the recent development of Pt coordination chemistry: a case study. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(98)00192-1] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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35
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Reed MW, Wald A, Meyer RB. Triplex-Directed Interstrand DNA Cross-Linking by Diaziridinylquinone−Oligonucleotide Conjugates. J Am Chem Soc 1998. [DOI: 10.1021/ja973819u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael W. Reed
- Contribution from Epoch Pharmaceuticals Incorporated, 1725 220th Street SE, #104, Bothell, Washington 98021
| | - Ansel Wald
- Contribution from Epoch Pharmaceuticals Incorporated, 1725 220th Street SE, #104, Bothell, Washington 98021
| | - Rich B. Meyer
- Contribution from Epoch Pharmaceuticals Incorporated, 1725 220th Street SE, #104, Bothell, Washington 98021
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36
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Berghoff U, Schmidt K, Janik M, Schröder G, Lippert B. Monofunctional trans-PtII(NH3)2 modification of pyrimidine-rich deoxyoligonucleotides: direct platination and use of a protective group. Inorganica Chim Acta 1998. [DOI: 10.1016/s0020-1693(97)05779-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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37
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Lampe JN, Kutyavin IV, Rhinehart R, Reed MW, Meyer RB, Gamper HB. Factors influencing the extent and selectivity of alkylation within triplexes by reactive G/A motif oligonucleotides. Nucleic Acids Res 1997; 25:4123-31. [PMID: 9321668 PMCID: PMC146991 DOI: 10.1093/nar/25.20.4123] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
G/A motif triplex-forming oligonucleotides (TFOs) complementary to a 21 base pair homopurine/homopyrimidine run were conjugated at one or both ends to chlorambucil. These TFOs were incubated with several synthetic duplexes containing the targeted homopurine run flanked by different sequences. The extent of mono and interstrand cross-linking was compared with the level of binding at equilibrium. Covalent modification took place within a triple-stranded complex and usually occurred at guanine residues in the flanking double-stranded DNA. The efficiency of alkylation was dependent upon the sequence of the flanking duplex, the solution conditions, and the rate of triplex formation relative to the rate of chlorambucil reaction. Self-association of the TFOs as parallel duplexes was demonstrated and this did not interfere with triple strand formation. With an optimal target, cross-linking of the triplex was very efficient when incubation was carried in a physiological buffer supplemented with the triplex selective intercalator coralyne.
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Affiliation(s)
- J N Lampe
- Epoch Pharmaceuticals, Inc., 1725 220th Street SE, #104, Bothell, WA 98021, USA
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