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Nair YS, Venkataraman SK, Joy F, Krishna PM, Agarwal AK, Vinod T, Madathil PK, Kurup M. Synthesis, spectral and DNA/Protein binding evaluation of novel Cu(II) chelates of an NNO donor tridentate aroylhydrazone: Halogen bonding directed close packing. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128453] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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2
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Kaczorowska A, Lamperska W, Frączkowska K, Masajada J, Drobczyński S, Sobas M, Wróbel T, Chybicka K, Tarkowski R, Kraszewski S, Podbielska H, Kałas W, Kopaczyńska M. Profound Nanoscale Structural and Biomechanical Changes in DNA Helix upon Treatment with Anthracycline Drugs. Int J Mol Sci 2020; 21:ijms21114142. [PMID: 32531996 PMCID: PMC7312087 DOI: 10.3390/ijms21114142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/16/2020] [Accepted: 06/04/2020] [Indexed: 11/16/2022] Open
Abstract
In our study, we describe the outcomes of the intercalation of different anthracycline antibiotics in double-stranded DNA at the nanoscale and single molecule level. Atomic force microscopy analysis revealed that intercalation results in significant elongation and thinning of dsDNA molecules. Additionally, using optical tweezers, we have shown that intercalation decreases the stiffness of DNA molecules, that results in greater susceptibility of dsDNA to break. Using DNA molecules with different GC/AT ratios, we checked whether anthracycline antibiotics show preference for GC-rich or AT-rich DNA fragments. We found that elongation, decrease in height and decrease in stiffness of dsDNA molecules was highest in GC-rich dsDNA, suggesting the preference of anthracycline antibiotics for GC pairs and GC-rich regions of DNA. This is important because such regions of genomes are enriched in DNA regulatory elements. By using three different anthracycline antibiotics, namely doxorubicin (DOX), epirubicin (EPI) and daunorubicin (DAU), we could compare their detrimental effects on DNA. Despite their analogical structure, anthracyclines differ in their effects on DNA molecules and GC-rich region preference. DOX had the strongest overall effect on the DNA topology, causing the largest elongation and decrease in height. On the other hand, EPI has the lowest preference for GC-rich dsDNA. Moreover, we demonstrated that the nanoscale perturbations in dsDNA topology are reflected by changes in the microscale properties of the cell, as even short exposition to doxorubicin resulted in an increase in nuclei stiffness, which can be due to aberration of the chromatin organization, upon intercalation of doxorubicin molecules.
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Affiliation(s)
- Aleksandra Kaczorowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
| | - Weronika Lamperska
- Department of Optics and Photonics, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (W.L.); (J.M.); (S.D.)
| | - Kaja Frączkowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
| | - Jan Masajada
- Department of Optics and Photonics, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (W.L.); (J.M.); (S.D.)
| | - Sławomir Drobczyński
- Department of Optics and Photonics, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (W.L.); (J.M.); (S.D.)
| | - Marta Sobas
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Wroclaw Medical University, Pasteura 4, 50-367 Wroclaw, Poland; (M.S.); (T.W.)
| | - Tomasz Wróbel
- Department of Hematology, Blood Neoplasms and Bone Marrow Transplantation, Wroclaw Medical University, Pasteura 4, 50-367 Wroclaw, Poland; (M.S.); (T.W.)
| | - Kinga Chybicka
- Department of Experimental Oncology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland; (K.C.); (W.K.)
| | - Radosław Tarkowski
- Department of Surgical Oncology, Provincial Specialist Hospital, Iwaszkiewicza 5, 59-220 Legnica, Poland;
| | - Sebastian Kraszewski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
| | - Halina Podbielska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
| | - Wojciech Kałas
- Department of Experimental Oncology, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland; (K.C.); (W.K.)
| | - Marta Kopaczyńska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, 27 Wybrzeze Wyspianskiego, 50-370 Wroclaw, Poland; (A.K.); (K.F.); (S.K.); (H.P.)
- Correspondence: ; Tel.: +48-71-320-46-17
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3
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Morgan KD, Andersen RJ, Ryan KS. Piperazic acid-containing natural products: structures and biosynthesis. Nat Prod Rep 2019; 36:1628-1653. [DOI: 10.1039/c8np00076j] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Piperazic acid is a cyclic hydrazine and a non-proteinogenic amino acid found in diverse non-ribosomal peptide (NRP) and hybrid NRP–polyketide (PK) structures.
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Affiliation(s)
- Kalindi D. Morgan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | | | - Katherine S. Ryan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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4
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Gomes A, Fernandes I, Teixeira C, Mateus N, Sottomayor MJ, Gomes P. A Quinacrine Analogue Selective Against Gastric Cancer Cells: Insight from Biochemical and Biophysical Studies. ChemMedChem 2016; 11:2703-2712. [PMID: 27863116 DOI: 10.1002/cmdc.201600477] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/11/2016] [Indexed: 12/29/2022]
Abstract
One of the earliest synthetic antimalarial drugs, quinacrine, was recently reported as interesting for the treatment of acute myeloid leukemia. Inspired by this and similar findings, we evaluated a set of quinacrine analogues against gastric (MKN-28), colon (Caco-2), and breast (MFC-7) cancer cell lines and one normal human fibroblast cell line (HFF-1). All the compounds, previously developed by us as dual-stage antimalarial leads, displayed antiproliferative activity, and one of the set stood out as selective toward the gastric cancer cell line, MKN-28. Interestingly, this compound was transported across an in vitro MKN-28 model cell line in low amounts, and approximately 80 % was trapped inside those cells. Nuclear targeting of the same compound and its interactions with calf thymus DNA were assessed through combined fluorescence microscopy, spectroscopy, and calorimetry studies, which provided evidence for the compound's ability to reach the nucleus and to interact with DNA.
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Affiliation(s)
- Ana Gomes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Iva Fernandes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Cátia Teixeira
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Nuno Mateus
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - M J Sottomayor
- CIQ-UP, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Paula Gomes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
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Fernández J, Marín L, Alvarez-Alonso R, Redondo S, Carvajal J, Villamizar G, Villar CJ, Lombó F. Biosynthetic modularity rules in the bisintercalator family of antitumor compounds. Mar Drugs 2014; 12:2668-99. [PMID: 24821625 PMCID: PMC4052310 DOI: 10.3390/md12052668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/05/2022] Open
Abstract
Diverse actinomycetes produce a family of structurally and biosynthetically related non-ribosomal peptide compounds which belong to the chromodepsipeptide family. These compounds act as bisintercalators into the DNA helix. They give rise to antitumor, antiparasitic, antibacterial and antiviral bioactivities. These compounds show a high degree of conserved modularity (chromophores, number and type of amino acids). This modularity and their high sequence similarities at the genetic level imply a common biosynthetic origin for these pathways. Here, we describe insights about rules governing this modular biosynthesis, taking advantage of the fact that nowadays five of these gene clusters have been made public (thiocoraline, triostin, SW-163 and echinomycin/quinomycin). This modularity has potential application for designing and producing novel genetic engineered derivatives, as well as for developing new chemical synthesis strategies. These would facilitate their clinical development.
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Affiliation(s)
- Javier Fernández
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Laura Marín
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Raquel Alvarez-Alonso
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Saúl Redondo
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Juan Carvajal
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Germán Villamizar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Claudio J Villar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Felipe Lombó
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
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Rackham BD, Howell LA, Round AN, Searcey M. Non-covalent duplex to duplex crosslinking of DNA in solution revealed by single molecule force spectroscopy. Org Biomol Chem 2013; 11:8340-7. [PMID: 24158749 DOI: 10.1039/c3ob42009d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Small molecules that interact with DNA, disrupting the binding of transcription factors or crosslinking DNA into larger structures, have significant potential as cancer therapies and in nanotechnology. Bisintercalators, including natural products such as echinomycin and rationally designed molecules such as the bis-9-aminoacridine-4-carboxamides, are key examples. There is little knowledge of the propensity of these molecules to crosslink duplex DNA. Here we use single molecule force spectroscopy to assay the crosslinking capabilities of bisintercalators. We show that bis-9-aminoacridine-4-carboxamides with both rigid and flexible linkers are able to crosslink duplex strands of DNA, and estimate the equilibrium free energy of a 9-aminoacridine-4-carboxamide bisintercalator from DNA at 5.03 kJ mol(-1). Unexpectedly, we find that echinomycin and its synthetic analogue TANDEM are capable of sequence-specific crosslinking of the terminal base pairs of two duplex DNA strands. In the crowded environment of the nucleosome, small molecules that crosslink neighbouring DNA strands may be expected to have significant effects on transcription, while a small molecule that facilitates sequence-specific blunt-end ligation of DNA may find applications in the developing field of DNA nanotechnology.
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Affiliation(s)
- Benjamin D Rackham
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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7
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Alonso-Sarduy L, Longo G, Dietler G, Kasas S. Time-lapse AFM imaging of DNA conformational changes induced by daunorubicin. NANO LETTERS 2013; 13:5679-5684. [PMID: 24125039 DOI: 10.1021/nl403361f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cancer is a major health issue that absorbs the attention of a large part of the biomedical research. Intercalating agents bind to DNA molecules and can inhibit their synthesis and transcription; thus, they are increasingly used as drugs to fight cancer. In this work, we show how atomic force microscopy in liquid can characterize, through time-lapse imaging, the dynamical influence of intercalating agents on the supercoiling of DNA, improving our understanding of the drug's effect.
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Affiliation(s)
- Livan Alonso-Sarduy
- Laboratoire de Physique de la Matière Vivante, École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne, Switzerland
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8
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Dutta S, Snyder MJ, Rosile D, Binz KL, Roll EH, Suryadi J, Bierbach U, Guthold M. PT-ACRAMTU, a platinum-acridine anticancer agent, lengthens and aggregates, but does not stiffen or soften DNA. Cell Biochem Biophys 2013; 67:1103-13. [PMID: 23636685 PMCID: PMC3767762 DOI: 10.1007/s12013-013-9614-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We used atomic force microscopy (AFM) to study the dose-dependent change in conformational and mechanical properties of DNA treated with PT-ACRAMTU ([PtCl(en)(ACRAMTU-S)](NO3)2, (en = ethane-1,2-diamine, ACRAMTU = 1-[2-(acridin-9-ylamino)ethyl]-1,3-dimethylthiourea. PT-ACRAMTU is the parent drug of a family of non-classical platinum-based agents that show potent activity in non-small cell lung cancer in vitro and in vivo. Its acridine moiety intercalates between DNA bases, while the platinum group forms mono-adducts with DNA bases. AFM images show that PT-ACRAMTU causes some DNA looping and aggregation at drug-to-base pair ratio (r b) of 0.1 and higher. Very significant lengthening of the DNA was observed with increasing doses of PT-ACRAMTU, and reached saturation at an r b of 0.15. At r b of 0.1, lengthening was 0.6 nm per drug molecule, which is more than one fully stretched base pair stack can accommodate, indicating that ACRAMTU also disturbs the stacking of neighboring base pair stacks. Analysis of the AFM images based on the worm-like chain (WLC) model showed that PT-ACRAMTU did not change the flexibility of (non-aggregated) DNA, despite the extreme lengthening. The persistence length of untreated DNA and DNA treated with PT-ACRAMTU was in the range of 49-65 nm. Potential consequences of the perturbations caused by this agent for the recognition and processing of the DNA adducts it forms are discussed.
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Affiliation(s)
- Samrat Dutta
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Matthew J. Snyder
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - David Rosile
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Kristen L. Binz
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Eric H. Roll
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Jimmy Suryadi
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109
| | - Ulrich Bierbach
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27109
| | - Martin Guthold
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
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9
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Oelke AJ, France DJ, Hofmann T, Wuitschik G, Ley SV. Piperazic acid-containing natural products: Isolation, biological relevance and total synthesis. Nat Prod Rep 2011; 28:1445-71. [DOI: 10.1039/c1np00041a] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Banerjee T, Mukhopadhyay R. Structural effects of nogalamycin, an antibiotic antitumour agent, on DNA. Biochem Biophys Res Commun 2008; 374:264-8. [DOI: 10.1016/j.bbrc.2008.07.053] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 07/03/2008] [Indexed: 11/28/2022]
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11
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Turner YTA, Roberts CJ, Davies MC. Scanning probe microscopy in the field of drug delivery. Adv Drug Deliv Rev 2007; 59:1453-73. [PMID: 17920719 DOI: 10.1016/j.addr.2007.08.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 08/10/2007] [Indexed: 01/14/2023]
Abstract
The scanning probe microscopes (SPMs) are a group of powerful surface sensitive instruments which when used complimentarily with traditional analytical techniques can provide invaluable, definitive information aiding our understanding and development of drug delivery systems. In this review, the main use of the SPMs (particularly the atomic force microscopy (AFM)) and their successes in forwarding drug delivery are highlighted and categorised into two interlinked sections namely, preformulation and formulation. SPM in preformulation concentrates on applications in pharmaceutical processes including, crystal morphology and modification, discriminating polymorphs, drug dissolution and release, solid state stability and interaction. The ability of the AFM to detect forces between different surfaces and at the same time to operate in liquids or controlled humidity and defined temperatures has also been particularly useful in the study of drug delivery. In formulation, the use of SPMs in different drug delivery systems is discussed in light of different host entry routes.
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Affiliation(s)
- Ya Tsz A Turner
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, The University of Nottingham, NG7 2RD, UK
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12
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Cherian AE, Sun FC, Sheiko SS, Coates GW. Formation of Nanoparticles by Intramolecular Cross-Linking: Following the Reaction Progress of Single Polymer Chains by Atomic Force Microscopy. J Am Chem Soc 2007; 129:11350-1. [PMID: 17722930 DOI: 10.1021/ja074301l] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna E Cherian
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853-1301, USA
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13
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Brabec V, Christofis P, Slámová M, Kostrhunová H, Nováková O, Najajreh Y, Gibson D, Kaspárková J. DNA interactions of new cytotoxic tetrafunctional dinuclear platinum complex trans,trans-[{PtCl2(NH3)}2(piperazine)]. Biochem Pharmacol 2007; 73:1887-900. [PMID: 17400194 DOI: 10.1016/j.bcp.2007.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 02/09/2007] [Accepted: 03/02/2007] [Indexed: 11/28/2022]
Abstract
A new tetrafunctional dinuclear platinum complex trans,trans-[{PtCl2(NH3)}2(piperazine)] with sterically rigid linking group was designed, synthesized and characterized. In this novel molecule, the DNA-binding features of two classes of the platinum compounds with proven antitumor activity are combined, namely trans oriented bifunctional mononuclear platinum complexes with a heterocyclic ligand and polynuclear platinum complexes. DNA-binding mode of this new complex was analyzed by various methods of molecular biology and biophysics. The complex coordinates DNA in a unique way and interstrand and intrastrand cross-links are the predominant lesions formed in DNA in cell-free media and in absence of proteins. An intriguing aspect of trans,trans-[{PtCl2(NH3)}2(piperazine)] is that, using a semi-rigid linker, interstrand cross-linking is diminished relative to other dinuclear platinum complexes with flexible linking groups and lesions that span several base pairs, such as tri- and tetrafunctional adducts, become unlikely. In addition, in contrast to the inability of trans,trans-[{PtCl2(NH3)}2(piperazine)] to cross-link two DNA duplexes, the results of the present work convincingly demonstrate that this dinuclear platinum complex forms specific DNA lesions which can efficiently cross-link proteins to DNA. The results substantiate the view that trans,trans-[{PtCl2(NH3)}2(piperazine)] or its analogues could be used as a tool for studies of DNA properties and their interactions or as a potential antitumor agent. The latter view is also corroborated by the observation that trans,trans-[{PtCl2(NH3)}2(piperazine)] is a more effective cytotoxic agent than cisplatin against human tumor ovarian cell lines.
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Affiliation(s)
- Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, CZ-61265 Brno, Czech Republic
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14
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Dawson S, Malkinson JP, Paumier D, Searcey M. Bisintercalator natural products with potential therapeutic applications: isolation, structure determination, synthetic and biological studies. Nat Prod Rep 2007; 24:109-26. [PMID: 17268609 DOI: 10.1039/b516347c] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Echinomycin is the prototypical bisintercalator, a molecule that binds to DNA by inserting two planar chromophores between the base-pairs of duplex DNA, placing its cyclic depsipeptide backbone in the minor groove. As such, it has been the focus of an extensive number of investigations into its biological activity, nucleic acid binding and, to some extent, its structure-activity relationships. However, echinomycin is also the parent member of an extended family of natural products that interact with DNA by a similar mechanism of bisintercalation. The structural variety in these compounds leads to changes in sequence selectivity and and biological activity, particularly as anti-tumour and anti-viral agents. One of the more recently identified marine natural products that is moving close to clinical development is thiocoraline, and it therefore seems timely to review the various bisintercalator natural products.
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Affiliation(s)
- Simon Dawson
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London, 29-39 Brunswick Square, London, WC1N 1AX, UK
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15
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Mihailovic A, Vladescu I, McCauley M, Ly E, Williams MC, Spain EM, Nuñez ME. Exploring the interaction of ruthenium(II) polypyridyl complexes with DNA using single-molecule techniques. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:4699-709. [PMID: 16649785 PMCID: PMC2519805 DOI: 10.1021/la053242r] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Here we explore DNA binding by a family of ruthenium(II) polypyridyl complexes using an atomic force microscope (AFM) and optical tweezers. We demonstrate using AFM that Ru(bpy)2dppz2+ intercalates into DNA (K(b) = 1.5 x 10(5) M(-1)), as does its close relative Ru(bpy)2dppx2+ (K(b) = 1.5 x 10(5) M(-1)). However, intercalation by Ru(phen)3(2+) and other Ru(II) complexes with K(b) values lower than that of Ru(bpy)2dppz2+ is difficult to determine using AFM because of competing aggregation and surface-binding phenomena. At the high Ru(II) concentrations required to evaluate intercalation, most of the DNA strands acquire a twisted, curled conformation that is impossible to measure accurately. The condensation of DNA on mica in the presence of polycations is well known, but it clearly precludes the accurate assessment by AFM of DNA intercalation by most Ru(II) complexes, though not by ethidium bromide and other monovalent intercalators. When stretching individual DNA molecules using optical tweezers, the same limitation on high metal concentration does not exist. Using optical tweezers, we show that Ru(phen)2dppz2+ intercalates avidly (K(b) = 3.2 x 10(6) M(-1)) whereas Ru(bpy)3(2+) does not intercalate, even at micromolar ruthenium concentrations. Ru(phen)3(2+) is shown to intercalate weakly (i.e., at micromolar concentrations (K(b) = 8.8 x 10(3) M(-1))). The distinct differences in DNA stretching behavior between Ru(phen)3(2+) and Ru(bpy)3(2+) clearly illustrate that intercalation can be distinguished from groove binding by pulling the DNA with optical tweezers. Our results demonstrate both the benefits and challenges of two single-molecule methods of exploring DNA binding and help to elucidate the mode of binding of Ru(phen)3(2+).
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Affiliation(s)
| | - Ioana Vladescu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115
| | - Micah McCauley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115
| | - Elaine Ly
- Department of Chemistry, Occidental College, Los Angeles, California 10021
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, Massachusetts 02115
| | - Eileen M. Spain
- Department of Chemistry, Occidental College, Los Angeles, California 10021
| | - Megan E. Nuñez
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 10075
- To whom correspondence should be addressed: Department of Chemistry, Mount Holyoke College, South Hadley, MA 10075. Telephone: (413) 538−2449; Fax: (413) 538−2327; E-mail:
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16
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Lee JWM, Chu JJH, Ng ML. Quantifying the Specific Binding between West Nile Virus Envelope Domain III Protein and the Cellular Receptor αVβ3 Integrin. J Biol Chem 2006; 281:1352-60. [PMID: 16275649 DOI: 10.1074/jbc.m506614200] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A previous study has illustrated that the alphaVbeta3 integrin served as the functional receptor for West Nile virus (WNV) entry into cells. Domain III (DIII) of WNV envelope protein (E) was postulated to mediate virus binding to the cellular receptor. In this study, the specificity and affinity binding of WNV E DIII protein to alphaVbeta3 integrin was confirmed with co-immunoprecipitation and receptor competition assay. Binding of WNV E DIII protein to alphaVbeta3 integrin induced the phosphorylation of focal adhesion kinase that is required to mediate ligand-receptor internalization into cells. A novel platform was then developed using the atomic force microscopy to measure this specific binding force between WNV E DIII protein and the cellular receptor, alphaVbeta3 integrin. The single protein pair-interacting force measured was in the range of 45 +/- 5 piconewtons. This interacting force was highly specific as minimal force was measured in the WNV E DIII protein interaction with alphaVbeta5 integrin molecules and heparan sulfate. These experiments provided an insight to quantitate virus-receptor interaction. Force measurement using atomic force microscopy can serve to quantitatively analyze the effect of candidate drugs that modulate virus-host receptor affinity.
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Affiliation(s)
- Jason Wei-Ming Lee
- Flavivirology Laboratory, Department of Microbiology, National University of Singapore, Singapore 117597
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Tseng YD, Ge H, Wang X, Edwardson JM, Waring MJ, Fitzgerald WJ, Henderson RM. Atomic force microscopy study of the structural effects induced by echinomycin binding to DNA. J Mol Biol 2005; 345:745-58. [PMID: 15588823 DOI: 10.1016/j.jmb.2004.10.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Revised: 10/08/2004] [Accepted: 10/18/2004] [Indexed: 10/26/2022]
Abstract
Atomic force microscopy (AFM) has been used to examine the conformational effects of echinomycin, a DNA bis-intercalating antibiotic, on linear and circular DNA. Four different 398 bp DNA fragments were synthesized, comprising a combination of normal and/or modified bases including 2,6-diaminopurine and inosine (which are the corresponding analogues of adenine and guanosine in which the 2-amino group that is crucial for echinomycin binding has been added or removed, respectively). Analysis of AFM images provided contour lengths, which were used as a direct measure of bis-intercalation. About 66 echinomycin molecules are able to bind to each fragment, corresponding to a site size of six base-pairs. The presence of base-modified nucleotides affects DNA conformation, as determined by the helical rise per base-pair. At the same time, the values obtained for the dissociation constant correlate with the types of preferred binding site available among the different DNA fragments; echinomycin binds to TpD sites much more tightly than to CpG sites. The structural perturbations induced when echinomycin binds to closed circular duplex pBR322 DNA were also investigated and a method for quantification of the structural changes is presented. In the presence of increasing echinomycin concentration, the plasmid can be seen to proceed through a series of transitions in which its supercoiling decreases, relaxes, and then increases.
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Affiliation(s)
- Yolanda D Tseng
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
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18
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Abstract
Atomic force microscopy is being used ever more widely in biological imaging, because of its unique ability to provide structural information at the single molecule level and under near-physiological conditions. Detailed topographic images of potential drug targets, such as proteins and DNA, have been produced, and the folding of modular proteins has been studied using single-molecule force spectroscopy. Recently, atomic force microscopy has been used to examine ligand-protein and ligand-DNA interactions, and to begin to determine the architecture of multi-subunit proteins, including a member of the superfamily of ionotropic receptors. Atomic force microscopy is fast becoming a valuable addition to the pharmaceutical industry's toolkit.
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Affiliation(s)
- J Michael Edwardson
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, UK CB2 1PD
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