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Ilieva S, Bozova N, Rangelov M, Todorova N, Vasilev A, Cheshmedzhieva D. Asymmetric Monomethine Cyanine Dyes with Hydrophobic Functionalities for Fluorescent Intercalator Displacement Assay. Molecules 2023; 29:114. [PMID: 38202697 PMCID: PMC10779803 DOI: 10.3390/molecules29010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
A new green procedure has been applied for the synthesis and purification of asymmetric monomethine cyanine dyes. The photophysical properties of the newly synthesized compounds have been examined by combined application of spectroscopic and theoretical methods. The structural characteristics of the molecules and dimer formation were characterized by quantum chemical computation and juxtaposed to the aggregachromism in UV/Vis spectra. The applicability of the dyes as fluorogenic nucleic acid probes has been proven by fluorescence titration, and their binding constants have been calculated. The mode of ligand-dsDNA/RNA interaction was rationalized by means of CD spectroscopy, molecular docking analysis, and fluorescent intercalator displacement experiments.
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Affiliation(s)
- Sonia Ilieva
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1 J. Bourchier Ave., 1164 Sofia, Bulgaria; (S.I.); (N.B.)
| | - Nadezhda Bozova
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1 J. Bourchier Ave., 1164 Sofia, Bulgaria; (S.I.); (N.B.)
| | - Miroslav Rangelov
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Nadezhda Todorova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria;
| | - Aleksey Vasilev
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1 J. Bourchier Ave., 1164 Sofia, Bulgaria; (S.I.); (N.B.)
- Institute of Polymers, Bulgarian Academy of Sciences, Akad. G. Bonchev St., Bl 103A, 1113 Sofia, Bulgaria
| | - Diana Cheshmedzhieva
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kliment Ohridski”, 1 J. Bourchier Ave., 1164 Sofia, Bulgaria; (S.I.); (N.B.)
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2
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Shi H, Hu X, Zhang J, Li W, Xu J, Hu B, Ma L, Lou L. Soil minerals and organic matters affect ARGs transformation by changing the morphology of plasmid and bacterial responses. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131727. [PMID: 37257383 DOI: 10.1016/j.jhazmat.2023.131727] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/18/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023]
Abstract
Soil environment is a vital place for the occurrence and spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Extracellular DNA-mediated transformation is an important pathway for ARGs horizontal transfer and widely exists in soil environment. However, little information is available on how common soil components affect ARGs transformation. Here, three minerals (quartz, kaolinite, and montmorillonite) and three organic matters (humic acid, biochar, and soot) were selected as typical soil components. A small amount in suspension (0.2 g/L) of most soil components (except for quartz and montmorillonite) promoted transformant production by 1.1-1.6 folds. For a high amount (8 g/L), biochar significantly promoted transformant production to 1.5 times, kaolinite exerted a 30 % inhibitory effect. From the perspective of plasmid, biochar induced a higher proportion of supercoiled plasmid than kaolinite; more dissolved organic matter and metal ions facilitated plasmid aggregation under the near-neutral pH, thus promoted transformation. As for the influence of materials on recipient, although biochar and kaolinite both increased reactive oxygen species (ROS) level and membrane permeability, biochar up-regulated more ROS related genes, resulting in intracellular ROS production and up-regulating the expression of carbohydrate metabolism and transformation related genes. While kaolinite inhibited transformation mainly by causing nutrient deficiency.
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Affiliation(s)
- Hongyu Shi
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Xinyi Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Jin Zhang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Wenxuan Li
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Jiang Xu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China
| | - Liping Ma
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, PR China.
| | - Liping Lou
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310029, PR China; Key Laboratory of Water Pollution Control and Environmental Safety of Zhejiang Province, Hangzhou 310020, PR China.
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3
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Gaeta M, Farini S, Gangemi CMA, Purrello R, D'Urso A. Interactions of mono spermine porphyrin derivative with DNAs. Chirality 2020; 32:1243-1249. [PMID: 32794305 DOI: 10.1002/chir.23272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/04/2020] [Accepted: 07/20/2020] [Indexed: 11/12/2022]
Abstract
In this work, we have characterized the interactions of monospermine porphyrin derivative with calf thymus DNA (ct-DNA) and poly (dG-dC)2 in both B and Z conformation. By several spectroscopic techniques (UV-vis, electronic circular dichroism and resonance light scattering), the binding modes of monospermine porphyrin derivative with different DNA sequences have been elucidated. In the presence of ct-DNA, the porphyrin binds along the external double helix as well as in the presence of B conformation of poly (dG-dC)2 . Whilst when the Z form of the poly (dG-dC)2 is induced, a slight intercalation of the porphyrin between the basis has been detected.
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Affiliation(s)
- Massimiliano Gaeta
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
| | - Salvatore Farini
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
| | - Chiara M A Gangemi
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
| | - Roberto Purrello
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
| | - Alessandro D'Urso
- Department of Chemical Sciences, University of Catania, Catania, 6 95125, Italy
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4
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May B, Naqi HA, Tipping M, Scott J, Husbands SM, Blagbrough IS, Pudney CR. Synthetic Cannabinoid Receptor Agonists Detection Using Fluorescence Spectral Fingerprinting. Anal Chem 2019; 91:12971-12979. [PMID: 31580647 PMCID: PMC7006962 DOI: 10.1021/acs.analchem.9b03037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
Synthetic
cannabinoid receptor agonists (SCRAs), termed “Spice”
or “K2”, are molecules that emulate the effects of the
active ingredient of marijuana, and they have gained enormous popularity
over the past decade. SCRAs are Schedule 1 drugs that are highly prevalent
in the U.K. prison system and among homeless populations. SCRAs are
highly potent and addictive. With no way to determine the dose/amount
at the point-of care, they pose severe health risks to users, including
psychosis, stroke, epileptic seizures, and they can kill. SCRAs are
chemically diverse, with over a hundred compounds used as recreational
drugs. The chemical diversity of SCRA structures presents a challenge
in developing detection modalities. Typically, GC-MS is used for chemical
identification; however, this cannot be in place in most settings
where detection is critical, e.g., in hospital Emergency Departments,
in custody suites/prisons, or among homeless communities. Ideally,
real time, point-of-care identification of SCRAs is desirable to direct
the care pathway of overdoses and provide information for informed
consent. Herein, we show that fluorescence spectral fingerprinting
can be used to identify the likely presence of SCRAs, as well as provide
more specific information on structural class and concentration (∼1
μg mL–1). We demonstrate that that fluorescence
spectral fingerprints, combined with numerical modeling, can detect
both parent and combusted material, and such fingerprinting is also
practical for detecting them in oral fluids. Our proof-of-concept
study suggests that, with development, the approach could be useful
in a range of capacities, notably in harm reduction for users of Spice/K2.
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5
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Safiarian MS, Sawoo S, Mapp CT, Williams DE, Gude L, Fernández M, Lorente A, Grant KB. Aminomethylanthracene Dyes as High‐Ionic‐Strength DNA‐Photocleaving Agents: Two Rings are Better than One. ChemistrySelect 2018. [DOI: 10.1002/slct.201703019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Sudeshna Sawoo
- Department of Chemistry Georgia State University, Atlanta GA 30302–3965 USA
| | - Carla T. Mapp
- Department of Chemistry Georgia State University, Atlanta GA 30302–3965 USA
| | | | - Lourdes Gude
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805-Alcalá de Henares Madrid Spain
| | - María‐José Fernández
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805-Alcalá de Henares Madrid Spain
| | - Antonio Lorente
- Departamento de Química Orgánica y Química Inorgánica Universidad de Alcalá 28805-Alcalá de Henares Madrid Spain
| | - Kathryn B. Grant
- Department of Chemistry Georgia State University, Atlanta GA 30302–3965 USA
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6
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Duprey JLHA, Bassani DM, Hyde EI, Jonusauskas G, Ludwig C, Rodger A, Spencer N, Vyle JS, Wilkie J, Zhao ZY, Tucker JHR. Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes. Org Biomol Chem 2018; 16:6576-6585. [DOI: 10.1039/c8ob01710g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.
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Affiliation(s)
| | - Dario M. Bassani
- Institut des Sciences Moléculaires, CNRS UMR 5255
- Université Bordeaux
- Talence 33405
- France
| | - Eva I. Hyde
- School of Biosciences
- The University of Birmingham
- Edgbaston
- UK
| | - Gediminas Jonusauskas
- Laboratoire Ondes et Matière d'Aquitaine
- UMR CNRS 5798
- Université Bordeaux
- Talence 33405
- France
| | - Christian Ludwig
- Henry Wellcome Building for Biomolecular NMR Spectroscopy
- Institute of Cancer & Genomic Sciences
- College of Medical & Dental Sciences
- University of Birmingham
- Edgbaston
| | - Alison Rodger
- Department of Molecular Sciences
- Faculty of Science and Engineering
- Macquarie University
- North Ryde
- Australia
| | - Neil Spencer
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
| | - Joseph S. Vyle
- School of Chemistry and Chemical Engineering
- Queen's University Belfast
- Belfast
- UK
| | - John Wilkie
- School of Chemistry
- University of Birmingham
- Edgbaston
- UK
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7
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Deiana M, Pokladek Z, Matczyszyn K, Mlynarz P, Buckle M, Samoc M. Effective control of the intrinsic DNA morphology by photosensitive polyamines. J Mater Chem B 2017; 5:1028-1038. [DOI: 10.1039/c6tb02732f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Changes occurring in the intrinsic B-DNA morphology upon binding to molecular photoswitches.
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Affiliation(s)
- M. Deiana
- Advanced Materials Engineering and Modelling Group
- Faculty of Chemistry
- Wroclaw University of Science and Technology
- 50-370 Wroclaw
- Poland
| | - Z. Pokladek
- Department of Bioorganic Chemistry
- Faculty of Chemistry
- Wroclaw University of Science and Technology
- 50-370 Wroclaw
- Poland
| | - K. Matczyszyn
- Advanced Materials Engineering and Modelling Group
- Faculty of Chemistry
- Wroclaw University of Science and Technology
- 50-370 Wroclaw
- Poland
| | - P. Mlynarz
- Department of Bioorganic Chemistry
- Faculty of Chemistry
- Wroclaw University of Science and Technology
- 50-370 Wroclaw
- Poland
| | - M. Buckle
- LBPA
- ENS Cachan
- CNRS Université Paris-Saclay
- Cachan
- France
| | - M. Samoc
- Advanced Materials Engineering and Modelling Group
- Faculty of Chemistry
- Wroclaw University of Science and Technology
- 50-370 Wroclaw
- Poland
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8
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Shahabadi N, Pourfoulad M, Moghadam NH. Experimental and computational studies on the effects of valganciclovir as an antiviral drug on calf thymus DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 36:31-48. [PMID: 27759493 DOI: 10.1080/15257770.2016.1218019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA-binding properties of an antiviral drug, valganciclovir (valcyte) was studied by using emission, absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, and computational studies. The drug bound to calf thymus DNA (ct-DNA) in a groove-binding mode. The calculated binding constant of UV-vis, Ka, is comparable to groove-binding drugs. Competitive fluorimetric studies with Hoechst 33258 showed that valcyte could displace the DNA-bound Hoechst 33258. The drug could not displace intercalated methylene blue from DNA double helix. Furthermore, the induced detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity confirm the groove-binding mode. In addition, an integrated molecular docking was employed to further investigate the binding interactions between valcyte and calf thymus DNA.
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Affiliation(s)
- Nahid Shahabadi
- a Department of Chemistry , Faculty of Science, Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Mehdi Pourfoulad
- a Department of Chemistry , Faculty of Science, Razi University , Kermanshah , Iran
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9
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Shankar BH, Jayaram DT, Ramaiah D. Naphthalene Imide Conjugates: Formation of Supramolecular Assemblies, and the Encapsulation and Release of Dyes through DNA-Mediated Disassembly. Chemistry 2015; 21:17657-63. [PMID: 26490366 DOI: 10.1002/chem.201502955] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Indexed: 01/01/2023]
Abstract
We report the synthesis of two new amphiphilic conjugates 1 and 2 based on naphthalene di- and monoimide chromophores and the investigation of their photophysical, self-assembly and DNA-binding properties. These conjugates showed aqueous good solubility and exhibited strong interactions with DNA and polynucleotides such as poly(dG⋅dC)-poly(dG⋅dC) and poly(dA⋅dT)-poly(dA⋅dT). The interaction of these conjugates with DNA was evaluated by photo- and biophysical techniques. These studies revealed that the conjugates interact with DNA through intercalation with association constants in the order of 5-8×10(4) M(-1) . Of these two conjugates, bolaamphiphile 1 exhibited a supramolecular assembly that formed vesicles with an approximate diameter of 220 nm in the aqueous medium at a critical aggregation concentration of 0.4 mM, which was confirmed by SEM and TEM. These vesicular structures showed a strong affinity for hydrophobic molecules such as Nile red through encapsulation. Uniquely, when exposed to DNA the vesicles disassembled, and therefore this transformation could be utilised for the encapsulation and release of hydrophobic molecules by employing DNA as a stimulus.
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Affiliation(s)
- Balaraman H Shankar
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019 (India)
| | - Dhanya T Jayaram
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019 (India)
| | - Danaboyina Ramaiah
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019 (India). , , .,CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785 006, Assam (India). , ,
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10
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Razmkhah K, Chmel NP, Gibson MI, Rodger A. Oxidized polyethylene films for orienting polar molecules for linear dichroism spectroscopy. Analyst 2015; 139:1372-82. [PMID: 24482800 DOI: 10.1039/c3an02322b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stretched polyethylene (PE) films have been used to orient small molecules for decades by depositing solutions on their surface and allowing the solvent to evaporate leaving the analyte absorbed on the polymer film. However, the non-polar hydrophobic nature of PE is an obstacle to aligning polar molecules and biological samples. In this work PE film was treated with oxygen plasma in order to increase surface hydrophilicity. Different treatment conditions were evaluated using contact angle measurement and X-ray photoelectron spectroscopy. Treated PE (PE(OX)) films are shown to be able to align molecules of different polarities including progesterone, 1-pyrenecarboxaldehyde, 4',6-diamidino-2-phenylindole (DAPI) and anthracene. The degree of alignment of each molecule was studied by running series of linear dichroism (LD) experiments and the polarizations of electronic transition moments were determined. For the first time optimal conditions (such as stretching factor and concentration of the sample) for stretched film LD were determined. PE(OX) aligning ability was compared to that of normal PE films. Progesterone showed a slightly better alignment on PE(OX) than PE. 1-Pyrenecarboxaldehyde oriented differently on the two different films which enabled transition moment assignment for this low symmetry molecule. DAPI (which does not align on PE) aligned well on PE(OX) and enabled us to obtain better LD data than had previously been collected with polyvinyl alcohol. Anthracene alignment and formation of dimers and higher order structures were studied in much more detail than previously possible, showing a variety of assemblies on PE and PE(OX) films.
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Affiliation(s)
- Kasra Razmkhah
- Department of Chemistry and Warwick Analytical Science Centre, University of Warwick, Coventry, CV4 7AL, UK.
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11
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Ang DL, Jones NC, Stootman F, Ghadirian B, Aldrich-Wright JR. Improved DNA equilibrium binding affinity determinations of platinum(ii) complexes using synchrotron radiation circular dichroism. Analyst 2015; 140:4162-9. [DOI: 10.1039/c5an00066a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The DNA binding affinity of a range of Pt(ii) complexes was reinvestigated using SRCD and a new method was implemented for determining the binding constant, saving time and minimising data collection.
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Affiliation(s)
- Dale L. Ang
- Nanoscale Organisation and Dynamics Group
- School of Science and Health
- University of Western Sydney
- Penrith
- Australia
| | - Nykola C. Jones
- ISA
- Department of Physics and Astronomy
- Aarhus University
- DK 8000 Aarhus C
- Denmark
| | - Frank Stootman
- Nanoscale Organisation and Dynamics Group
- School of Science and Health
- University of Western Sydney
- Penrith
- Australia
| | - Bahman Ghadirian
- Nanoscale Organisation and Dynamics Group
- School of Science and Health
- University of Western Sydney
- Penrith
- Australia
| | - Janice R. Aldrich-Wright
- Nanoscale Organisation and Dynamics Group
- School of Science and Health
- University of Western Sydney
- Penrith
- Australia
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12
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Hicks MR, Rodger A, Lin YP, Jones NC, Hoffmann SV, Dafforn TR. Rapid Injection Linear Dichroism for Studying the Kinetics of Biological Processes. Anal Chem 2012; 84:6561-6. [DOI: 10.1021/ac300842h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Matthew R. Hicks
- Department of Chemistry and
Warwick Centre for Analytical Science, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Alison Rodger
- Department of Chemistry and
Warwick Centre for Analytical Science, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Yu-pin Lin
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United
Kingdom
| | - Nykola C. Jones
- Institute for Storage
Ring Facilities
(ISA), Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Søren Vrønning Hoffmann
- Institute for Storage
Ring Facilities
(ISA), Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Timothy R. Dafforn
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United
Kingdom
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13
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Zhao C, Ren J, Gregoliński J, Lisowski J, Qu X. Contrasting enantioselective DNA preference: chiral helical macrocyclic lanthanide complex binding to DNA. Nucleic Acids Res 2012; 40:8186-96. [PMID: 22675072 PMCID: PMC3439914 DOI: 10.1093/nar/gks524] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
There is great interest in design and synthesis of small molecules which selectively target specific genes to inhibit biological functions in which particular DNA structures participate. Among these studies, chiral recognition has been received much attention because more evidences have shown that conversions of the chirality and diverse conformations of DNA are involved in a series of important life events. Here, we report that a pair of chiral helical macrocyclic lanthanide (III) complexes, (M)-Yb[LSSSSSS]3+ and (P)-Yb[LRRRRRR]3+, can enantioselectively bind to B-form DNA and show remarkably contrasting effects on GC-rich and AT-rich DNA. Neither of them can influence non-B-form DNA, nor quadruplex DNA stability. Our results clearly show that P-enantiomer stabilizes both poly(dG-dC)2 and poly(dA-dT)2 while M-enantiomer stabilizes poly(dA-dT)2, however, destabilizes poly(dG-dC)2. To our knowledge, this is the best example of chiral metal compounds with such contrasting preference on GC- and AT-DNA. Ligand selectively stabilizing or destabilizing DNA can interfere with protein–DNA interactions and potentially affect many crucial biological processes, such as DNA replication, transcription and repair. As such, bearing these unique capabilities, the chiral compounds reported here may shed light on the design of novel enantiomers targeting specific DNA with both sequence and conformation preference.
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Affiliation(s)
- Chuanqi Zhao
- Division of Biological Inorganic Chemistry, State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Graduate School of Chinese Academy of Sciences, Changchun, Jilin 130022, China
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14
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Phillips T, Haq I, Thomas JA. Water-soluble amino derivatives of free-base dppz – syntheses and DNA binding studies. Org Biomol Chem 2011; 9:3462-70. [DOI: 10.1039/c0ob00869a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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15
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Doi I, Tsuji G, Kawakami K, Nakagawa O, Taniguchi Y, Sasaki S. The Spermine–Bisaryl Conjugate as a Potent Inducer of B‐ to Z‐DNA Transition. Chemistry 2010; 16:11993-9. [DOI: 10.1002/chem.201000947] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Issei Doi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Genichiro Tsuji
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Kyoko Kawakami
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Yosuke Taniguchi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3‐1‐1 Maidashi, Higashi‐ku, Fukuoka, 812‐8582 (Japan), Fax: (+81) 92‐642‐6615
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16
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Banerjee T, Dubey P, Mukhopadhyay R. Compacting effect of BBR3464, a new-generation trisplatinum anticancer agent, on DNA. Biochimie 2010; 92:846-51. [DOI: 10.1016/j.biochi.2010.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 01/18/2010] [Indexed: 11/26/2022]
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17
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Lau V, Heyne B. Does the DNA Binding Mode of a Molecule Affect its Ability to Interact With Singlet Oxygen? Photochem Photobiol 2009; 85:1110-5. [DOI: 10.1111/j.1751-1097.2009.00559.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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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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19
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Thermoresponsive polymeric gel as a medium for examining interactions between dsDNA and an anticancer drug. Anal Bioanal Chem 2008; 392:463-9. [PMID: 18716762 DOI: 10.1007/s00216-008-2278-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 07/01/2008] [Accepted: 07/02/2008] [Indexed: 10/21/2022]
Abstract
A piece of dry N-isopropylacrylamide polymer was soaked in phosphate buffer to obtain a hydrogel which was then employed in the examination of interactions between an anticancer drug C-1311 (5-diethylaminoethyl-amino-8-hydroxyimidazoacridinone) and dsDNA. dsDNA was introduced into the polymer at the polymerization stage. The drug was added to the buffer. Using the volume phase transition of the gel at 40 degrees C, the unbound drug could be determined in the solution released during the transition, which made the calculations more reliable. The interaction parameters were calculated using the McGhee and von Hippel model. It appeared that in the gel medium, the interaction between the drug and dsDNA is spatially limited, since the number of binding units of the polymer chain occupied by one drug molecule was found to be one, while it was two in the regular buffer solution.
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20
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Garbett NC, Ragazzon PA, Chaires JB. Circular dichroism to determine binding mode and affinity of ligand-DNA interactions. Nat Protoc 2008; 2:3166-72. [PMID: 18079716 DOI: 10.1038/nprot.2007.475] [Citation(s) in RCA: 243] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Circular dichroism (CD) is a useful technique for an assessment of DNA-binding mode, being a more accessible, low-resolution complement to NMR and X-ray diffraction methods. Ligand-DNA interactions can be studied by virtue of the interpretation of induced ligand CD signals resulting from the coupling of electric transition moments of the ligand and DNA bases within the asymmetric DNA environment. This protocol outlines methods to determine the binding mode and affinity of ligand-DNA interactions and takes approximately 7.5 h.
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Affiliation(s)
- Nichola C Garbett
- James Graham Brown Cancer Center, Health Sciences Campus, University of Louisville, 529 S. Jackson Street, Louisville, Kentucky 40202, USA
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21
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Strekowski L, Wilson B. Noncovalent interactions with DNA: an overview. Mutat Res 2007; 623:3-13. [PMID: 17445837 DOI: 10.1016/j.mrfmmm.2007.03.008] [Citation(s) in RCA: 303] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 03/14/2007] [Accepted: 03/15/2007] [Indexed: 05/15/2023]
Abstract
Over the last four decades, intense research has focused on the effects of small organic compounds that noncovalently bind to nucleic acids. These interactions have been shown to disrupt replication and/or transcription culminating in cellular death. Accordingly, DNA binding compounds have potential applications as anti-cancer and anti-viral agents. This report provides an overview of the different DNA-binding modes with an emphasis on DNA groove specificity for the groove-binding and intercalation modes. While most DNA-interacting agents selectively bind to DNA by either groove binding or intercalation, some compounds can exhibit both binding modes. The binding mode with the most favorable free energy for complex formation depends on the DNA sequence and structural features of the bound ligand.
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Affiliation(s)
- Lucjan Strekowski
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-4098, United States.
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22
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Duff MR, Tan WB, Bhambhani A, Perrin BS, Thota J, Rodger A, Kumar CV. Contributions of Hydroxyethyl Groups to the DNA Binding Affinities of Anthracene Probes. J Phys Chem B 2006; 110:20693-701. [PMID: 17034261 DOI: 10.1021/jp063997m] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Contributions of hydroxyethyl functions to the DNA binding affinities of substituted anthracenes are evaluated by calorimetry and spectroscopy. Isothermal titration calorimetry indicated that binding of the ligands to calf thymus DNA (5 mM Tris buffer, 50 mM NaCl, pH 7.2, 25 degrees C) is exothermic. The binding constants increased from 1.5 x 10(4) to 1.7 x 10(6) M(-1) as a function of increase in the number of hydroxyethyl functions (0-4). DNA binding was accompanied by red-shifted absorption (approximately 630 cm(-1)), strong hypochromism (>65%), positive induced-circular dichroism bands, and negative linear dichroism signals. DNA binding, in general, increased the helix stabilities to a significant extent (DeltaT(m) approximately 7 degrees C, DeltaDeltaH approximately 3 kcal/mol, DeltaDeltaS approximately 6-20 cal/K.mol). The binding constants showed a strong correlation with the number of hydroxyethyl groups present on the anthracene ring system. Analysis of the binding data using the hydrophobicity parameter (Log P) showed a poor correlation between the binding affinity and hydrophobicity. This observation was also supported by a comparison of the affinities of probes carrying N-ethyl (Kb = 0.8 x 10(5) M(-1)) versus N-hydroxyethyl side chains (Kb = 5.5 x 10(5) M(-1)). These are the very first examples of a strong quantitative correlation between the DNA binding affinity of a probe and the number of hydroxyethyl groups present on the probe. These quantitative findings are useful in the rational design of new ligands for high-affinity binding to DNA.
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Affiliation(s)
- Michael R Duff
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, USA
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23
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Tan WB, Bhambhani A, Duff MR, Rodger A, Kumar CV. Spectroscopic identification of binding modes of anthracene probes and DNA sequence recognition. Photochem Photobiol 2006; 82:20-30. [PMID: 16194126 DOI: 10.1562/2005-05-24-ra-539] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The binding properties of two anthracene derivatives with calf thymus DNA (CT DNA), poly(dA-dT), and poly(dG) x poly(dC) are reported. One contained bulky, cyclic cationic substituents at the 9 and 10 positions, and the other carried acylic, branched, cationic substituents. Binding of the probes to the DNA was examined by calorimetry, spectroscopy and helix melting studies. The cyclic derivative indicated exothermic binding, strong hypochromism, bathochromism, positive induced circular dichroism (CD, 300-400 nm), significant unwinding of the helix, large increases in the helix melting temperature, strong but negative linear dichroism (LD, 300-400 nm) and considerable stabilization of the helix. In contrast, the acyclic analog indicated thermoneutral binding, smaller hypochromism, no bathochromism, very weak induced CD, and no change in the helix melting temperature with any of the DNA polymers. A sharp distinction between the binding properties of the two probes is indicated, and both have intrinsic binding constants of approximately 10(6) M(-1) for the three polymers. However, when the ionic strength of the medium was lowered (10 mM NaCl), the absorption as well as CD spectral changes associated with the binding of the acyclic derivative corresponded with those of the cyclic derivative. The acyclic derivative showed large preference (10-fold) for poly(dG) x poly(dC) over poly(dA-dT), whereas the cyclic analog showed no preference. The characteristic spectroscopic signatures of the two distinct binding modes of these probes will be helpful in deciphering the interaction of other anthracene derivatives with DNA.
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Affiliation(s)
- Willy B Tan
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, USA
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24
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Rodger A, Marrington R, Geeves MA, Hicks M, de Alwis L, Halsall DJ, Dafforn TR. Looking at long molecules in solution: what happens when they are subjected to Couette flow? Phys Chem Chem Phys 2006; 8:3161-71. [PMID: 16902709 DOI: 10.1039/b604810m] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Knowing the structure of a molecule is one of the keys to deducing its function in a biological system. However, many biomacromolecules are not amenable to structural characterisation by the powerful techniques often used namely NMR and X-ray diffraction because they are too large, or too flexible or simply refuse to crystallize. Long molecules such as DNA and fibrous proteins are two such classes of molecule. In this article the extent to which flow linear dichroism (LD) can be used to characterise the structure and function of such molecules is reviewed. Consideration is given to the issues of fluid dynamics and light scattering by such large molecules. A range of applications of LD are reviewed including (i) fibrous proteins with particular attention being given to actin; (ii) a far from comprehensive discussion of the use of LD for DNA and DNA-ligand systems; (iii) LD for the kinetics of restriction digestion of circular supercoiled DNA; and (iv) carbon nanotubes to illustrate that LD can be used on any long molecules with accessible absorption transitions.
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Affiliation(s)
- Alison Rodger
- Department of Chemistry, University of Warwick, Coventry, UKCV4 7AL
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25
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Stootman FH, Fisher DM, Rodger A, Aldrich-Wright JR. Improved curve fitting procedures to determine equilibrium binding constants. Analyst 2006; 131:1145-51. [PMID: 17003863 DOI: 10.1039/b604686j] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
For ligand-biomacromolecule titration experiments it has been traditional practice to extract parameters such as the equilibrium binding constant K and the number of bases per ligand binding site n with relatively labour intensive methods, usually based on single wavelength data, such as the difference method by Rodger and Nordén coupled together with a Scatchard plot. Presented in this paper are both the theory and a least squares fitting method to derive parameters such as K and n more directly from all spectral non-linear experimental data. Both the case of non competitive binding of a metal complex ligand to DNA and the case of displacement by a metal complex ligand of an ethidium marker attached to the DNA are considered. This work may be applied directly to reduce experimental data produced by a spectropolarimeter (for circular or linear dichroism) or a spectrophotometer (for fluorescence or UV-Vis spectroscopy).
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Affiliation(s)
- Frank H Stootman
- University of Western Sydney, PO Box 1797, Penrith South DC, NSW 1797, Australia.
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26
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Delcros JG, Tomasi S, Duhieu S, Foucault M, Martin B, Le Roch M, Eifler-Lima V, Renault J, Uriac P. Effect of Polyamine Homologation on the Transport and Biological Properties of Heterocyclic Amidines. J Med Chem 2005; 49:232-45. [PMID: 16392808 DOI: 10.1021/jm050018q] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Five sets of heterocyclic derivatives of various sizes and complexities coupled by an amidine function to putrescine, spermidine, or spermine were prepared. They were essentially tested to determine the influence of the polyamine chain on their cellular transport. To comment on affinity and on selective transport via the polyamine transport system (PTS), K(i) values for polyamine uptake were determined in L1210 cells, and the cytotoxicity and accumulation of the conjugates were determined in CHO and polyamine transport-deficient mutant CHO-MG cells, as well as in L1210 and alpha-difluoromethylornithine- (DFMO-) treated L1210 cells. Unlike spermine, putrescine and spermidine were clearly identified as selective motifs that enable cellular entry via the PTS. However, this property was clearly limited by the size of substituents: these polyamines were able to ferry a dihydroquinoline system via the PTS but did not impart any selectivity to bulkier substituents.
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Affiliation(s)
- Jean-Guy Delcros
- Groupe de Recherche en Thérapeutique Anticancéreuse, Faculté de Médecine, Université Rennes 1, 2 Avenue du Professeur Léon Bernard, 35043 Rennes Cedex, France.
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27
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Maheswari PU, Palaniandavar M. DNA binding and cleavage activity of [Ru(NH3)4(diimine)]Cl2 complexes. Inorganica Chim Acta 2004. [DOI: 10.1016/j.ica.2003.07.010] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Delcros JG, Tomasi S, Carrington S, Martin B, Renault J, Blagbrough IS, Uriac P. Effect of spermine conjugation on the cytotoxicity and cellular transport of acridine. J Med Chem 2002; 45:5098-111. [PMID: 12408721 DOI: 10.1021/jm020843w] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polyamines are believed to be potent vectors for the selective delivery of chemotherapeutic agents into cancer cells. In this paper, we report the effect of spermine conjugation on the cytotoxic and transport properties of acridine. Six derivatives, composed of a spermine chain attached at its N(1) position to an acridine via an aliphatic chain, were synthesized. The aliphatic linker, comprised of 3-5 methylene units, was connected to the position-9 of the heterocycle through either an amide (amidoacridines 8-10) or an amine (aminoacridines 11-13) linkage. Independently of their architecture, all ligands showed a high affinity for DNA binding but a limited DNA sequence selectivity. In a whole cell assay with L1210 and Chinese hamster ovary (CHO) cells, the aminoacridines (IC(50) values around 2 microM) were more potent than the amidoacridines (IC(50) values between 20 and 40 microM). This was related to a less efficient transport for the latter. As determined from competitive uptake studies with [(14)C]spermidine, all conjugates had a high affinity for the polyamine transport system (PTS). However, on the basis of competitive studies with an excess of spermidine and on the differential effect on cell growth and accumulation in CHO and in the mutant PTS deficient CHO-MG cells, the accumulation of the conjugates through the PTS was found to be poor but still more efficient for the aminoacridines. alpha-Difluoromethylornithine (DFMO), an inhibitor of ornithine decarboxylase, which induces an up-regulation of the activity of the PTS, enhanced accumulation of all acridine conjugates through the PTS and had a synergistic effect on the potency of the acridine conjugates to inhibit cell growth. Despite their high affinity for the PTS, the low amount of derivatives transiting through the PTS is likely to be related to their ability to repress rapidly and efficiently the activity of the PTS and, consequently, to inhibit their own uptake via this system.
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Affiliation(s)
- Jean-Guy Delcros
- Groupe de Recherche en Thérapeutiques Anticancéreuses, UPR ESA CNRS 6027, Faculté de Médecine, Université Rennes 1, 2 Avenue du Professeur Léon Bernard, 35043 Rennes Cédex, France.
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29
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Patel KK, Plummer EA, Darwish M, Rodger A, Hannon MJ. Aryl substituted ruthenium bis-terpyridine complexes: intercalation and groove binding with DNA. J Inorg Biochem 2002; 91:220-9. [PMID: 12121779 DOI: 10.1016/s0162-0134(01)00423-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The non-covalent interaction of five novel ruthenium(II) bis-terpyridine complexes with calf thymus DNA and, where appropriate, with poly[d(G-C)](2) and poly[d(A-T)](2) is described. Each complex is functionalised with aryl tail groups in the 4' position of the terpyridine ligands ((i) 9-anthracenyl, (ii) 4,4'-biphenyl, (iii) beta-naphthyl, (iv) 9-phenanthrenyl, and (v) 1-pyrenyl). Circular dichroism and linear dichroism show that the binding of three of the complexes (phenanthrenyl, anthracenyl and pyrenyl) at low metal complex concentration is dominated by intercalation of the aryl tail groups between the DNA bases. The complex with the biphenyl tail predominantly exhibits groove binding with no significant tail intercalation. The naphthyl derivative binds both by intercalation and a non-intercalative mode even at low metal complex concentrations. At high metal complex concentrations, aggregation of the complexes on the DNA is observed. Resonance light scattering indicates that the aggregates are of low nuclearity along the groove.
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Affiliation(s)
- Kirti K Patel
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7Al, UK
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30
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Cheno-, Urso- and Deoxycholic Acid Spermine Conjugates: Relative Binding Affinities for Calf Thymus DNA. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00265-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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31
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Geall AJ, Blagbrough IS. Homologation of Polyamines in the Rapid Synthesis of Lipospermine Conjugates and Related Lipoplexes. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(99)01082-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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32
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Ismail MA, Rodger PM, Rodger A. Drug Self-Assembly on DNA: Sequence Effects withtrans-bis-(4-N-methylpyridiniumyl)diphenyl Porphyrin and Hoechst 33258. J Biomol Struct Dyn 2000; 17 Suppl 1:335-48. [DOI: 10.1080/07391102.2000.10506639] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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33
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Coggan DZM, Haworth IS, Bates PJ, Robinson A, Rodger A. DNA Binding of Ruthenium Tris(1,10-phenanthroline): Evidence for the Dependence of Binding Mode on Metal Complex Concentration. Inorg Chem 1999; 38:4486-4497. [PMID: 11671161 DOI: 10.1021/ic990654c] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interaction with calf thymus DNA, poly(dA-dT)(2) and poly(dG-dC)(2) of the two enantiomers (Lambda and Delta) of [Ru(1,10-phenanthroline)(3)](2+), denoted PHEN, and of [Ru(4,7-dimethyl-1,10-phenanthroline)(3)](2+), denoted [4,7], [Ru(5,6-dimethyl-1,10-phenanthroline)(3)](2+), denoted [5,6], and [Ru(3,4,7,8-tetramethyl-1,10-phenanthroline)(3)](2+), denoted [3,4,7,8], has been investigated by normal absorption, linear dichroism (LD), circular dichroism (CD), and computer modeling. These studies have been performed at the saturated binding limit and the "isolated" limit where the DNA is in excess. The binding mode is dependent upon the enantiomer (Lambda or Delta), the DNA base sequence, the ring substituent pattern, and, for the Delta enantiomer, the relative concentrations of DNA and metal complex. Both the Lambda and Delta enantiomers of PHEN and [4,7] show at least two binding regimes. One binding regime operates below a metal complex:DNA phosphate mixing ratio, R, of 1:4-6. The average site size (number of DNA bases per bound metal complex) also decreases from 8-12 bases per metal complex at low R to 3 bases at high R. The average angle (alpha(eff)) between the metal complex 3-fold axis and the DNA helical axis was derived from the LD. At high R (saturated metal complex binding) for both enantiomers of both compounds, this angle is 55 degrees +/- 3 degrees. For low R (isolated metal complex binding), the average binding orientations for the enantiomers are different for PHEN (Lambda, alpha(eff) = 59 degrees; Delta, alpha(eff) = 38 degrees ) and for [4,7] (Lambda, alpha(eff) = 84 degrees; Delta, alpha(eff) = 42 degrees ). Under the low-R conditions the Delta enantiomer of both compounds binds to calf thymus DNA more strongly than the Lambda enantiomer. [3,4,7,8] binds to DNA but is not oriented in the LD experiment. There is no evidence that [5,6] binds to DNA. To explain the LD results for PHEN several possible binding orientations were considered in computer modeling studies. These have the metal complex located with (i) a single phenanthroline chelate approximately parallel to the base pair planes in the major groove (referred to as partially inserted); (ii) a single chelate along the minor groove (referred to as slotted); (iii) two chelates in the minor groove (referred to as minor facial). Using orientations adopted in energy-minimized complexes it was possible to deduce the approximate relative occupancy of the different modes. For Lambda-PHEN the partially inserted mode is favored at all mixing ratios. For Delta-PHEN at low-R minor groove binding is preferred for most sequences with most metal complexes adopting a minor facial orientation. However, at high R (close packed metal complexes) the slotted mode becomes more favorable and some major groove partial insertion also occurs. For both Delta- and Lambda-[4,7] the minor facial mode is favored at low R. As R increases, the slotted mode becomes more favorable for both enantiomers of [4,7].
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Affiliation(s)
- Delia Z. M. Coggan
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K., Department of Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90033, and Department of Medicine, Division of Hematology/Oncology, 1824 Sixth Avenue South, University of Alabama at Birmingham, Birmingham, Alabama 35294
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Moon JH, Kim SK, Sehlstedt U, Rodger A, Nordén B. DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258. Biopolymers 1998. [DOI: 10.1002/(sici)1097-0282(199605)38:5<593::aid-bip5>3.0.co;2-n] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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36
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Pandya U, Saxena JK, Shukla OP. Filarial DNA and its interaction with polyamines and antifilarial drugs. J Helminthol 1997; 71:325-32. [PMID: 9443951 DOI: 10.1017/s0022149x0001614x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The interaction of DNA from filarial parasite Setaria cervi with polyamines was monitored by melting temperature (Tm) profile, condensation and B to Z DNA transition and compared with DNA of Escherichia coli, Micrococcus luteus and calf thymus having different GC content. Polyamines, viz. spermine and spermidine, stabilized the secondary structure of all DNAs as indicated by increase in Tm value. UV absorption studies indicated B to Z DNA transition in the presence of polyamines. The amount of polyamines required for B to Z transition was dependent upon base composition of DNA and charge of the polyamine. Filarial DNA (AT rich) required six times higher concentration of spermine as compared to GC rich DNA for B to Z DNA transition. Spermidine was not effective in causing transition of S. cervi DNA even at Spd:DNA-P ratio of 20. The antifilarial compound suramin significantly decreased melting temperature of filarial DNA as compared to GC rich DNAs of other parasites. Suramin adversely affected condensation and B to Z DNA transition of various DNAs but prior addition of polyamines protected the DNAs from the destabilizing effect of suramin.
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Affiliation(s)
- U Pandya
- Division of Biochemistry, Central Drug Research Institute, Lucknow 226 001, India
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37
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Harding MM, Krippner GY, Shelton CJ, Rodger A, Sanders KJ, Mackay JP, Prakash AS. DNA-binding studies of XSPTSPSZ, derivatives of the intercalating heptad repeat of RNA polymerase II. Biopolymers 1997; 42:387-98. [PMID: 9283289 DOI: 10.1002/(sici)1097-0282(19971005)42:4<387::aid-bip2>3.0.co;2-m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The synthesis, solution conformation, and interaction with DNA of three 8-residue peptides structurally related to the heptad repeat unit found at the C-terminus of RNA polymerase II are reported. Peptides QQ, XQ, and PQ are derived from the parent sequence YSPTSPSY (peptide YY), which was reported to bind to DNA by bisintercalation [M. Suzuki (1990) Nature, Vol. 344, pp. 562-565], and contain either a 2-quinolyl (Q), 2-quinoxolyl (X), or 5-phenanthrolyl (P) group in place of the aromatic side chains of the N- and C-terminal tyrosine residues present in the parent sequence. The combined results of linear dichroism and induced CD measurements of peptides QQ, XQ, and PQ with calf thymus DNA are consistent with weak binding of the peptides to DNA in a preferred orientation in which the chromophores are intercalated. Small increases in the melting temperatures of poly[d(A-T)2] are also consistent with the peptides interacting with DNA. While enzymatic footprinting with DNase I showed no protection from cleavage by the enzyme, chemical footprinting with fotemustine showed that the peptides modify the reactivity of the major groove, presumably via minor groove binding. Peptide QQ inhibited fotemustine alkylation significantly more than either XQ or PQ, and slightly more than YY. In aqueous solution, nmr experiments on QQ, XQ, and PQ show a significant population of a conformation in which Ser2-Pro3-Thr4-Ser5 form both type I and type II beta-turn conformations in equilibrium with open chain conformations. Nuclear magnetic resonance titration experiments of PQ with (GCGTACGC)2 showed small changes in chemical shifts, consistent with the formation of a weak nonspecific complex. Analogous experiments, using peptides QQ and XQ with (GCGTACGC)2, and peptide YY with (CGTACG)2, showed no evidence for the interaction of the peptides with these oligonucleotides. These results show that peptides of general structure XSPTSPSZ are weak nonspecific DNA binders that differ significantly from previously characterized S(T)PXX DNA-binding motifs that are generally AT-selective minor groove binders.
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Affiliation(s)
- M M Harding
- School of Chemistry, University of Sydney, NSW, Australia
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38
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Esposito D, Del Vecchio P, Barone G. Interactions with Natural Polyamines and Thermal Stability of DNA. A DSC Study and a Theoretical Reconsideration. J Am Chem Soc 1997. [DOI: 10.1021/ja962449r] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Diego Esposito
- Contribution from the Department of Chemistry, University “Federico II” of Naples, Via Mezzocannone 4, 80134 Naples, Italy
| | - Pompea Del Vecchio
- Contribution from the Department of Chemistry, University “Federico II” of Naples, Via Mezzocannone 4, 80134 Naples, Italy
| | - Guido Barone
- Contribution from the Department of Chemistry, University “Federico II” of Naples, Via Mezzocannone 4, 80134 Naples, Italy
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39
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Moon JH, Kim SK, Sehlstedt U, Rodger A, Nordén B. DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258. Biopolymers 1996; 38:593-606. [PMID: 8722229 DOI: 10.1002/(sici)1097-0282(199605)38:5%3c593::aid-bip5%3e3.0.co;2-n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The complexes of Hoechst 33258 with poly[d(A-T)2], poly[d(I-C)2], and poly[d(G-C)2], and poly[d(G-m5C)2] were studied using linear dichroism, CD, and fluorescence spectroscopies. The Hoechst-poly[d(I-C)2] complex, in which there is no guanine amino group protruding in the minor groove, exhibits spectroscopic properties that are very similar to those of the Hoechst-poly[d(A-T)2] complex. When bound to both of these polynucleotides, Hoechst exhibits an average orientation angle of near 45 degrees relative to the DNA helix axis for the long-axis polarized low-energy transition, a relatively strong positive induced CD, and a strong increase in fluorescence intensity--leading us to conclude that this molecule also binds in the minor groove of poly[d(I-C)2]. By contrast, when bound to poly[d(G-C)2] and poly[d(G-m5C)2], Hoechst shows a distinctively different behavior. The strongly negative reduced linear dichroism in the ligand absorption region is consistent with a model in which part of the Hoechst chromophore is intercalculated between DNA bases. From the low drug:base ratio onset of excitonic effects in the CD and fluorescence emission spectra, it is inferred that another part of the Hoechst molecule may sit in the major groove of poly[d(G-C)2] and poly[d(G-m5C)2] and preferentially stacks into dimers, though this tendency is strongly reduced for the latter polynucleotide. Based on these results, the importance of the interactions of Hoechst with the exocyclic amino group of guanine and the methyl group of cytosine in determining the binding modes are discussed.
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Affiliation(s)
- J H Moon
- Department of Chemistry, Yeungnam University, Kyoungbuk, Republic of Korea
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Rodger A, Taylor S, Adlam G, Blagbrough IS, Haworth IS. Multiple DNA binding modes of anthracene-9-carbonyl-N1-spermine. Bioorg Med Chem 1995; 3:861-72. [PMID: 7582962 DOI: 10.1016/0968-0896(95)00086-v] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The poly(dAdT)2 complex of anthracene-9-carbonyl-N1-spermine, a spermine derivative terminally substituted with an anthracene moiety, has been studied using fluorescence, linear dichroism, circular dichroism, normal absorption spectroscopy (as a function of temperature) and computer modelling. For comparison, some data are also provided for the same ligand with poly(dGdC)2 and calf thymus DNA. Following detailed fluorescence and CD spectroscopic studies, we propose that anthracene-9-carbonyl-N1-spermine intercalates in at least two different binding orientations with poly(dAdT)2. Based on computer simulation data, we deduce that the ligand can intercalate from both the minor groove and the major groove. In contrast, intercalation with poly(dGdC)2 probably occurs only from the major groove. At high ligand concentrations, the CD spectra suggest anthracene-anthracene interactions, whilst the LD data point towards a groove-bound anthracene. Again from computer simulations, we propose binding modes consistent with these observations. Other data from the LD spectra suggest a sequential nature to the binding of the ligand to calf thymus DNA, with GC-rich sites being occupied first. At low ligand concentrations, anthracene-9-carbonyl-N1-spermine is able to stabilize poly(dAdT)2 against thermal decomposition, but not as effectively as spermine. The reverse is found to be true with calf thymus DNA. Both the anthracene-9-carbonyl-N1-spermine and spermine complexes of poly(dAdT)2 show pre-melt transitions in their melting curves. The anthracene-9-carbonyl-N1-spermine complex with poly(dAdT)2 also shows a post-melt transition.
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Affiliation(s)
- A Rodger
- Department of Medicinal Chemistry, School of Pharmacy and Pharmacology, University of Bath, Claverton Down, U.K
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Adlam G, Blagbrough IS, Taylor S, Latham HC, Haworth IS, Rodger A. Multiple binding modes with DNA of anthracene-9-carbonyl-N1-spermine probed by LD, CD, normal absorption, and molecular modelling compared with those of spermidine and spermine. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80405-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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