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Andrushchenko V, Bouř P. Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides. Chirality 2011; 22 Suppl 1:E96-E114. [PMID: 21038400 DOI: 10.1002/chir.20872] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Prague, Czech Republic.
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Froehlich E, Mandeville JS, Weinert CM, Kreplak L, Tajmir-Riahi HA. Bundling and Aggregation of DNA by Cationic Dendrimers. Biomacromolecules 2010; 12:511-7. [DOI: 10.1021/bm1013102] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- E. Froehlich
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7, and Department of Physics, Sir James Dunn Building, Dalhousie University Lord Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - J. S. Mandeville
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7, and Department of Physics, Sir James Dunn Building, Dalhousie University Lord Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - C. M. Weinert
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7, and Department of Physics, Sir James Dunn Building, Dalhousie University Lord Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - L. Kreplak
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7, and Department of Physics, Sir James Dunn Building, Dalhousie University Lord Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - H. A. Tajmir-Riahi
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7, and Department of Physics, Sir James Dunn Building, Dalhousie University Lord Dalhousie Drive, Halifax, Canada NS B3H 3J5
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Nafisi S, Malekabady ZM, Khalilzadeh MA. Interaction of β-Carboline Alkaloids with RNA. DNA Cell Biol 2010; 29:753-61. [DOI: 10.1089/dna.2010.1087] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Nafisi S, Bonsaii M, Maali P, Khalilzadeh MA, Manouchehri F. β-Carboline alkaloids bind DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2010; 100:84-91. [DOI: 10.1016/j.jphotobiol.2010.05.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 04/27/2010] [Accepted: 05/12/2010] [Indexed: 12/01/2022]
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Arakawa H, Dovbeshko G, Diamantoglou S, Tajmir-Riahi HA. Oxovanadium Ions Bind Transfer RNA at Multiple Sites. DNA Cell Biol 2010; 29:459-64. [DOI: 10.1089/dna.2010.1028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hirohumi Arakawa
- Department of Chemistry-Biology, University of Québec at Trois-Riviéres, Trois-Riviéres, Quebec, Canada
| | - Galina Dovbeshko
- Department of Physics of Biological Systems, Institute of Physics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Stavroula Diamantoglou
- Department of Chemistry-Biology, University of Québec at Trois-Riviéres, Trois-Riviéres, Quebec, Canada
| | - Heidar-Ali Tajmir-Riahi
- Department of Chemistry-Biology, University of Québec at Trois-Riviéres, Trois-Riviéres, Quebec, Canada
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Dias RS, Pais AACC. Polyelectrolyte condensation in bulk, at surfaces, and under confinement. Adv Colloid Interface Sci 2010; 158:48-62. [PMID: 20347064 DOI: 10.1016/j.cis.2010.02.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 02/05/2010] [Accepted: 02/14/2010] [Indexed: 11/18/2022]
Abstract
In this review we discuss recent results from computer simulations based on coarse-grained polyion models representing aqueous solutions of polyelectrolytes. The focus will be directed to the conformation of the polyions and, in particular, their condensation in bulk, induced by multivalent ions and oppositely charged polyelectrolytes, at responsive surfaces and under confinement.
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Affiliation(s)
- R S Dias
- Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
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Mandeville JS, N’soukpoé-Kossi CN, Neault JF, Tajmir-Riahi HA. Structural analysis of DNA interaction with retinol and retinoic acid. Biochem Cell Biol 2010; 88:469-77. [DOI: 10.1139/o09-158] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dietary constituents of fresh fruits and vegetables may play a relevant role in DNA adduct formation by inhibiting enzymatic activities. Studies have shown the important role of antioxidant vitamins A, C, and E in the protection against cancer and cardiovascular diseases. The antioxidant activity of vitamin A and beta-carotene may consist of scavenging oxygen radicals and preventing DNA damage. This study was designed to examine the interaction of calf-thymus DNA with retinol and retinoic acid in aqueous solution at physiological conditions using a constant DNA concentration and various retinoid contents. Fourier transform infrared (FTIR), circular dichroism (CD), and fluorescence spectroscopic methods were used to determine retinoid binding mode, the binding constant, and the effects of retinol and retinoic acid complexation on DNA conformation and aggregation. Structural analysis showed that retinol and retinoic acid bind DNA via G-C and A-T base pairs and the backbone phosphate groups with overall binding constants of Kret = 3.0 (±0.50) × 103 (mol·L–1)–1 and Kretac = 1.0 (±0.20) × 104 (mol·L–1)–1. The number of bound retinoids per DNA were 0.84 for retinol and 1.3 for retinoic acid. Hydrophobic interactions were also observed at high retinol and retinoic acid contents. At a high retinoid concentration, major DNA aggregation occurred, while DNA remained in the B-family structure.
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Affiliation(s)
- J. S. Mandeville
- Department of Chemistry-Biology, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
| | - C. N. N’soukpoé-Kossi
- Department of Chemistry-Biology, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
| | - J. F. Neault
- Department of Chemistry-Biology, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
| | - H. A. Tajmir-Riahi
- Department of Chemistry-Biology, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
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Urbanová M. Bioinspired interactions studied by vibrational circular dichroism. Chirality 2010; 21 Suppl 1:E215-30. [PMID: 19937957 DOI: 10.1002/chir.20803] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.
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Affiliation(s)
- Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Czech Republic.
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Jangir DK, Tyagi G, Mehrotra R, Kundu S. Carboplatin interaction with calf-thymus DNA: A FTIR spectroscopic approach. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.01.052] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nafisi S, Norouzi Z. A comparative study on the interaction of cis- and trans-platin with DNA and RNA. DNA Cell Biol 2009; 28:469-77. [PMID: 19558218 DOI: 10.1089/dna.2009.0894] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cis-diamminedichloroplatinum(II) is a frequently used and very effective chemotherapeutic drug for treatment of various malignancies; however, the trans isomer is clinically ineffective. Cis-platin exerts its antitumor activity by binding to DNA via intrastrand cross-links to d(GpG) (dG = deoxyguanosine) and to d(ApG) (dA = deoxyadenosine), interfering with DNA replication and transcription and causing cell death. The trans-diamminedichloroplatinum(II) isomer also binds DNA, but is clinically ineffective. This study was designed to examine the interactions of cis- and trans-platin with calf thymus DNA and yeast RNA in aqueous solution at physiological conditions, using a constant DNA and RNA concentration (6.25 mM) and various platin salts/polynucleotide (phosphate) ratios of 1/100, 1/50, 1/25, and 1/12.5. Fourier transform infrared, ultraviolet-visible spectroscopic methods were used to determine the drug binding modes, the binding constants, and the stability of cis- and trans-platin-DNA and -RNA complexes in aqueous solution. Spectroscopic evidence showed that cis- and trans-platin bind to the major and minor grooves of DNA (via G, A, T, and C bases), while RNA binding is through G, U, A, and C bases with some degree of the pt-phosphate (PO(2)) interaction for both isomers and overall binding constants of K((cis-platin-DNA)) = 5.51 x 10(4) M(-1), K((trans-platin-DNA)) = 2.26 x 10(4) M(-1), K((cis-platin-RNA)) = 1.9 x 10(4) M(-1), and K((trans-platin-RNA)) = 1.75 x 10(4) M(-1). DNA and RNA aggregations occurred at high platin concentrations. No biopolymer conformational changes were observed upon cis- and trans-platin interactions, while DNA remains in the B-family, and RNA retains its A-family structure. The order of platin compound-polymer stability was cis-platin-DNA > trans-platin-DNA > cis-platin-RNA > trans-platin-RNA.
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Affiliation(s)
- Shohreh Nafisi
- Department of Chemistry, Azad University, Central Tehran Branch, Tehran, Iran.
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N’soukpoé-Kossi CN, Ahmed Ouameur A, Thomas T, Thomas TJ, Tajmir-Riahi HA. Interaction of tRNA with antitumor polyamine analogues. Biochem Cell Biol 2009; 87:621-30. [DOI: 10.1139/o09-036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We studied the interaction between tRNA and three polyamine analogues (1,11-diamino-4,8-diazaundecane·4HCl (333), 3,7,11,15-tetrazaheptadecane·4HCl (BE-333), and 3,7,11,15,19-pentazahenicosane·5HCl (BE-3333)) using FTIR, UV-visible, and CD spectroscopic methods. Spectroscopic evidence showed that polyamine analogues bound tRNA via guanine N7, adenine, uracil O2, and the backbone phosphate (PO 2– ) groups, while the most reactive sites for biogenic polyamines were guanine N7/O6, adenine N7, uracil O2, and sugar 2′-OH groups as well as the backbone phosphate group. The binding constants of polyamine analogue – tRNA recognition were lower than those of the biogenic polyamine – tRNA complexes, with K333 = 2.8 (±0.5) × 104, KBE-333 = 3.7 (±0.7) × 104, KBE-3333 = 4.0 (±0.9) × 104, Kspm = 8.7 (±0.9) × 105, Kspd = 6.1 (±0.7) × 105, and Kput = 1.0 (±0.3) × 105 mol/L. tRNA remained in the A-family conformation; however, it aggregated at high polyamine analogue concentrations.
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Affiliation(s)
- C. N. N’soukpoé-Kossi
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
- Department of Environmental and Occupational Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - A. Ahmed Ouameur
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
- Department of Environmental and Occupational Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - T. Thomas
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
- Department of Environmental and Occupational Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - T. J. Thomas
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
- Department of Environmental and Occupational Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
| | - H. A. Tajmir-Riahi
- Département de Chimie-Biologie, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
- Department of Environmental and Occupational Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
- The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA
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Marty R, N’soukpoé-Kossi CN, Charbonneau DM, Kreplak L, Tajmir-Riahi HA. Structural characterization of cationic lipid-tRNA complexes. Nucleic Acids Res 2009; 37:5197-207. [PMID: 19561199 PMCID: PMC2731917 DOI: 10.1093/nar/gkp543] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 06/08/2009] [Accepted: 06/09/2009] [Indexed: 01/22/2023] Open
Abstract
Despite considerable interest and investigations on cationic lipid-DNA complexes, reports on lipid-RNA interaction are very limited. In contrast to lipid-DNA complexes where lipid binding induces partial B to A and B to C conformational changes, lipid-tRNA complexation preserves tRNA folded state. This study is the first attempt to investigate the binding of cationic lipid with transfer RNA and the effect of lipid complexation on tRNA aggregation and condensation. We examine the interaction of tRNA with cholesterol (Chol), 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), dioctadecyldimethylammoniumbromide (DDAB) and dioleoylphosphatidylethanolamine (DOPE), at physiological condition, using constant tRNA concentration and various lipid contents. FTIR, UV-visible, CD spectroscopic methods and atomic force microscopy (AFM) were used to analyze lipid binding site, the binding constant and the effects of lipid interaction on tRNA stability, conformation and condensation. Structural analysis showed lipid-tRNA interactions with G-C and A-U base pairs as well as the backbone phosphate group with overall binding constants of K(Chol) = 5.94 (+/- 0.8) x 10(4) M(-1), K(DDAB) = 8.33 (+/- 0.90) x 10(5) M(-1), K(DOTAP) = 1.05 (+/- 0.30) x 10(5) M(-1) and K(DOPE) = 2.75 (+/- 0.50) x 10(4) M(-1). The order of stability of lipid-tRNA complexation is DDAB > DOTAP > Chol > DOPE. Hydrophobic interactions between lipid aliphatic tails and tRNA were observed. RNA remains in A-family structure, while biopolymer aggregation and condensation occurred at high lipid concentrations.
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Affiliation(s)
- Regis Marty
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, G9A 5H7 and Department of Physics and Atmospheric Science, Sir James Dunn Building, Dalhousie University, Lord Dalhousie Drive, Halifax, NS B3H 3J5, Canada
| | - Christophe N. N’soukpoé-Kossi
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, G9A 5H7 and Department of Physics and Atmospheric Science, Sir James Dunn Building, Dalhousie University, Lord Dalhousie Drive, Halifax, NS B3H 3J5, Canada
| | - David M. Charbonneau
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, G9A 5H7 and Department of Physics and Atmospheric Science, Sir James Dunn Building, Dalhousie University, Lord Dalhousie Drive, Halifax, NS B3H 3J5, Canada
| | - Laurent Kreplak
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, G9A 5H7 and Department of Physics and Atmospheric Science, Sir James Dunn Building, Dalhousie University, Lord Dalhousie Drive, Halifax, NS B3H 3J5, Canada
| | - Heidar-Ali Tajmir-Riahi
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec, G9A 5H7 and Department of Physics and Atmospheric Science, Sir James Dunn Building, Dalhousie University, Lord Dalhousie Drive, Halifax, NS B3H 3J5, Canada
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Nafisi S, Adelzadeh M, Norouzi Z, Sarbolouki MN. Curcumin Binding to DNA and RNA. DNA Cell Biol 2009; 28:201-8. [DOI: 10.1089/dna.2008.0840] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Shohreh Nafisi
- Department of Chemistry, Azad University, Central Tehran Branch (IAUCTB), Tehran, Iran
| | - Maryam Adelzadeh
- Department of Chemistry, Azad University, Omidieh Branch, Omidieh, Iran
| | - Zeinab Norouzi
- Department of Chemistry, Azad University, Central Tehran Branch (IAUCTB), Tehran, Iran
| | - Mohammad Nabi Sarbolouki
- Biomaterials Research Center (BRC), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Andrushchenko V, Bour P. Infrared absorption detection of metal ion-deoxyguanosine monophosphate binding: experimental and theoretical study. J Phys Chem B 2009; 113:283-91. [PMID: 19063657 DOI: 10.1021/jp8058678] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metal ion interactions with nucleic acids attract attention because of the environmental and biological consequences. The formation of the complex is often monitored by the vibrational spectroscopy. To identify characteristic binding patterns and marker bands on a model DNA component, infrared absorption spectra of the deoxyguanosine monophosphate complexes with Na(+), Mg(2+), Ca(2+), Ni(2+), Cu(2+), Zn(2+), and Cd(2+) cations were recorded and interpreted on the basis of density-functional computations. The aqueous environment was simulated by continuum and combined continuum-explicit solvent models. For the binding to the N7 position of the guanine base, the computation predicted a characteristic frequency upshift and splitting of the 1578 cm(-1) band, which is in accord with available experimental data. Contrary to the expectation, the modeling suggests that the binding to the carbonyl group might not be detectable, as the metal causes smaller spectral changes if compared to the hydrogen-bound water molecules. The binding to the phosphate group causes significant spectral changes in the sugar-phosphate vibrating region ( approximately 800-1200 cm(-1)), but also notable frequency shifts of the carbonyl vibrations. The Cu(2+) and Zn(2+) ions induced the largest alterations in observed vibrational absorption, which corresponds to the calculated strong interaction energies in the N7-complexes and to previous experimental experience. Additional changes in the vibrational spectra of the copper complexes were observed under high metal concentration, corresponding to the simultaneous binding to the phosphate residue. The two-step Cu(2+) binding process was also confirmed by the microcalorimetry titration curve. The computations and combination of more techniques thus help us to assign and localize spectral changes caused by the metal ion binding to nucleic acids.
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Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610, Praha 6, Czech Republic
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Kypr J, Kejnovská I, Renciuk D, Vorlícková M. Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 2009; 37:1713-25. [PMID: 19190094 PMCID: PMC2665218 DOI: 10.1093/nar/gkp026] [Citation(s) in RCA: 1272] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Here we review studies that provided important information about conformational properties of DNA using circular dichroic (CD) spectroscopy. The conformational properties include the B-family of structures, A-form, Z-form, guanine quadruplexes, cytosine quadruplexes, triplexes and other less characterized structures. CD spectroscopy is extremely sensitive and relatively inexpensive. This fast and simple method can be used at low- as well as high-DNA concentrations and with short- as well as long-DNA molecules. The samples can easily be titrated with various agents to cause conformational isomerizations of DNA. The course of detected CD spectral changes makes possible to distinguish between gradual changes within a single DNA conformation and cooperative isomerizations between discrete structural states. It enables measuring kinetics of the appearance of particular conformers and determination of their thermodynamic parameters. In careful hands, CD spectroscopy is a valuable tool for mapping conformational properties of particular DNA molecules. Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA.
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Affiliation(s)
- Jaroslav Kypr
- Institute of Biophysics, vvi Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Froehlich E, Gupta A, Provencher-Mandeville J, Asselin É, Bariyanga J, Bérubé G, Tajmir-Riahi HA. Study of DNA Interactions with Steroidal and Nonsteroidal Estrogen–Platinum (II)–Based Anticancer Drugs. DNA Cell Biol 2009; 28:31-9. [DOI: 10.1089/dna.2008.0804] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Emilie Froehlich
- Département de Chimie-Biologie, Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - Atul Gupta
- Département de Chimie-Biologie, Groupe de Recherche en Oncologie et en Endocrinologie Moléculaires, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - Josée Provencher-Mandeville
- Département de Chimie-Biologie, Groupe de Recherche en Oncologie et en Endocrinologie Moléculaires, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - éric Asselin
- Département de Chimie-Biologie, Groupe de Recherche en Oncologie et en Endocrinologie Moléculaires, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - Joseph Bariyanga
- Department of Chemistry, University of Hawaii-West O'ahu, Pearl City, Hawaii
| | - Gervais Bérubé
- Département de Chimie-Biologie, Groupe de Recherche en Oncologie et en Endocrinologie Moléculaires, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
| | - Heidar-Ali Tajmir-Riahi
- Département de Chimie-Biologie, Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, Canada
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Marty R, N'soukpoé-Kossi CN, Charbonneau D, Weinert CM, Kreplak L, Tajmir-Riahi HA. Structural analysis of DNA complexation with cationic lipids. Nucleic Acids Res 2008; 37:849-57. [PMID: 19103664 PMCID: PMC2647290 DOI: 10.1093/nar/gkn1003] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Complexes of cationic liposomes with DNA are promising tools to deliver genetic information into cells for gene therapy and vaccines. Electrostatic interaction is thought to be the major force in lipid–DNA interaction, while lipid-base binding and the stability of cationic lipid–DNA complexes have been the subject of more debate in recent years. The aim of this study was to examine the complexation of calf-thymus DNA with cholesterol (Chol), 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), dioctadecyldimethylammoniumbromide (DDAB) and dioleoylphosphatidylethanolamine (DOPE), at physiological condition, using constant DNA concentration and various lipid contents. Fourier transform infrared (FTIR), UV-visible, circular dichroism spectroscopic methods and atomic force microscopy were used to analyse lipid-binding site, the binding constant and the effects of lipid interaction on DNA stability and conformation. Structural analysis showed a strong lipid–DNA interaction via major and minor grooves and the backbone phosphate group with overall binding constants of KChol = 1.4 (±0.5) × 104 M−1, KDDAB = 2.4 (±0.80) × 104 M−1, KDOTAP = 3.1 (±0.90) × 104 M−1 and KDOPE = 1.45 (± 0.60) × 104 M−1. The order of stability of lipid–DNA complexation is DOTAP>DDAB>DOPE>Chol. Hydrophobic interactions between lipid aliphatic tails and DNA were observed. Chol and DOPE induced a partial B to A-DNA conformational transition, while a partial B to C-DNA alteration occurred for DDAB and DOTAP at high lipid concentrations. DNA aggregation was observed at high lipid content.
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Affiliation(s)
- Regis Marty
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
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68
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Andrushchenko V, Bouř P. Circular dichroism enhancement in large DNA aggregates simulated by a generalized oscillator model. J Comput Chem 2008; 29:2693-703. [DOI: 10.1002/jcc.21015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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69
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Wan L, Manickam DS, Oupický D, Mao G. DNA release dynamics from reducible polyplexes by atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:12474-82. [PMID: 18839970 PMCID: PMC2825055 DOI: 10.1021/la802088y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Controlled intracellular disassembly of polyelectrolyte complexes of polycations and DNA (polyplexes) is a crucial step for the success of nonviral gene delivery. Motivated by our previous observation of different gene delivery performances among multiblock reducible copolypeptide vectors ( Manickam, D. S. ; Oupicky, D. Bioconjugate Chem. 2006, 17, 1395- 1403 ), atomic force microscopy is used to visualize plasmid DNA in various decondensed states from reducible polypeptide polyplexes under simulated physiological reducing conditions. DNA decondensation is triggered by reductive degradation of disulfide-containing cationic polypeptides. Striking differences in DNA release dynamics between polyplexes based on polypeptides of histidine-rich peptide (HRP, CKHHHKHHHKC) and nuclear localization signal (NLS, CGAGPKKKRKVC) peptide are presented. The HRP and NLS polyplexes are similar to each other in their initial morphology with a majority of them containing only one DNA plasmid. Upon reductive degradation by dithiothreitol, DNA is released from NLS abruptly regardless of the initial polyplex morphology, while DNA release from HRP polyplexes displays a gradual decondensation that is dependent on the size of polyplexes. The release rate is higher for larger HRP polyplexes. The smaller HRP polyplexes become unstable when they are in contact with expanding chains nearby. The results reveal potentially rich DNA release dynamics that can be controlled by subtle variation in multivalent counterion binding to DNA as well as the cellular matrix.
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Affiliation(s)
- Lei Wan
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202
| | - Devika S. Manickam
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48202
| | - David Oupický
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48202
| | - Guangzhao Mao
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202
- Corresponding author:
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70
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Nafisi S, Hashemi M, Rajabi M, Tajmir-Riahi HA. DNA adducts with antioxidant flavonoids: morin, apigenin, and naringin. DNA Cell Biol 2008; 27:433-42. [PMID: 18491957 DOI: 10.1089/dna.2008.0735] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Flavonoids have recently attracted a great interest as potential therapeutic drugs against a wide range of free-radical-mediated diseases. The anticancer and antiviral activities of these natural products are implicated in their mechanism of actions. While the antioxidant activity of these natural polyphenolic compounds is well known, their bindings to DNA are not fully investigated. This study was designed to examine the interactions of morin (Mor), naringin (Nar), and apigenin (Api) with calf thymus DNA in aqueous solution at physiological conditions, using constant DNA concentration (6.25 mM) and various drug/DNA(phosphate) ratios of 1/40 to 1. FTIR and UV-Vis spectroscopic methods were used to determine the ligand binding modes, the binding constant, and the stability of DNA in flavonoid-DNA complexes in aqueous solution. Spectroscopic evidence shows both intercalation and external binding of flavonoids to DNA duplex with overall binding constants of K(morin) = 5.99 x 10(3) M(-1), K(apigenin) = 7.10 x 10(4) M(-1), and K(naringin) = 3.10 x 10(3) M(-1). The affinity of ligand-DNA binding is in the order of apigenin > morin > naringin. DNA aggregation and a partial B- to A-DNA transition occurs upon morin, apigenin, and naringin complexation.
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Affiliation(s)
- Shohreh Nafisi
- Department of Chemistry, Azad University, Central Tehran Branch (IAUCTB), Tehran, Iran.
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71
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Nafisi S, Shadaloi A, Feizbakhsh A, Tajmir-Riahi HA. RNA binding to antioxidant flavonoids. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2008; 94:1-7. [PMID: 18922698 DOI: 10.1016/j.jphotobiol.2008.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 08/08/2008] [Accepted: 08/25/2008] [Indexed: 10/21/2022]
Abstract
Flavonoids are an interesting group of natural polyphenolic compounds that exhibit extensive bioactivities such as scavenging free radical, antitumor and antiproliferative effects. The anticancer and antiviral effects of these natural products are attributed to their potential biomedical applications. While flavonoids complexation with DNA is known, their bindings to RNA are not fully investigated. This study was designed to examine the interactions of three flavonoids; morin (Mor), apigenin (Api) and naringin (Nar) with yeast RNA in aqueous solution at physiological conditions, using constant RNA concentration (6.25 mM) and various pigment/RNA (phosphate) ratios of 1/120 to 1/1. FTIR, UV-visible spectroscopic methods were used to determine the ligand binding modes, the binding constant and the stability of RNA in flavonoid-RNA complexes in aqueous solution. Spectroscopic evidence showed major binding of flavonoids to RNA with overall binding constants of K(morin) = 9.150 x 10(3) M(-1), K(apigenin)=4.967 x 10(4) M(-1), and K(naringin)=1.144 x 10(4) M(-1). The affinity of flavonoid-RNA binding is in the order of apigenin>naringin>morin. No biopolymer secondary structural changes were observed upon flavonoid interaction and RNA remains in the A-family structure in these pigment complexes.
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Affiliation(s)
- Sh Nafisi
- Department of Chemistry, Azad University, Central Tehran Branch (IAUCTB), Tehran 1467686831, Iran.
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72
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N’soukpoé-Kossi CN, Ouameur AA, Thomas T, Shirahata A, Thomas TJ, Tajmir-Riahi HA. DNA Interaction with Antitumor Polyamine Analogues: A Comparison with Biogenic Polyamines. Biomacromolecules 2008; 9:2712-8. [DOI: 10.1021/bm800412r] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- C. N. N’soukpoé-Kossi
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - A. Ahmed Ouameur
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - T. Thomas
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - A. Shirahata
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - T. J. Thomas
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
| | - H. A. Tajmir-Riahi
- Département de Chimie-Biologie, Université du Québec á Trois-Rivières, C. P. 500, Trois-Rivières (Québec), G9A 5H7, Canada, Department of Environmental and Occupational Medicine, Environmental and Occupational Health Sciences Institute, Department of Medicine, and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey 08903, and Department of Biochemistry and Cellular Physiology, Josai University, Saitama, Japan
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73
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N'soukpoé-Kossi CN, Diamantoglou S, Tajmir-Riahi HA. DNase I - DNA interaction alters DNA and protein conformations. Biochem Cell Biol 2008; 86:244-50. [PMID: 18523485 DOI: 10.1139/o08-039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Human DNase I is an endonuclease that catalyzes the hydrolysis of double-stranded DNA predominantly by a single-stranded nicking mechanism under physiological conditions in the presence of divalent Mg and Ca cations. It binds to the minor groove and the backbone phosphate group and has no contact with the major groove of the right-handed DNA duplex. The aim of this study was to examine the effects of DNase I - DNA complexation on DNA and protein conformations. We monitored the interaction of DNA with DNase I under physiological conditions in the absence of Mg2+, with a constant DNA concentration (12.5 mmol/L; phosphate) and various protein concentrations (10-250 micromol/L). We used Fourier transfrom infrared, UV-visible, and circular dichroism spectroscopic methods to determine the protein binding mode, binding constant, and effects of polynucleotide-enzyme interactions on both DNA and protein conformations. Structural analyses showed major DNase-PO2 binding and minor groove interaction, with an overall binding constant, K, of 5.7 x 10(5) +/- 0.78 x 10(5) (mol/L)-1. We found that the DNase I - DNA interaction altered protein secondary structure, with a major reduction in alpha helix and an increase in beta sheet and random structures, and that a partial B-to-A DNA conformational change occurred. No DNA digestion was observed upon protein-DNA complexation.
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Affiliation(s)
- C N N'soukpoé-Kossi
- Department of Chemistry-Biology, University of QC at Trois-Rivieres, CP 500, Trois-Rivieres, QC, Canada
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74
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N'soukpoé-Kossi CN, Descôteaux C, Asselin É, Bariyanga J, Tajmir-Riahi HA, Bérubé G. Transfer RNA Bindings to Antitumor Estradiol-Platinum(II) Hybrid and Cisplatin. DNA Cell Biol 2008; 27:337-43. [DOI: 10.1089/dna.2008.0727] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Christophe N. N'soukpoé-Kossi
- Groupe de Recherche en Biologie Végétale, Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Caroline Descôteaux
- Groupe de Recherche en Biopathologies Cellulaires et Moléculaires, Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Éric Asselin
- Groupe de Recherche en Biopathologies Cellulaires et Moléculaires, Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Joseph Bariyanga
- Department of Chemistry, University of Hawaii-West O'ahu, Pearl City, Hawaii
| | - Heidar-Ali Tajmir-Riahi
- Groupe de Recherche en Biologie Végétale, Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Gervais Bérubé
- Groupe de Recherche en Biopathologies Cellulaires et Moléculaires, Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
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75
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Abstract
Deoxyribonuclease I (DNase I) binds right-handed DNA duplex via a minor groove and the backbone phosphate group with no contact to the major groove. It hydrolyses double-stranded DNA predominantly by a single-stranded nicking mechanism under physiological conditions, in the presence of divalent Mg and Ca cations. Even though DNase-RNA interaction was observed, less is known about the protein-RNA binding mode and the effect of such complexation on both protein and RNA conformations. The aim of this study was to examine the effects of DNase I-tRNA interaction on tRNA and protein conformations. The interaction of DNase I with tRNA is monitored under physiological conditions, in the absence of Mg2+, using constant DNA concentration of 12.5 mM (phosphate) and various protein contents (10 microM to 250 microM). FTIR, UV-visible, and CD spectroscopic methods were used to analyze the protein binding mode, the binding constant, and the effects of polynucleotide-enzyme interaction on both tRNA and protein conformations. Spectroscopic evidence showed major DNase-PO2 and minor groove interactions with overall binding constant of K = 2.1 (+/-0.7) x 10(4) M(-1). The DNase I-tRNA interaction alters protein secondary structure with major reduction of the alpha-helix, and increases the random coil, beta-anti and turn structures, while tRNA remains in the A-conformation. No digestion of tRNA by DNase I was observed in the protein-tRNA complexes.
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Affiliation(s)
- C N N'soukpoé-Kossi
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, Trois-Rivières (Québec) Canada G9A 5H7
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76
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77
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N'soukpoé-Kossi CN, Descôteaux C, Asselin É, Tajmir-Riahi HA, Bérubé G. DNA Interaction with Novel Antitumor Estradiol–Platinum(II) Hybrid Molecule: A Comparative Study with Cisplatin Drug. DNA Cell Biol 2008; 27:101-7. [DOI: 10.1089/dna.2007.0669] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Christophe N. N'soukpoé-Kossi
- Département de Chimie-Biologie, Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Caroline Descôteaux
- Département de Chimie-Biologie, Groupe de Recherche en Biophatologies Cellulaires et Moléculaires, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Éric Asselin
- Département de Chimie-Biologie, Groupe de Recherche en Biophatologies Cellulaires et Moléculaires, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Heidar-Ali Tajmir-Riahi
- Département de Chimie-Biologie, Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Gervais Bérubé
- Département de Chimie-Biologie, Groupe de Recherche en Biophatologies Cellulaires et Moléculaires, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
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78
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Kanakis CD, Tarantilis PA, Tajmir-Riahi HA, Polissiou MG. Interaction of tRNA with Safranal, Crocetin, and Dimethylcrocetin. J Biomol Struct Dyn 2007; 24:537-46. [PMID: 17508775 DOI: 10.1080/07391102.2007.10507142] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Saffron is the red dried stigmas of Crocus sativus L. flowers and used both as a spice and as a drug in traditional therapeutic. The biological activity of saffron in modern medicine is in development. Its numerous applications as an anti-oxidant and anti-cancer agent are due to its secondary metabolites and their derivatives (safranal, crocins, crocetin, dimethylcrocetin). The aim of this study was to examine the interaction of transfer RNA with safranal, crocetin, and dimethylcrocetin in aqueous solution at physiological conditions. Constant tRNA concentration (6.25 mM) and various drug/tRNA (phosphate) molar ratios of 1/48 to 1/8 were used. FT-IR and UV-Visible difference spectroscopic methods have been applied to determine the drug binding mode, the binding constants and the effects of drug complexation on the stability and conformation of tRNA duplex. External binding mode was observed for safranal crocetin and dimethylcrocetin, with overall binding constants K(safranal) = 6.8 (+/- 0.34) x 10(3) M(-1), K(CRT) = 1.4 (+/- 0.31) x 10(4) M(-1), and K(DMCRT) = 3.4 (+/- 0.30) x 10(4) M(-1). Transfer RNA remains in the A-family structure, upon safranal, crocetin and dimethylcrocetin complexation.
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Affiliation(s)
- Charalabos D Kanakis
- Laboratory of Chemistry, Department of Science, Agricultural University of Athens, 75 Iera Odos, 118 55 Athens, Greece
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79
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N'soukpoé-Kossi CN, Ragi C, Tajmir-Riahi HA. RNase A – tRNA binding alters protein conformation. Biochem Cell Biol 2007; 85:311-8. [PMID: 17612625 DOI: 10.1139/o07-050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bovine pancreatic ribonuclease A (RNase A) catalyzes the cleavage of P-O5′ bonds in RNA on the 3′ side of pyrimidine to form cyclic 2′,5′-phosphates. Even though extensive structural information is available on RNase A complexes with mononucleotides and oligonucleotides, the interaction of RNase A with tRNA has not been fully investigated. We report the complexation of tRNA with RNase A in aqueous solution under physiological conditions, using a constant RNA concentration and various amounts of RNase A. Fourier transform infrared, UV-visible, and circular dichroism spectroscopic methods were used to determine the RNase binding mode, binding constant, sequence preference, and biopolymer secondary structural changes in the RNase–tRNA complexes. Spectroscopic results showed 2 major binding sites for RNase A on tRNA, with an overall binding constant of K = 4.0 × 105(mol/L)–1. The 2 binding sites were located at the G-C base pairs and the backbone PO2group. Protein–RNA interaction alters RNase secondary structure, with a major reduction in α helix and β sheets and an increase in the turn and random coil structures, while tRNA remains in the A conformation upon protein interaction. No tRNA digestion was observed upon RNase A complexation.
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Affiliation(s)
- C N N'soukpoé-Kossi
- Department of Chemistry-Biology, Université du Québec at Trois-Rivières, C.P. 500 Trois-Rivières, QC G9A 5H7, Canada
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80
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Stability and structural features of DNA intercalation with ethidium bromide, acridine orange and methylene blue. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2006.05.004] [Citation(s) in RCA: 324] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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81
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Besteman K, van Eijk K, Vilfan ID, Ziese U, Lemay SG. Influence of charged surfaces on the morphology of DNA condensed with multivalent ions. Biopolymers 2007; 87:141-8. [PMID: 17626297 DOI: 10.1002/bip.20806] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
DNA in solution can be condensed into dense aggregates by multivalent counterions. Here we investigate the effect of a nearby surface on the morphology of DNA condensates. We show that, contrary to what has often been assumed, interactions between DNA condensates and the surface can strongly influence the observed morphology. This limits the usefulness of surface probes such as atomic force microscopy for studying the morphology of condensates in bulk solution. Surprisingly, we find that the most negatively charged surface disturbs the condensate morphology most, suggesting that the microscopic mechanism resulting in DNA condensation is also responsible for the attractive force between DNA and the surface.
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Affiliation(s)
- K Besteman
- Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
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82
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Ahmed Ouameur A, Arakawa H, Tajmir-Riahi HA. Binding of oxovanadium ions to the major and minor grooves of DNA duplex: stability and structural models. Biochem Cell Biol 2006; 84:677-83. [PMID: 17167530 DOI: 10.1139/o06-043] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Vanadate induces DNA strand breaks in cultured human fibroblasts at doses that are relative to the occupational exposure. Oxovanadium compounds also exert preventive effects against chemical carcinogenesis in animals and form complexes with DNA in vivo. This study was designed to examine the interaction of calf-thymus DNA with VO2+and VO3¯ions in aqueous solution at physiological pH, with a constant DNA concentration of 12.5 mmol/L and vanadium–DNA (phosphate) molar ratios (r) of 1:160 to 1:2. Capillary electrophoresis and Fourier transform infrared difference spectroscopy were used to determine the cation binding site, the binding constant, the helix stability, and DNA conformation in the oxovanadium–DNA complexes. Structural analysis showed that VO2+binds DNA through guanine and adenine N-7 atoms and the backbone PO2group with apparent binding constants of KG= 8.8 × 105(mol/L)–1and KA= 3.4 × 105(mol/L)–1. The VO3¯shows weaker binding through thymine, adenine, and guanine bases, with K = 1.9 × 104(mol/L)–1and no interaction with the backbone phosphate group. A partial B-to-A DNA transition occurred upon VO–DNA complexation, while DNA remains in the B-family structure in the VO3¯complexes.
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Affiliation(s)
- A Ahmed Ouameur
- Department of Chemistry-Biology, Université de Québec à Trois-Rivières, C.P. 500, Trois-Rivières, QC, G9A 5H7, Canada
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83
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Petrovic AG, Polavarapu PL. Structural transitions in polyriboadenylic acid induced by the changes in pH and temperature: vibrational circular dichroism study in solution and film states. J Phys Chem B 2006; 109:23698-705. [PMID: 16375350 DOI: 10.1021/jp054280m] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A correlation of the changes in vibrational absorption and vibrational circular dichroism (VCD) spectral features with the structural changes of polyriboadenylic acid (polyA) as a function of pH is reported. Analysis of the solution spectral data as a function of pH led us to establishing the importance of a previously unrecognized absorption band at approximately 1665 cm(-1). The present studies indicate that this absorption band and associated VCD originate from the double-helical structure of polyA. The observed changes in solution-state VCD features are indicative of the pH-dependent transitions among the three acidic forms of polyA (A, B, and "frozen" form). In addition to the solution-state spectral data, pH-dependent absorption and VCD spectra for films of polyA, derived from dilute H2O solutions, are also presented. The pH-dependent changes in the absorption and VCD spectra of films are also correlated to the polyA structural changes.
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Affiliation(s)
- Ana G Petrovic
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
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84
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Malonga H, Neault JF, Tajmir-Riahi HA. Transfer RNA Binding to Human Serum Albumin: A Model for Protein–RNA Interaction. DNA Cell Biol 2006; 25:393-8. [PMID: 16848680 DOI: 10.1089/dna.2006.25.393] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein-RNA complexation is essential in cell biological functions. Transfer RNAs are bound to aminoacyl-tRNA synthetases for the translation of the genetic code during protein synthesis, while ribonucleoproteins bind RNA in posttranscriptional regulation of gene expression. A recent report showed the interacton of human serum albumin (HSA) with DNA duplex, in which two binding sites with strong and weak association constants were detected. We now examine the interaction of tRNA with human serum albumin (HSA) in aqueous solution at physiological conditions, using a constant RNA concentration of 12.5 mM (phosphate) and various HSA contents of 0.04 to 0.6 mM. Affinity capillary electrophoresis and FTIR spectroscopic methods were used to determine the protein binding mode, the association constant, sequence preference, and the biopolymer secondary structural changes in the HSA-RNA complexes. Spectroscopic evidence showed two types of HSA-RNA complexes with an overall binding constant of K = 1.45 x 10(4) M(-1). The major binding sites were located on the G-C bases and the backbone PO2 group. The protein-RNA interaction stabilizes the HSA secondary structure, and no major alterations of A-RNA structure or protein conformation occurred.
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Affiliation(s)
- Herman Malonga
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, Québec, Canada
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85
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Kanakis CD, Tarantilis PA, Polissiou MG, Tajmir-Riahi HA. Interaction of Antioxidant Flavonoids with tRNA: Intercalation or External Binding and Comparison with Flavonoid-DNA Adducts. DNA Cell Biol 2006; 25:116-23. [PMID: 16460235 DOI: 10.1089/dna.2006.25.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Antioxidants are essential to good health. Flavonoids are powerful antioxidants, and prevent DNA damage. The antioxidative protections are related to their binding modes to a DNA duplex and complexation with free radicals in vivo. Recently we reported the interaction of flavonoids with DNA in vitro (Kanakis et al., J. Biomol. Struct. Dyn. 22, 719-724, 2005), where polyphenol different binding modes were discussed. The aim of this study was to examine the interaction of transfer RNA with quercetin (que), kaempferol (kae), and delphinidin (del) in aqueous solution at physiological conditions and to make a comparison with the corresponding pigment-DNA adducts. Constant tRNA concentration (6.25 mM) and various drug/RNA(phosphate) molar ratios of 1/48 to 1/8 were used. FTIR and UV-visible difference spectroscopic methods have been applied to determine the drug binding mode, the binding constants, and the effects of drug complexation on the stability and conformation of tRNA duplex. Both intercalative and external binding modes were observed. Structural analysis showed que, kae, and a del intercalate tRNA duplex with minor external binding to the major or minor groove and the backbone phosphate group with overall binding constants K (que) = 4.80 x 10(4) M(1), K (kae) = 4.65 x 10(4) M(1), and K (del) = 9.47 x 10(4) M(1). The stability of adduct formation is in the order of del > que > kae. A comparison with flavonoids-DNA adducts showed both intercalation and external bindings with the stability order K (que) = 7.25 x 10(4) M(1), K (kae) = 3.60 x 10(4) M(1), and K (del) = 1.66 x 10(4) M(1). Low flavonoid concentration induces helical stabilization, whereas high pigment content causes helix opening. A partial Bto A-DNA transition occurs at high drug concentration, while tRNA remains in the A-family structure.
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Affiliation(s)
- Charalabos D Kanakis
- Laboratory of Chemistry, Department of Science, Agricultural University of Athens, Athens, Greece
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86
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Polyanichko AM, Chikhirzhina EV, Andrushchenko VV, Vorob'ev VI, Wieser H. The effect of manganese(II) on the structure of DNA/HMGB1/H1 complexes: Electronic and vibrational circular dichroism studies. Biopolymers 2006; 83:182-92. [PMID: 16732569 DOI: 10.1002/bip.20544] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The interactions were studied of DNA with the nonhistone chromatin protein HMGB1 and histone H1 in the presence of manganese(II) ions at different protein to DNA and manganese to DNA phosphate ratios by using absorption and optical activity spectroscopy in the electronic [ultraviolet (UV) and electronic circular dichroism ECD)] and vibrational [infrared (IR) and vibrational circular dichroism (VCD)] regions. In the presence of Mn2+, the protein-DNA interactions differ from those without the ions and cause prominent DNA compaction and formation of large intermolecular complexes. At the same time, the presence of HMGB1 and H1 also changed the mode of interaction of Mn2+ with DNA, which now takes place mostly in the major groove of DNA involving N7(G), whereas interactions between Mn2+ and DNA phosphate groups are weakened by histone molecules. Considerable interactions were also detected of Mn2+ ions with aspartic and glutamic amino acid residues of the proteins.
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Affiliation(s)
- A M Polyanichko
- Department of Chemistry, University of Calgary, Calgary, Canada.
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87
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Malonga H, Neault JF, Arakawa H, Tajmir-Riahi HA. DNA Interaction with Human Serum Albumin Studied by Affinity Capillary Electrophoresis and FTIR Spectroscopy. DNA Cell Biol 2006; 25:63-8. [PMID: 16405401 DOI: 10.1089/dna.2006.25.63] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The question addressed in this study is how does the protein-DNA complexation affect the structure and dynamics of DNA and protein in aqueous solution. We examined the interaction of calf-thymus DNA with human serum albumin (HSA) in aqueous solution at physiological conditions, using constant DNA concentration of 12.5 mM (phosphate) and various HSA contents 0.25 to 2% or 0.04 to 0.3 mM. Affinity capillary electrophoresis and FTIR spectroscopic methods were used to determine the protein binding mode, the association constant, sequence preference, and the biopolymer secondary structural changes in the HSA-DNA complexes. Spectroscopic evidence showed two types of HSA-DNA complexes with strong binding of K(1) = 4.5 x 10(5) M(-1) and weak binding of K(2) = 6.10 x 10(4) M(-1). The two major binding sites were located on the G-C bases and the backbone PO(2) group. The protein-DNA interaction stabilizes the HSA secondary structure. A minor alteration of B-DNA structure was observed, while no major protein conformational changes occurred.
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Affiliation(s)
- H Malonga
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, Canada
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88
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Nafisi S, Sobhanmanesh A, Alimoghaddam K, Ghavamzadeh A, Tajmir-Riahi HA. Interaction of arsenic trioxide As2O3 with DNA and RNA. DNA Cell Biol 2005; 24:634-40. [PMID: 16225394 DOI: 10.1089/dna.2005.24.634] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Arsenic salts have been used for centuries to treat a variety of medical conditions ranging from infectious disease to cancer. More recently, trivalent arsenic trioxide was found to exhibit high antitumor activity towards hematological malignancies. Even though much is known about antitumor activity and DNA damage by As2O3, there has been no report on the interaction of arsenic trioxide with isolated DNA or RNA. Therefore, it was of interest to examine the interaction of As2O3 with DNA and RNA in aqueous solution at physiological pH. FTIR and UV-visible difference spectroscopic methods were used to characterize the nature of drug-DNA and drug-RNA interactions and to determine the As binding site, the binding constant, the sequence selectivity, the helix stability, and the biopolymer secondary structure in the As2O3-polynucleotide complexes in vitro. The FTIR spectroscopic studies were conducted with As2O3-polynucleotide (phosphate) ratios of 1/40, 1/20, 1/10, and 1/5, with a final DNA (P) or RNA (P) concentration of 6.25 mmol/l. Spectroscopic results showed As2O3 binds to DNA and RNA at G-C, A-T, and A-U bases, and no interaction with the backbone PO2 group. As2O3-DNA and -RNA adducts showed one type of binding with overall binding constant of K(As2O3-DNA) = 1.24 x 10(5) M(-1) and K(As2O3-RNA) = 2.60 x 10(5) M(-1). The As2O3-polynucleotide complexation is associated with a partial biopolymer aggregation and no major alterations of B-DNA or A-RNA structure.
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Affiliation(s)
- Shohreh Nafisi
- Deparment of Chemistry, Azad University, Tehran Central Branch, Tehran, Iran.
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89
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Ouameur AA, Arakawa H, Ahmad R, Naoui M, Tajmir-Riahi HA. A Comparative study of Fe(II) and Fe(III) interactions with DNA duplex: major and minor grooves bindings. DNA Cell Biol 2005; 24:394-401. [PMID: 15941392 DOI: 10.1089/dna.2005.24.394] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The involvement of the Fe cations in autoxidation in cells and tissues is well documented. DNA is a major target in such reaction, and can chelate Fe cation in many ways. The present study was designed to examine the interaction of calf-thymus DNA with Fe(II) and Fe(III), in aqueous solution at pH 6.5 with cation/DNA (P) (P = phosphate) molar ratios (r) of 1:160 to 1:2. Capillary electrophoresis and Fourier transform infrared (FTIR) difference spectroscopic methods were used to determine the cation binding site, the binding constant, helix stability and DNA conformation in Fe-DNA complexes. Structural analysis showed that at low cation concentration (r = 1/80 and 1/40), Fe(II) binds DNA through guanine N-7 and the backbone PO(2) group with specific binding constants of K(G) = 5.40 x 10(4) M(1) and K(P) = 2.40 x 10(4) M(1). At higher cation content, Fe(II) bindings to adenine N-7 and thymine O-2 are included. The Fe(III) cation shows stronger interaction with DNA bases and the backbone phosphate group. At low cation concentration (r = 1:80), Fe(III) binds mainly to the backbone phosphate group, while at higher metal ion content, cation binding to both guanine N-7 atom and the backbone phosphate group is prevailing with specific binding constants of K(G) = 1.36 x 10(5) M(-1) and K(P) = 5.50 x 10(4) M(-1). At r = 1:10, Fe(II) binding causes a minor helix destabilization, whereas Fe(III) induces DNA condensation. No major DNA conformational changes occurred upon iron complexation and DNA remains in the B-family structure.
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Affiliation(s)
- A Ahmed Ouameur
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, Quebec, Canada
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90
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Vibrational and electronic circular dichroism and absorption spectral study of the DNA–5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin interaction. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2005.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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91
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Polyanichko A, Wieser H. Fourier transform infrared/vibrational circular dichroism spectroscopy as an informative tool for the investigation of large supramolecular complexes of biological macromolecules. Biopolymers 2005; 78:329-39. [PMID: 15912505 DOI: 10.1002/bip.20299] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A combination of ultraviolet (UV) and infrared (IR) absorption and circular dichroism (CD) spectroscopy was applied to investigate the structure and formation of large supramolecular DNA-protein complexes. This combination of techniques was used to overcome limitations of UV-CD (electronic, or ECD) spectroscopy due to considerable light scattering in such solutions. Based on the analysis of FTIR and UV-CD spectra, the interaction of DNA with nonhistone chromatin protein HMGB1 and linker histone H1 was studied. The data obtained showed that under the conditions of the experiment (15 mM NaCl, protein/DNA ratio r < 1 w/w) the proteins did not reveal any AT or GC specificity in binding to DNA. In the presence of both proteins, mainly interactions in the DNA minor groove were observed, which were attributed to HMGB1 binding. Histone H1 facilitated binding of HMGB1 to DNA by interacting with the negatively charged groups of the sugar-phosphate backbone and binding of aspartic and glutamic amino acid residues of HMGB1. Acting together, HMGB1 and H1 stimulated the assemblage of supramolecular DNA-protein structures. The structural organization of the ternary complexes depended not only on the properties of the protein-DNA interactions but also on the interactions between HMGB1 and H1 molecules.
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92
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Pandyra AA, Yamniuk AP, Andrushchenko VV, Wieser H, Vogel HJ. Isotope-labeled vibrational circular dichroism studies of calmodulin and its interactions with ligands. Biopolymers 2005; 79:231-7. [PMID: 16013055 DOI: 10.1002/bip.20339] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this work we have studied ligand-induced secondary structure changes in the small calcium regulatory protein calmodulin (CaM) using vibrational circular dichroism (VCD) spectroscopy. We find that, due to its chiral sensitivity, VCD spectroscopy has increased ability over IR spectroscopy to detect changes in the structure and flexibility of secondary structure elements upon ligand binding. Moreover, we demonstrate that the uniform isotope labeling of CaM with (13)C shifts its amide I' VCD band by about approximately 43 cm(-1) to lower wavenumbers, which opens up a spectral window to simultaneously visualize a bound target protein. Therefore this study also provides the first example of how isotope labeling enables protein-protein interactions to be studied by VCD with good separation of the signals for both isotope-labeled and unlabeled proteins.
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93
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Nový J, Urbanová M, Volka K. The DNA-Porphyrin Interactions Studied by Vibrational and Electronic Circular Dichroism Spectroscopy. ACTA ACUST UNITED AC 2005. [DOI: 10.1135/cccc20051799] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The interactions of three different porphyrins, without axial ligands - 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Cu(II) tetrachloride (Cu(II)TMPyP), with axial ligands - 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin-Fe(III) pentachloride (Fe(III)TMPyP), and with bulky meso substituents - 5,10,15,20-tetrakis(N,N,N-trimethylanilinium-4-yl)-porphyrin tetrachloride (TMAP), with calf thymus DNA were studied by combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopy, and by IR and UV-VIS absorption spectroscopy. It has been shown that Cu(II)TMPyP prefers the intercalative binding mode with DNA in the GC-rich regions and the intercalative sites are saturated at the c(DNA)/c(Cu(II)TMPyP) ratio ~3:1, where c(DNA) and c(Cu(II)TMPyP) are total molar concentrations of nucleic acid in base pairs and porphyrin, respectively. Fe(III)TMPyP does not intercalate between the GC base pairs but binds to DNA in the minor groove. At higher c(DNA)/c(TMAP) ratios, TMAP interacts with DNA in the minor groove, but at lower ratios in the major groove and by the external binding mode accompanied by self-stacking of porphyrins along the phosphate backbone. VCD spectroscopy reliably discriminates the binding modes and specifies the conformational changes of the DNA matrices. It has been also shown that VCD spectroscopy is an effective tool for the conformational studies of DNA-porphyrin complexes. New spectroscopic "markers" in VCD spectra have been found for the specific DNA-porphyrin interactions.
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94
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Polyanichko AM, Andrushchenko VV, Chikhirzhina EV, Vorob'ev VI, Wieser H. The effect of manganese(II) on DNA structure: electronic and vibrational circular dichroism studies. Nucleic Acids Res 2004; 32:989-96. [PMID: 14872058 PMCID: PMC373386 DOI: 10.1093/nar/gkh242] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The interaction of DNA with Mn2+ was studied in absorbance and optical activity in the electronic and vibrational regions. Based on the data, several stages of the interaction were identified. Con formational transition towards the C-form of DNA was observed in solution at the molar ratio Mn2+/DNA-phosphates between 0.1 and 1.5. The exact ratio depended on the ionic strength and increased with increasing NaCl concentration. Although manganese interacted with the phosphates and bases of DNA at higher metal concentrations, it is unlikely that direct chelation occurred. A model for the interaction between manganese ions and DNA mediated by water is suggested destabilizing the double helix and partially breaking the hydrogen bonds between the base pairs. At high Mn2+ concentrations DNA aggregation was observed.
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Affiliation(s)
- A M Polyanichko
- Department of Physics, St Petersburg State University, St Petersburg, Russian Federation
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95
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Andrushchenko V, van de Sande JH, Wieser H. Vibrational circular dichroism and IR absorption of DNA complexes with Cu2+ ions. Biopolymers 2003; 72:374-90. [PMID: 12949828 DOI: 10.1002/bip.10439] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Vibrational circular dichroism (VCD) spectroscopy and simultaneous IR absorption measurements are applied to study the interaction of natural calf thymus DNA with Cu2+ ions at room temperature in a Cu2+ concentration range of 0-0.4M (a Cu2+/phosphate molar ratio [Cu]/[P] of 0-0.7). In some important instances, VCD provides more detailed insights than previous IR investigations whereas in several others it leads to the same interpretations. The Cu2+ ions bind to phosphate groups at a low metal concentration. Upon increasing the ion concentration, chelates are formed in which Cu2+ binds to the N7 of guanine (G) and a phosphate group. Detectable only by VCD, significant distortion of most guanine-cytosine (GC) base pairs occurs at a [Cu]/[P] ratio of 0.5 with only a minor affect on adenine-thymine (AT) base pairs, which favors a "sandwich" complex in which a Cu2+ ion is inserted between two adjacent guanines in a GpG sequence. The AT base pairs become significantly distorted when the metal concentration is increased to 0.7 [Cu]/[P]. A number of GC base pairs, which are possibly involved in sandwich complexes, remain stacked and paired even at 0.7 [Cu]/[P], preventing complete strand separation. The DNA secondary structure changes considerably from the standard B-form geometry at a [Cu]/[P] ratio of 0.4 and higher. A further transition to some intermediate conformation that is inconsistent with either the A- or Z-form or a completely denatured state is suggested in agreement with other works. In general, VCD proves to be a reliable indicator of the 3-dimensional structure of the DNA-metal ion complexes, which reveals structural details that cannot be deduced from the IR absorption spectra alone.
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Affiliation(s)
- V Andrushchenko
- Department of Chemistry, Faculty of Science, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4, Canada
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96
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Andrushchenko V, Tsankov D, Wieser H. Vibrational circular dichroism spectroscopy and the effects of metal ions on DNA structure. J Mol Struct 2003. [DOI: 10.1016/j.molstruc.2003.08.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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97
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Lobo BA, Vetro JA, Suich DM, Zuckermann RN, Middaugh CR. Structure/function analysis of peptoid/lipitoid:DNA complexes. J Pharm Sci 2003; 92:1905-18. [PMID: 12950008 DOI: 10.1002/jps.10450] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Previous transfection studies of cationic peptoid polymers (N-substituted polyglycines) and cationic lipitoid polymers (peptoid-phospholipid conjugates) have shown that only the polymers which possessed a repeating (cationic, hydrophobic, hydrophobic) substituent sequence are efficient in gene transfer in vitro. To determine if there is a physical attribute of peptoid and lipitoid complexes that correlates with efficient gene transfection, biophysical, and transfection measurements were performed with polymer:DNA complexes containing each of seven structurally diverse peptoid polymers and two lipitoids that possess different hydrophobic substituents. These measurements revealed that the biophysical properties of these complexes (size, zeta-potential, ethidium bromide exclusion) varied with polymer structure and complex (+/-) charge ratio but were not directly predictive of transfection efficiency. Unique alterations in the circular dichroism spectra of DNA were observed in complexes containing several of the peptoids and both lipitoids, although FTIR spectroscopy demonstrated that the DNA remained in the B-form. The lack of correlations between the physical properties and the transfection activities of these polyplexes suggests that a further subpopulation examination of these complexes by these methods may reveal hidden structure-activity relationships.
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Affiliation(s)
- Brian A Lobo
- Department of Pharmaceutical Chemistry, 2095 Constant Avenue, University of Kansas, Lawrence, Kansas 66047, USA
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98
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Andrushchenko V, Van De Sande H, Wieser H. DNA interaction with Mn2+ ions at elevated temperatures: VCD evidence of DNA aggregation. Biopolymers 2003; 69:529-45. [PMID: 12879498 DOI: 10.1002/bip.10419] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Interaction of natural calf thymus DNA with Mn(2+) ions was studied at room temperature and at elevated temperatures in the range from 23 degrees C to 94 degrees C by means of IR absorption and vibrational circular dichroism (VCD) spectroscopy. The Mn(2+) concentration was varied between 0 and 1.3M (0 and 10 [Mn]/[P]). The secondary structure of DNA remained in the frame of the B-form family in the whole ion concentration range at room temperature. No significant DNA denaturation was revealed at room temperature even at the highest concentration of metal ions studied. However at elevated temperatures, DNA denaturation and a significant decrease of the melting temperature of DNA connected with a decrease of the stability of DNA induced by Mn(2+) ions occurred. VCD demonstrated sensitivity to DNA condensation and aggregation as well as an ability to distinguish between these two processes. No condensation or aggregation of DNA was observed at room temperature at any of the metal ion concentrations studied. DNA condensation was revealed in a very narrow range of experimental conditions at around 2.4 [Mn]/[P] and about 55 degrees C. DNA aggregation was observed in the presence of Mn(2+) ions at elevated temperatures during or after denaturation. VCD spectroscopy turned out to be useful for studying DNA condensation and aggregation due to its ability to distinguish between these two processes, and for providing information about DNA secondary structure in a condensed or aggregated state.
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Affiliation(s)
- Valery Andrushchenko
- Department of Chemistry, Faculty of Science, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
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99
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Tsankov D, Kalisch B, van de Sande H, Wieser H. Cisplatin-DNA Adducts by Vibrational Circular Dichroism Spectroscopy: Structure and Isomerization of d(CCTG*G*TCC)·d(GGACCAGG) Intrastrand Cross-Linked by Cisplatin. J Phys Chem B 2003. [DOI: 10.1021/jp034246c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dimiter Tsankov
- Department of Chemistry, Faculty of Science, and Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Berndt Kalisch
- Department of Chemistry, Faculty of Science, and Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Hans van de Sande
- Department of Chemistry, Faculty of Science, and Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Hal Wieser
- Department of Chemistry, Faculty of Science, and Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, T2N 1N4, Canada
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