1
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Joshi S, Singh A, Kukreti S. Porphyrin induced structural destabilization of a parallel DNA G-quadruplex in human MRP1 gene promoter. J Mol Recognit 2022; 35:e2950. [PMID: 34990028 DOI: 10.1002/jmr.2950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/01/2023]
Abstract
Porphyrins are among the first ligands that have been tested for their quadruplex binding and stabilization potential. We report the differential interaction of the positional cationic porphyrin isomers TMPyP3 and TMPyP4 with a parallel G-quadruplex (GQ) formed by 33-mer (TP) regulatory sequence present in the promoter region of the human multidrug resistance protein 1 (MRP1) transporter gene. This GQ element encompasses the three evolutionary conserved SP1 transcription factor binding sites. Taking into account that SP1 binds to a non-canonical GQ motif with higher affinity than to a canonical duplex DNA consensus motif, it is suggestive that GQ distortion by cationic porphyrin will have important implications in the regulation of MRP1 expression. Herein, we employed biophysical analysis using circular dichroism, visible absorption, UV-thermal melting and steady-state fluorescence spectroscopy, reporting destabilization of MRP1 GQ by cationic porphyrins. Results suggest that TMPyP4 and TMPyP3 interact with GQ with a binding affinity of 106 to 107 M-1 . Thermodynamic analysis indicated a significant decrease in melting temperature of GQ (ΔTm of 15.5°C-23.5°C), in the presence of 2 times excess of porphyrins. This study provides the biophysical evidence indicating the destabilisation of a parallel DNA G-quadruplex by cationic porphyrins.
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Affiliation(s)
- Savita Joshi
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
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2
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Plata CA, Marni S, Maritan A, Bellini T, Suweis S. Statistical physics of DNA hybridization. Phys Rev E 2021; 103:042503. [PMID: 34005886 DOI: 10.1103/physreve.103.042503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/23/2021] [Indexed: 11/07/2022]
Abstract
Deoxyribonucleic acid (DNA) hybridization is at the heart of countless biological and biotechnological processes. Its theoretical modeling played a crucial role, since it has enabled extracting the relevant thermodynamic parameters from systematic measurements of DNA melting curves. In this article, we propose a framework based on statistical physics to describe DNA hybridization and melting in an arbitrary mixture of DNA strands. In particular, we are able to analytically derive closed expressions of the system partition functions for any number N of strings and explicitly calculate them in two paradigmatic situations: (i) a system made of self-complementary sequences and (ii) a system comprising two mutually complementary sequences. We derive the melting curve in the thermodynamic limit (N→∞) of our description, which provides a full justification for the extra entropic contribution that in classic hybridization modeling was required to correctly describe within the same framework the melting of sequences either self-complementary or not. We thus provide a thorough study comprising limit cases and alternative approaches showing how our framework can give a comprehensive view of hybridization and melting phenomena.
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Affiliation(s)
- Carlos A Plata
- Dipartimento di Fisica "G. Galilei," INFN, Università di Padova, 35131 Padova, Italy
- Université Paris-Saclay, CNRS, LPTMS, 91405 Orsay, France
| | - Stefano Marni
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, MI I-20090, Italy
| | - Amos Maritan
- Dipartimento di Fisica "G. Galilei," INFN, Università di Padova, 35131 Padova, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Segrate, MI I-20090, Italy
| | - Samir Suweis
- Dipartimento di Fisica "G. Galilei," INFN, Università di Padova, 35131 Padova, Italy
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3
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Machha VR, Mikek CG, Wellman S, Lewis EA. Temperature and osmotic stress dependence of the thermodynamics for binding linker histone H1 0, Its carboxyl domain (H1 0-C) or globular domain (H1 0-G) to B-DNA. Biochem Biophys Rep 2017; 12:158-165. [PMID: 29090277 PMCID: PMC5645174 DOI: 10.1016/j.bbrep.2017.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
Linker histones (H1) are the basic proteins in higher eukaryotes that are responsible for the final condensation of chromatin. In contrast to the nucleosome core histone proteins, the role of H1 in compacting DNA is not clearly understood. In this study ITC was used to measure the binding constant, enthalpy change, and binding site size for the interactions of H10, or its C-terminal (H10-C) and globular (H10-G) domains to highly polymerized calf-thymus DNA at temperatures from 288 K to 308 K. Heat capacity changes, ΔCp, for these same H10 binding interactions were estimated from the temperature dependence of the enthalpy changes. The enthalpy changes for binding H10, H10-C, or H10-G to CT-DNA are all endothermic at 298 K, becoming more exothermic as the temperature is increased. The ΔH for binding H10-G to CT-DNA is exothermic at temperatures above approximately 300 K. Osmotic stress experiments indicate that the binding of H10 is accompanied by the release of approximately 35 water molecules. We estimate from our naked DNA titration results that the binding of the H10 to the nucleosome places the H10 protein in close contact with approximately 41 DNA bp. The breakdown is that the H10 carboxyl terminus interacts with 28 bp of linker DNA on one side of the nucleosome, the H10 globular domain binds directly to 7 bp of core DNA, and shields another 6 linker DNA bases, 3 bp on either side of the nucleosome where the linker DNA exits the nucleosome core.
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Affiliation(s)
- V R Machha
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - C G Mikek
- Department of Chemistry, Mississippi State University, Mississippi, MS 39762, USA
| | - S Wellman
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, 2500 N. State Street, Jackson, MS 39216, USA
| | - E A Lewis
- Department of Chemistry, Mississippi State University, Mississippi, MS 39762, USA
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4
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Iizuka N, Nakai M, Nakabayashi Y. Mixed-ligand ruthenium(II) complexes capable of hydrogen-bonding interactions with DNA: DNA binding, nuclease activity, cytotoxicity, and topoisomerase inhibition. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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5
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Yano T, Hishida S, Nakai M, Nakabayashi Y. Anticancer activity of heterodinuclear ruthenium(II)–platinum(II) complexes as photochemotherapeutic agents. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Matsui T, Sugiyama H, Nakai M, Nakabayashi Y. DNA Interaction and Cytotoxicity of Cyclometalated Ruthenium(II) Complexes as Potential Anticancer Drugs. Chem Pharm Bull (Tokyo) 2016; 64:282-6. [PMID: 26936054 DOI: 10.1248/cpb.c15-00903] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To evaluate the anticancer activity of the cyclometalated ruthenium(II) complexes [Ru(bpy)2(C^N)]Cl, we have studied the interaction of these complexes using calf thymus DNA (CT-DNA) and cytotoxicity assays with two tumor (L1210 and HeLa) and a non-tumor (BALB/3T3 clone A31) cell lines. It is suggested that the complexes act as intercalators and/or DNA minor groove binders. Moreover, the complexes display favorable cytotoxicity activities with L1210 and HeLa, which in all cases were significantly more favorable than cisplatin. In contrast, the complexes exhibit appreciably lower cytotoxicity toward BALB/3T3 clone A31.
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Affiliation(s)
- Takahiro Matsui
- Department of Chemistry and Materials Engineering, Kansai University
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7
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Turaga G, Edmondson SP, Smith K, Shriver JW. Insights into the Structure of Sulfolobus Nucleoid Using Engineered Sac7d Dimers with a Defined Orientation. Biochemistry 2016; 55:6230-6237. [PMID: 27766846 DOI: 10.1021/acs.biochem.6b00810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The structure of Archaeal chromatin or nucleoid is believed to have characteristics similar to that found in both eukaryotes and bacteria. Recent comparative studies have suggested that DNA compaction in Archaea requires a bridging protein (e.g., Alba) along with either a wrapping protein (e.g., a histone) or a bending protein such as Sac7d. While X-ray crystal structures demonstrate that Sac7d binds as a monomer to create a significant kink in duplex DNA, the structure of a multiprotein-DNA complex has not been established. Using cross-linked dimers of Sac7d with a defined orientation, we present evidence that indicates that Sac7d is able to largely coat duplex DNA in vivo by binding in alternating head-to-head and tail-to-tail orientations. Although each Sac7d monomer promotes a significant kink of nearly 70°, coated DNA is expected to be largely extended because of compensation of repetitive kinks with helical symmetry.
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Affiliation(s)
- Gokul Turaga
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - Stephen P Edmondson
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - Kelley Smith
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
| | - John W Shriver
- Departments of Chemistry and Biological Sciences, University of Alabama in Huntsville , Huntsville, Alabama 35899, United States
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8
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Jha JK, Ramachandran R, Chattoraj DK. Opening the Strands of Replication Origins-Still an Open Question. Front Mol Biosci 2016; 3:62. [PMID: 27747216 PMCID: PMC5043065 DOI: 10.3389/fmolb.2016.00062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022] Open
Abstract
The local separation of duplex DNA strands (strand opening) is necessary for initiating basic transactions on DNA such as transcription, replication, and homologous recombination. Strand opening is commonly a stage at which these processes are regulated. Many different mechanisms are used to open the DNA duplex, the details of which are of great current interest. In this review, we focus on a few well-studied cases of DNA replication origin opening in bacteria. In particular, we discuss the opening of origins that support the theta (θ) mode of replication, which is used by all chromosomal origins and many extra-chromosomal elements such as plasmids and phages. Although the details of opening can vary among different origins, a common theme is binding of the initiator to multiple sites at the origin, causing stress that opens an adjacent and intrinsically unstable A+T rich region. The initiator stabilizes the opening by capturing one of the open strands. How the initiator binding energy is harnessed for strand opening remains to be understood.
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Affiliation(s)
- Jyoti K Jha
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
| | - Dhruba K Chattoraj
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD, USA
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9
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Wambang N, Schifano-Faux N, Martoriati A, Henry N, Baldeyrou B, Bal-Mahieu C, Bousquet T, Pellegrini S, Meignan S, Cailliau K, Goossens JF, Bodart JF, T. Ndifon P, Pélinski L. Synthesis, Structure, and Antiproliferative Activity of Ruthenium(II) Arene Complexes of Indenoisoquinoline Derivatives. Organometallics 2016. [DOI: 10.1021/acs.organomet.6b00440] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Nathalie Wambang
- University of Lille, CNRS, ENSCL, UMR 8181-UCCS-Unité
de Catalyse et Chimie du Solide, F-59000 Lille, France
- University of Yaoundé 1, Laboratoire de Chimie
de Coordination, BP 812, Yaoundé, Cameroun
| | - Nadège Schifano-Faux
- University of Lille, EA 7365-GRITA-Groupe de Recherche
sur les formes Injectables et les Technologies Associées, F-59000 Lille, France
| | - Alain Martoriati
- University of Lille, CNRS, UMR 8576-UGSF-Unité
de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Natacha Henry
- University of Lille, CNRS, ENSCL, UMR 8181-UCCS-Unité
de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Brigitte Baldeyrou
- University of Lille, Inserm, U908-CPAC-Cell Plasticity
and Cancer, F-59000 Lille, France
| | - Christine Bal-Mahieu
- University of Lille, Inserm, U908-CPAC-Cell Plasticity
and Cancer, F-59000 Lille, France
| | - Till Bousquet
- University of Lille, CNRS, ENSCL, UMR 8181-UCCS-Unité
de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Sylvain Pellegrini
- University of Lille, CNRS, ENSCL, UMR 8181-UCCS-Unité
de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Samuel Meignan
- University of Lille, Inserm, U908-CPAC-Cell Plasticity
and Cancer, F-59000 Lille, France
| | - Katia Cailliau
- University of Lille, CNRS, UMR 8576-UGSF-Unité
de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Jean-François Goossens
- University of Lille, EA 7365-GRITA-Groupe de Recherche
sur les formes Injectables et les Technologies Associées, F-59000 Lille, France
| | - Jean-François Bodart
- University of Lille, CNRS, UMR 8576-UGSF-Unité
de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Peter T. Ndifon
- University of Yaoundé 1, Laboratoire de Chimie
de Coordination, BP 812, Yaoundé, Cameroun
| | - Lydie Pélinski
- University of Lille, CNRS, ENSCL, UMR 8181-UCCS-Unité
de Catalyse et Chimie du Solide, F-59000 Lille, France
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10
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Ivanov AA, Salyanov VI, Zhuze AL. DNA sequence-specific ligands: XV. Synthesis and spectral characteristics of a new series of dimeric bisbenzimidazoles DB(1, 2, 6, 8, 9, 10, 12). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016020059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Synthesis and biological activity of ferrocenyl indeno[1,2-c]isoquinolines as topoisomerase II inhibitors. Bioorg Med Chem 2016; 24:651-60. [DOI: 10.1016/j.bmc.2015.12.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/18/2022]
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12
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Blázquez-Sánchez MT, Marcelo F, Fernández-Alonso MDC, del Villar-Guerra R, Samadi A, Cañada FJ, Jiménez-Barbero J, Vicent C. D- andL-Mannose-Containingglyco-Oligoamides Show Distinct Recognition Properties When Interacting with DNA. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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13
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Marušič M, Plavec J. The Effect of DNA Sequence Directionality on G-Quadruplex Folding. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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14
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Marušič M, Plavec J. The Effect of DNA Sequence Directionality on G‐Quadruplex Folding. Angew Chem Int Ed Engl 2015; 54:11716-9. [DOI: 10.1002/anie.201505348] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/20/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Maja Marušič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia)
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana (Slovenia)
- EN‐FIST Center of Excellence, 1000 Ljubljana (Slovenia)
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana (Slovenia)
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15
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Karapetyan NH, Torosyan AL, Malakyan M, Bajinyan SA, Haroutiunian SG. Investigation of irradiated rats DNA in the presence of Cu(II) chelates of amino acids Schiff bases. J Biomol Struct Dyn 2015; 34:177-83. [PMID: 26101796 DOI: 10.1080/07391102.2015.1020876] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The new synthesized Cu(II) chelates of amino acids Schiff bases were studied as a potential radioprotectors. Male albino rats of Wistar strain were exposed to X-ray whole-body irradiation at 4.8 Gy. This dose caused 30% mortality of the animals (LD30). The survival of animals exposed to radiation after preliminary administration of 10 mg/kg Cu(II)(Nicotinyl-L-Tyrosinate)2 or Cu(II)(Nicotinyl-L-Tryptophanate)2 prior to irradiation was registered about 80 and 100% correspondingly. Using spectrophotometric melting and agarose gel electrophoresis methods, the differences between the DNA isolated from irradiated rats and rats pretreated with Cu(II) chelates were studied. The fragments of DNA with different breaks were revealed in DNA samples isolated from irradiated animals. While, the repair of the DNA structure was observed for animals pretreated with the Cu(II) chelates. The results suggested that pretreatment of the irradiated rats with Cu(II)(Nicotinyl-L-Tyrosinate)2 and Cu(II)(Nicotinyl-L-Tryptophanate)2 compounds improves the liver DNA characteristics.
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Affiliation(s)
- N H Karapetyan
- a Department of Physics , Yerevan State University , Al. Manoogian 1, Yerevan 0025 , Armenia
| | - A L Torosyan
- a Department of Physics , Yerevan State University , Al. Manoogian 1, Yerevan 0025 , Armenia
| | - M Malakyan
- b Centre of Radiation Medicine and Burns , P.O. Box 25, Davidashen, Yerevan 0048 , Armenia
| | - S A Bajinyan
- b Centre of Radiation Medicine and Burns , P.O. Box 25, Davidashen, Yerevan 0048 , Armenia
| | - S G Haroutiunian
- a Department of Physics , Yerevan State University , Al. Manoogian 1, Yerevan 0025 , Armenia
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16
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Ge S, Zhao Y, Sui B, Shangguan G. Studies on the interaction of novel organogermanium sesquioxides with DNA. Chem Res Chin Univ 2015. [DOI: 10.1007/s40242-015-4198-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Betanzos-Lara S, Chmel NP, Zimmerman MT, Barrón-Sosa LR, Garino C, Salassa L, Rodger A, Brumaghim JL, Gracia-Mora I, Barba-Behrens N. Redox-active and DNA-binding coordination complexes of clotrimazole. Dalton Trans 2015; 44:3673-85. [DOI: 10.1039/c4dt02883j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The coordination compounds bind to DNA by two different binding modes depending on the concentration, sequence of the DNA, and the structure of the complex.
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Affiliation(s)
- Soledad Betanzos-Lara
- Departamento de Química Inorgánica
- Facultad de Química
- Universidad Nacional Autónoma de México
- México
- Mexico
| | - Nikola P. Chmel
- Department of Chemistry
- University of Warwick CV4 7AL Coventry
- England
- UK
| | | | - Lidia R. Barrón-Sosa
- Departamento de Química Inorgánica
- Facultad de Química
- Universidad Nacional Autónoma de México
- México
- Mexico
| | - Claudio Garino
- Department of Chemistry and NIS Centre of Excellence
- University of Turin
- 10125 Turin
- Italy
| | - Luca Salassa
- CIC biomaGUNE
- 20009 Donostia
- Spain
- Kimika Fakultatea
- Euskal Herriko Unibertsitatea and Donostia International Physics Center (DIPC)
| | - Alison Rodger
- Department of Chemistry
- University of Warwick CV4 7AL Coventry
- England
- UK
| | | | - Isabel Gracia-Mora
- Departamento de Química Inorgánica
- Facultad de Química
- Universidad Nacional Autónoma de México
- México
- Mexico
| | - Norah Barba-Behrens
- Departamento de Química Inorgánica
- Facultad de Química
- Universidad Nacional Autónoma de México
- México
- Mexico
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18
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Le VH, McGuire MR, Ahuja P, MacDonnell FM, Lewis EA. Thermodynamic Investigations of [(phen)2Ru(tatpp)Ru(phen)2]4+ Interactions with B-DNA. J Phys Chem B 2014; 119:65-71. [DOI: 10.1021/jp509569s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Vu H. Le
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Matthew R. McGuire
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Pooja Ahuja
- Department
of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Frederick M. MacDonnell
- Department
of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Edwin A. Lewis
- Department
of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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19
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Nakabayashi Y, Nakamura H, Kubota Y, Morimoto M, Kawasaki T, Nakai M, Yamauchi O. DNA interaction with dipolar ruthenium(II) ammine complexes containing 4,4′-bipyridinium as photochemotherapeutic agents. Inorganica Chim Acta 2014. [DOI: 10.1016/j.ica.2014.07.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Ornstein RL, Rein R. An optimized potential function for the calculation of nucleic acid interaction energies I. base stacking. Biopolymers 2014; 17:2341-60. [PMID: 24624489 DOI: 10.1002/bip.1978.360171005] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An optimized potential function for base-stacking interactions is constructed. Stacking energies between the complementary pairs of a dimer are calculated as a function of the rotational angle and separation distance. Using several different sets of atomic charges, the electrostatic component in the monopole-monopole approximation (MMA) is compared to the more refined segmented multipole-multipole representation (SMMA); the general features of the stacking minima are found to be correctly reproduced with IEHT or CNDO atomic charges. The electrostatic component is observed to control the location of stacking minima.The MMA, in general, is not a reliable approximation of the SMMA in regions away from minima; however, the MMA is reliable in predicting the location and nature of stacking minima.The attractive part of the Lennard-Jones 6-12 potential is compared to and parameterized against the expressions for the second-order interaction terms composed of multipole-bond polarizability for the polarization energy and transition-dipole bond polariz abilities for approximation of the dispersion energy. The repulsive part of the Lennard-Jones potential is compared to a Kitaygorodski-type repulsive function; changing the exponent from its usual value of 12 to 11.7 gives significantly better agreement with the more refined repulsive function.Stacking minima calculated with the optimized potential method are compared with various perturbation-type treatments. The optimized potential method yields results that compare as well with melting data as do any of the more recent and expensive perturbation methods.
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21
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Dutta S, Lahiri S, Banerjee A, Saha S, Dasgupta D. Association of antitumor antibiotic Mithramycin with Mn2+ and the potential cellular targets of Mithramycin after association with Mn2+. J Biomol Struct Dyn 2014; 33:434-46. [PMID: 24559512 DOI: 10.1080/07391102.2014.887031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Mithramycin (MTR), an aureolic acid group of antitumor antibiotic is used for the treatment of several types of tumors. We have reported here the association of MTR with an essential micronutrient, manganese (Mn(2+)). Spectroscopic methods have been used to characterize and understand the kinetics and mechanism of complex formation between them. MTR forms a single type of complex with Mn(2+) in the mole ratio of 2:1 [MTR: Mn(2+)] via a two step kinetic process. Circular dichroism (CD) spectroscopic study indicates that the complex [(MTR)2 Mn(2+)] has a right-handed twist conformation similar in structure with the complexes reported for Mg(2+) and Zn(2+). This conformation allows binding via minor groove of DNA with (G, C) base preference during the interaction with double-stranded B-DNA. Using absorbance, fluorescence, and CD spectroscopy we have shown that [(MTR)2 Mn(2+)] complex binds to double-stranded DNA with an apparent dissociation constant of 32 μM and binding site size of 0.2 (drug/nucleotide). It binds to chicken liver chromatin with apparent dissociation constant value 298 μM. Presence of histone proteins in chromatin inhibits the accessibility of the complex for chromosomal DNA. We have also shown that MTR binds to Mn(2+) containing metalloenzyme manganese superoxide dismutase from Escherichia coli.
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Affiliation(s)
- Shreyasi Dutta
- a Biophysics & Structural Genomics Division , Saha Institute of Nuclear Physics , Block-AF, Sector-I, Bidhan Nagar, Kolkata - 700 064 , India
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Jacques A, Kirsch-De Mesmaeker A, Elias B. Selective DNA purine base photooxidation by bis-terdentate iridium(III) polypyridyl and cyclometalated complexes. Inorg Chem 2014; 53:1507-12. [PMID: 24446771 DOI: 10.1021/ic402476b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two bis-terdentate iridium(III) complexes with polypyridyl and cyclometalated ligands have been prepared and characterized. Their spectroscopic and electrochemical properties have been studied, and a photophysical scheme addressing their properties is proposed. Different types of excited states have been considered to account for the deactivation processes in each complex. Interestingly, in the presence of mono- or polynucleotides, a photoinduced electron-transfer process from a DNA purine base (i.e., guanine or adenine) to the excited complex is shown through luminescence quenching experiments. For the first time, this work reports evidence for selective DNA purine bases oxidation by excited iridium(III) bis-terdentate complexes.
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Affiliation(s)
- Alexandre Jacques
- Institut de la Matière Condensée et des Nanosciences, Université Catholique de Louvain , Place Louis Pasteur 2, Box L4.01.02, B-1348 Louvain-la-Neuve, Belgium
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23
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Wang S, Long Y, Wang J, Ge Y, Guo P, Liu Y, Tian T, Zhou X. Systematic investigations of different cytosine modifications on CpG dinucleotide sequences: the effects on the B-Z transition. J Am Chem Soc 2013; 136:56-9. [PMID: 24364741 DOI: 10.1021/ja4107012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have first demonstrated the distinctive effects of three newly reported epigenetic modifications, including 5hmC, 5fC, and 5caC, on B-Z transition of CpG dinucleotide DNAs. We have performed detailed assays and compared their effects. We further studied the regulation of B-Z transition of CpG dinucleotide dodecamers by alternating oxidation and alternating reduction.
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Affiliation(s)
- Shaoru Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan, Hubei 430072, P. R. China
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24
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Machha VR, Jones SB, Waddle JR, Le VH, Wellman S, Lewis EA. Exploring the energetics of histone H1.1 and H1.4 duplex DNA interactions. Biophys Chem 2013; 185:32-8. [PMID: 24317196 DOI: 10.1016/j.bpc.2013.11.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/28/2013] [Accepted: 11/18/2013] [Indexed: 01/11/2023]
Abstract
H1.1 and H1.4 bind tightly to both short DNA oligomers and to CT-DNA (Ka≈1×10(7)). Binding is accompanied by an unfavorable enthalpy change (∆H≈+22 kcal/mol) and a favorable entropy change (-T∆S≈-30 kcal/mol). The Tm for the H1.4/CT-DNA complex is increased by 9 °C over the Tm for the free DNA. H1.4 titrations of the DNA oligomers yield stoichiometries (H1/DNA) of 0.64, 0.96, 1.29, and 2.04 for 24, 36, 48, and 72-bp DNA oligomers. The stoichiometries are consistent with a binding site size of 37±1 bp. CT-DNA titration data are consistent with binding site sizes of 32 bp for H1.1 and 36 bp for H1.4. The heat capacity changes, ΔCp, for formation of the H1.1 and H1.4/CT-DNA complexes are -160 cal mol(-1) K(-1) and -192 cal mol(-1)K(-1) respectively. The large negative ΔCp values indicate the loss of water from the protein DNA interface in the complex.
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Affiliation(s)
- V R Machha
- Department of Chemistry, Mississippi State University, Box 9573, Mississippi State, MS 39762, USA
| | - S B Jones
- Department of Chemistry, Mississippi State University, Box 9573, Mississippi State, MS 39762, USA
| | - J R Waddle
- Department of Chemistry, Mississippi State University, Box 9573, Mississippi State, MS 39762, USA
| | - V H Le
- Department of Chemistry, Mississippi State University, Box 9573, Mississippi State, MS 39762, USA
| | - S Wellman
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216-4505, USA
| | - E A Lewis
- Department of Chemistry, Mississippi State University, Box 9573, Mississippi State, MS 39762, USA.
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Abbehausen C, Peterson EJ, de Paiva REF, Corbi PP, Formiga ALB, Qu Y, Farrell NP. Gold(I)-Phosphine-N-Heterocycles: Biological Activity and Specific (Ligand) Interactions on the C-Terminal HIVNCp7 Zinc Finger. Inorg Chem 2013; 52:11280-7. [DOI: 10.1021/ic401535s] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Camilla Abbehausen
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box
6154, CEP 13083-970, Campinas, São Paulo, Brazil
| | - Erica J. Peterson
- Goodwin Laboratory, Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23298, United States
| | - Raphael E. F. de Paiva
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box
6154, CEP 13083-970, Campinas, São Paulo, Brazil
| | - Pedro P. Corbi
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box
6154, CEP 13083-970, Campinas, São Paulo, Brazil
| | - André L. B. Formiga
- Institute of Chemistry, University of Campinas—UNICAMP, P.O. Box
6154, CEP 13083-970, Campinas, São Paulo, Brazil
| | - Yun Qu
- Goodwin Laboratory, Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23298, United States
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284-2006, United States
| | - Nicholas P. Farrell
- Goodwin Laboratory, Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23298, United States
- Department of Chemistry, Virginia Commonwealth University, 1001 W. Main Street, Richmond, Virginia 23284-2006, United States
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Machha VR, Waddle JR, Turner AL, Wellman S, Le VH, Lewis EA. Calorimetric studies of the interactions of linker histone H1(0) and its carboxyl (H1(0)-C) and globular (H1(0)-G) domains with calf-thymus DNA. Biophys Chem 2013; 184:22-8. [PMID: 24036047 DOI: 10.1016/j.bpc.2013.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 01/04/2023]
Abstract
Histone H1 is a chromatin protein found in most eukaryotes. ITC and CD have been used to study the binding of H1(0) and its C-terminal, H1(0)-C, and globular, H1(0)-G, domains to a highly polymerized DNA. ITC results indicate that H1(0) and H1(0)-C bind tightly to DNA (Ka≈1×10(7)), with an unfavorable ΔH (ΔH≈+22kcal/mol) and a favorable ΔS (-TΔS≈-30kcal/mol). Binding H1(0)-G to DNA at 25°C is calorimetrically silent. A multiple independent site model fits the ITC data, with the anomaly in the data near saturation attributed to rearrangement of bound H1, maximizing the number of binding sites. CD experiments indicate that H1(0)/DNA and H1(0)-C/DNA complexes form with little change in protein structure but with some DNA restructuring. Salt dependent ITC experiments indicate that the electrostatic contribution to binding H1(0) or H1(0)-C is small ranging from 6% to 17% of the total ΔG.
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Affiliation(s)
- V R Machha
- Department of Chemistry, Mississippi State University, Box 9573, Mississippi State, MS 39762, United States
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Abstract
To reveal protective role of the new Mn(II) complexes with Nicotinyl-L-Tyrosinate and Nicotinyl-L-Tryptophanate Schiff Bases against ionizing radiation. The DNA of the rats liver was isolated on 7, 14, and 30 days after X-ray irradiation. The differences between the DNA of irradiated rats and rats pre-treated with Mn(II) complexes were studied using the melting, microcalorimetry, and electrophoresis methods. The melting parameters and the melting enthalpy of rats livers DNA were changed after the X-ray irradiation: melting temperature and melting enthalpy were decreased and melting interval was increased. These results can be explained by destruction of DNA molecules. It was shown that pre-treatment of rats with Mn(II) complexes approximates the melting parameters to norm. Agarose gel electrophoresis data confirmed the results of melting studies. The separate DNA fragments were revealed in DNA samples isolated from irradiated animals. The DNA isolated from animals pre-treated with the Mn(II) chelates had better electrophoretic characteristics, which correspond to healthy DNA. Pre-treatment of the irradiated rats with Mn(II)(Nicotinil-L-Tyrosinate) and Mn(II)(Nicotinil-L-Tryptophanate)2 improves the DNA characteristics.
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Yamada T, Noguchi Y, Nakai M, Yamauchi O, Nakabayashi Y, Sato T, Tamai Y, Chikuma M, Mino Y. Solvolysis and cytotoxicity of dinuclear ruthenium(II)-2,2′-bipyridine complexes with various bridged-ligands. Inorganica Chim Acta 2013. [DOI: 10.1016/j.ica.2012.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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Metallo-supramolecular Polymers: Versatile DNA Binding and Their Cytotoxicity. J Inorg Organomet Polym Mater 2012. [DOI: 10.1007/s10904-012-9752-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Busto N, García B, Leal JM, Secco F, Venturini M. The mode of binding ACMA–DNA relies on the base-pair nature. Org Biomol Chem 2012; 10:2594-602. [DOI: 10.1039/c2ob06889c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Xi H, Davis E, Ranjan N, Xue L, Hyde-Volpe D, Arya DP. Thermodynamics of nucleic acid "shape readout" by an aminosugar. Biochemistry 2011; 50:9088-113. [PMID: 21863895 PMCID: PMC3673541 DOI: 10.1021/bi201077h] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized as playing an equally important role in DNA recognition. Competition dialysis, UV, flourescent intercalator displacement (FID), computational docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, the results suggest the following. (1) Neomycin binds three RNA structures [16S A site rRNA, poly(rA)·poly(rA), and poly(rA)·poly(rU)] with high affinities (K(a) ~ 10(7) M(-1)). (2) The binding of neomycin to A-form GC-rich oligomer d(A(2)G(15)C(15)T(2))(2) has an affinity comparable to those of RNA structures. (3) The binding of neomycin to DNA·RNA hybrids shows a 3-fold variance that can be attributed to their structural differences [for poly(dA)·poly(rU), K(a) = 9.4 × 10(6) M(-1), and for poly(rA)·poly(dT), K(a) = 3.1 × 10(6) M(-1)]. (4) The interaction of neomycin with DNA triplex poly(dA)·2poly(dT) yields a binding affinity (K(a)) of 2.4 × 10(5) M(-1). (5) Poly(dA-dT)(2) shows the lowest association constant for all nucleic acids studied (K(a) < 10(5)). (6) Neomycin binds to G-quadruplexes with K(a) values of ~10(4)-10(5) M(-1). (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin's affinity for various nucleic acid structures can be ranked as follows: RNAs and GC-rich d(A(2)G(15)C(15)T(2))(2) structures > poly(dA)·poly(rU) > poly(rA)·poly(dT) > T·A-T triplex, G-quadruplex, B-form AT-rich, or GC-rich DNA sequences. The results illustrate the first example of a small molecule-based "shape readout" of different nucleic acid conformations.
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Affiliation(s)
- Hongjuan Xi
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Erik Davis
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Liang Xue
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - David Hyde-Volpe
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
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Airoldi M, Gennaro G, Giomini M, Giuliani AM, Giustini M, Palazzo G. The CdCl2 effects on synthetic DNAs encaged in the nanodomains of a cationic water-in-oil microemulsion. Phys Chem Chem Phys 2011; 13:12293-304. [PMID: 21643617 DOI: 10.1039/c1cp20770a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The present work is dedicated to the study of the interactions of CdCl(2) with the synthetic polynucleotides polyAT and polyGC confined in the nanoscopic aqueous compartment of the water-in-oil microemulsion CTAB/pentanol/hexane/water, with the goal to mimic in vitro the situation met by the nucleic acids in vivo. In biological structures, in fact, very long strings of nucleic acids are segregated into very small compartments having a radius exceedingly smaller than the length of the encapsulated macromolecule. For comparison, the behaviour of polyGC was also studied in aqueous solutions of matched composition. The conformational and thermal stabilities of both polynucleotides enclosed in the inner compartment of the microemulsion are scarcely affected by the presence of CdCl(2), whereas in solution immediate and large effects were observed also at room temperature. The lack of effects of CdCl(2) on the properties of the biopolymers entrapped in the aqueous core of the microemulsion has been attributed to the peculiar characteristics of the medium (low dielectric constant, in particular) which cause a total repression of the CdCl(2) dissociation that is not complete even in water. In fact, several of the numerous effects of CdCl(2) observed on the conformational stability of polyGC in aqueous solutions have also been ascribed to the limited dissociation of the cadmium salt.
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Affiliation(s)
- Marta Airoldi
- Dipartimento di Chimica S. Cannizzaro, Università di Palermo, Palermo, Italy
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Zhu XJ, Wang P, Leung HWC, Wong WK, Wong WY, Kwong DWJ. Synthesis, Characterization, and DNA-Binding and -Photocleavage Properties of Water-Soluble Lanthanide Porphyrinate Complexes. Chemistry 2011; 17:7041-52. [DOI: 10.1002/chem.201003342] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2010] [Indexed: 11/07/2022]
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Díaz-Espinosa Y, Crespo-Hernández CE, Alegría AE, García C, Arce R. Quenching enhancement of the singlet excited state of pheophorbide-a by DNA in the presence of the quinone carboquone. Photochem Photobiol 2010; 87:275-83. [PMID: 21138440 DOI: 10.1111/j.1751-1097.2010.00869.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Changes in the emission fluorescence intensity of pheophorbide-a (PHEO) in the presence of carboquone (CARBOQ) were used to obtain the association constant, the number of CARBOQ molecules interacting with PHEO, and the fluorescence quantum yield of the complex. Excitation spectra of mixtures of PHEO and CARBOQ in ethanol (EtOH) show an unresolved doublet in the red-most excitation band of PHEO, indicating the formation of a loose ground-state complex. The 1:1 CARBOQ-PHEO complex shows a higher fluorescence quantum yield in EtOH (0.41 ± 0.02) than in buffer solution (0.089 ± 0.002), which is also higher than that of the PHEO monomer (0.28). Quenching of the PHEO fluorescence by DNA nucleosides and double-stranded oligonucleotides was also observed and the bimolecular quenching rate constants were determined. The quenching rate constant increase as the oxidation potential of the DNA nucleoside increases. Larger quenching constants were obtained in the presence of CARBOQ suggesting that CARBOQ enhances DNA photo-oxidation, presumably by inhibiting the back-electron-transfer reaction from the photoreduced PHEO to the oxidized base. Thus, the enhanced DNA-base photosensitized oxidation by PHEO in the presence of CARBOQ may be related to the large extent by which this quinone covalently binds to DNA, as previously reported.
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Wahyuni ET, Tjahjono DH, Yoshioka N, Inoue H. Spectroscopic studies on the thermodynamic and thermal denaturation of the ct-DNA binding of methylene blue. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 77:528-534. [PMID: 20637684 DOI: 10.1016/j.saa.2010.06.032] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 06/16/2010] [Accepted: 06/18/2010] [Indexed: 05/29/2023]
Abstract
The ct-DNA binding properties of methylene blue (MB) including binding constant, thermodynamic parameter and thermal denaturation (T(m)) have been systematically studied by spectrophotometric method. The binding of MB to ct-DNA is quite strong as indicated by remarkable hypochromicity, red shift and equilibrium binding constant (K(b)). Van't Hoff plot of 1/T versus lnK(b) suggests that the MB dye binds exothermically to ct-DNA which is characterized by large negative enthalpy and entropy changes. According to polyelectrolyte theory, the charge release (Z) when ct-DNA interacts with MB is +1.09 which corresponds very well to the one positive charge carried by the MB dye. The K(b) at a low concentration of salt is dominated by electrostatic interaction (90%) while that at a high concentration of salt is mostly controlled by non-electrostatic process (85%). However, the stabilization of the DNA binding event in both cases is governed by non-electrostatic process. A moderate stabilization of double helix ct-DNA occurs when the MB dye binds to ct-DNA as indicated by the increase in T(m) of ct-DNA of about 5.5 degrees C in the presence of MB. This suggests that MB dye possibly binds to ct-DNA via electrostatic and intercalation modes.
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Tapia-Rojo R, Mazo JJ, Falo F. Thermal and mechanical properties of a DNA model with solvation barrier. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:031916. [PMID: 21230117 DOI: 10.1103/physreve.82.031916] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Indexed: 05/30/2023]
Abstract
We study the thermal and mechanical behaviors of DNA denaturation in the frame of the mesoscopic Peyrard-Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we are able to set suitable values of the parameters of the model and study the formation and stability of bubbles in the system. Then, we focus on the case of the P5 promoter sequence and use the principal component analysis of the trajectories to extract the main information on the dynamical behavior of the system. We find that this analysis method gives an excellent agreement with previous biological results.
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Affiliation(s)
- R Tapia-Rojo
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
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Li XQ, Fan P. A duplex DNA model with regular inter-base-pair hydrogen bonds. J Theor Biol 2010; 266:374-9. [PMID: 20621103 DOI: 10.1016/j.jtbi.2010.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 04/15/2010] [Accepted: 07/04/2010] [Indexed: 10/19/2022]
Abstract
It is well known that base-pair stacking is the main factor in stabilizing DNA duplex and plays an important role in determining DNA sequence-dependence. What is the dominant force in base-pair stacking? This fundamental biological question remains a challenging problem. Here, based on recent studies about the non-planarity of amino groups on DNA bases, we propose a new duplex DNA model, in which all base amino groups are non-planar and participate in forming regular inter-base-pair hydrogen bonds (IBP H-bonds). This model implies that IBP H-bonds are the dominant force stabilizing base-pair stacking and play a crucial role in determining the geometry and physical properties of sequence-dependent twisted stacking between adjacent base pairs. The model presents a new insight into the link, through regular IBP H-bonds, between base-sequence, fine structure and physical properties at dinucleotide step level, and provides an attractively concise, uniform and quantitative interpretation for various experimentally observed DNA sequence-dependent properties in terms of regular IBP H-bonds. It would provide a new approach to understanding the dynamics and underlying mechanisms of DNA sequence-dependent biological processes, sequence-structure-property relationships, DNA strand separation during replication and transcriptions, etc.
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Affiliation(s)
- Xu-Qing Li
- Department of Biomedical Engineering, Kunming University of Science and Technology, Kunming 650051, China.
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Electrochemical detection of aberrant methylated gene using naphthalene diimide derivative carrying four ferrocene moieties. J Organomet Chem 2010. [DOI: 10.1016/j.jorganchem.2010.04.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Klump H. Experimental Evaluation of the B-DNA → Z-DNA Transition: Energetics of a Reversible, Thermally Induced Helix/Helix Transition of Poly dG-m5dC in Physiological Mg2± Concentrations. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19860900512] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Zulkefeli M, Sogon T, Takeda K, Kimura E, Aoki S. Design and synthesis of a stable supramolecular trigonal prism formed by the self-assembly of a linear tetrakis(Zn2+-cyclen) complex and trianionic trithiocyanuric acid in aqueous solution and its complexation with DNA (cyclen = 1,4,7,10-tetraazacyclododecane). Inorg Chem 2010; 48:9567-78. [PMID: 19743814 DOI: 10.1021/ic901407d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new supramolecular complex, {(Zn(4)L(4))(3)-(TCA(3-))(4)}(12+), was designed and synthesized by the 3:4 self-assembly of a linear tetrakis(Zn(2+)-cyclen) complex (Zn(4)L(4))(8+) and trianionic trithiocyanurate (TCA(3-)) in aqueous solution (cyclen = 1,4,7,10-tetraazacyclododecane). The {(Zn(4)L(4))(3)-(TCA(3-))(4)}(12+) complex, which should have a trigonal prism configuration, was found to be very stable in aqueous solution at neutral pH and 25 degrees C, as evidenced by (1)H NMR titration, potentiometric pH and UV titrations, and MS measurements. The complex does not dissociate into the starting building blocks in the presence of Zn(2+)-binding anions such as phosphates and double-stranded DNA. The results of the competitive binding assays with ethidium bromide and calf-thymus DNA, thermal melting experiments, gel mobility shift assays, and dynamic light-scattering data strongly indicated that the trigonal prism functions as a polycationic template to induce the aggregation of double-stranded DNA.
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Affiliation(s)
- Mohd Zulkefeli
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510 Japan
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Schilter D, Urathamakul T, Beck JL, Harding MM, Rendina LM. ESI-MS and thermal melting studies of nanoscale platinum(ii) metallomacrocycles with DNA. Dalton Trans 2010; 39:11263-71. [DOI: 10.1039/c0dt00754d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Alexandrov BS, Gelev V, Yoo SW, Alexandrov LB, Fukuyo Y, Bishop AR, Rasmussen KØ, Usheva A. DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation. Nucleic Acids Res 2009; 38:1790-5. [PMID: 20019064 PMCID: PMC2847213 DOI: 10.1093/nar/gkp1084] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We assess the role of DNA breathing dynamics as a determinant of promoter strength and transcription start site (TSS) location. We compare DNA Langevin dynamic profiles of representative gene promoters, calculated with the extended non-linear PBD model of DNA with experimental data on transcription factor binding and transcriptional activity. Our results demonstrate that DNA dynamic activity at the TSS can be suppressed by mutations that do not affect basal transcription factor binding–DNA contacts. We use this effect to establish the separate contributions of transcription factor binding and DNA dynamics to transcriptional activity. Our results argue against a purely ‘transcription factor-centric’ view of transcription initiation, suggesting that both DNA dynamics and transcription factor binding are necessary conditions for transcription initiation.
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Affiliation(s)
- Boian S Alexandrov
- Los Alamos National Laboratory, Theoretical Division and Center for Nonlinear Studies, Los Alamos, NM, USA
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43
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Pressure-induced helix–coil transition of DNA copolymers is linked to water activity. Biophys Chem 2009; 144:62-6. [DOI: 10.1016/j.bpc.2009.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 06/17/2009] [Accepted: 06/17/2009] [Indexed: 11/18/2022]
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44
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Manono J, Marzilli PA, Marzilli LG. New Porphyrins Bearing Positively Charged Peripheral Groups Linked by a Sulfonamide Group to meso-Tetraphenylporphyrin: Interactions with Calf Thymus DNA. Inorg Chem 2009; 48:5636-47. [DOI: 10.1021/ic900385y] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Janet Manono
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Patricia A. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Luigi G. Marzilli
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
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Alexandrov BS, Gelev V, Yoo SW, Bishop AR, Rasmussen KØ, Usheva A. Toward a detailed description of the thermally induced dynamics of the core promoter. PLoS Comput Biol 2009; 5:e1000313. [PMID: 19282962 PMCID: PMC2645506 DOI: 10.1371/journal.pcbi.1000313] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 01/30/2009] [Indexed: 11/19/2022] Open
Abstract
Establishing the general and promoter-specific mechanistic features of gene transcription initiation requires improved understanding of the sequence-dependent structural/dynamic features of promoter DNA. Experimental data suggest that a spontaneous dsDNA strand separation at the transcriptional start site is likely to be a requirement for transcription initiation in several promoters. Here, we use Langevin molecular dynamic simulations based on the Peyrard-Bishop-Dauxois nonlinear model of DNA (PBD LMD) to analyze the strand separation (bubble) dynamics of 80-bp-long promoter DNA sequences. We derive three dynamic criteria, bubble probability, bubble lifetime, and average strand separation, to characterize bubble formation at the transcriptional start sites of eight mammalian gene promoters. We observe that the most stable dsDNA openings do not necessarily coincide with the most probable openings and the highest average strand displacement, underscoring the advantages of proper molecular dynamic simulations. The dynamic profiles of the tested mammalian promoters differ significantly in overall profile and bubble probability, but the transcriptional start site is often distinguished by large (longer than 10 bp) and long-lived transient openings in the double helix. In support of these results are our experimental transcription data demonstrating that an artificial bubble-containing DNA template is transcribed bidirectionally by human RNA polymerase alone in the absence of any other transcription factors. Accessing the information encoded in DNA requires that RNA polymerases recognize the core promoter, a sequence that marks the start of a gene. Statistical analysis of known promoter sequences has failed to reveal a simple code for identifying promoters, leading to the suggestion that promoter DNA is distinguished by certain structural/dynamic properties encoded in nonobvious ways by the literal sequence. Because the DNA strands at the promoter need to be separated for transcription to begin, we previously proposed that promoter sequences exhibit a propensity for spontaneous strand separation. Here, we conduct simulations of the ultrafast, small-scale strand separation motions of eight mammalian promoters and show that start sites tend to form larger and more stable openings in the double helix compared to other sequences. Experimentally, we show that an artificial permanent opening in the double helix is sufficient for transcription in the absence of sequence-specific protein–DNA contacts. These findings support a view of DNA as a structurally active participant in gene expression, rather than the commonly envisioned passive digital storage device. Our analysis suggests that functionally relevant structural variation in genomic DNA occurs at the level of fast motions not readily observed by traditional molecular structure analysis.
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Affiliation(s)
- Boian S. Alexandrov
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Vladimir Gelev
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sang Wook Yoo
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alan R. Bishop
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Kim Ø. Rasmussen
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anny Usheva
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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46
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Alexandrov BS, Gelev V, Monisova Y, Alexandrov LB, Bishop AR, Rasmussen KØ, Usheva A. A nonlinear dynamic model of DNA with a sequence-dependent stacking term. Nucleic Acids Res 2009; 37:2405-10. [PMID: 19264801 PMCID: PMC2673413 DOI: 10.1093/nar/gkp016] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
No simple model exists that accurately describes the melting behavior and breathing dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially true for homogenous and periodic DNA sequences, which exhibit large deviations in melting temperature from predictions made by additive thermodynamic contributions. Currently, no method exists for analysis of the DNA breathing dynamics of repeats and of highly G/C- or A/T-rich regions, even though such sequences are widespread in vertebrate genomes. Here, we extend the nonlinear Peyrard-Bishop-Dauxois (PBD) model of DNA to include a sequence-dependent stacking term, resulting in a model that can accurately describe the melting behavior of homogenous and periodic sequences. We collect melting data for several DNA oligos, and apply Monte Carlo simulations to establish force constants for the 10 dinucleotide steps (CG, CA, GC, AT, AG, AA, AC, TA, GG, TC). The experiments and numerical simulations confirm that the GG/CC dinucleotide stacking is remarkably unstable, compared with the stacking in GC/CG and CG/GC dinucleotide steps. The extended PBD model will facilitate thermodynamic and dynamic simulations of important genomic regions such as CpG islands and disease-related repeats.
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Affiliation(s)
- Boian S Alexandrov
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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47
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Nakabayashi Y, Inada H, Minoura Y, Iwamoto N, Yamauchi O. Effects of flexible bridging ligands on DNA-binding of dinuclear ruthenium(II)-2,2′-bipyridine complexes. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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48
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Taima H, Yoshioka N, Inoue H. Synthesis and DNA-binding properties of water-soluble cationic pyropheophorbides derived from chlorophyll a/b. Org Biomol Chem 2009; 7:1176-83. [DOI: 10.1039/b819700h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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49
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Airoldi M, Gennaro G, Giomini M, Giuliani AM, Giustini M. Circular dichroism of polynucleotides: Interactions of NiCl2 with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC) in a water-in-oil microemulsion. Chirality 2008; 20:951-60. [PMID: 18246552 DOI: 10.1002/chir.20531] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The thermal behavior of the synthetic, high molecular weight, double stranded polynucleotides poly(dA-dT).poly(dA-dT) [polyAT] and poly(dG-dC).poly(dG-dC) [polyGC] solubilized in the aqueous core of the quaternary water-in-oil cationic microemulsion CTAB|n-pentanol|n-hexane|water in the presence of increasing amounts of NiCl(2) at several constant ionic strength values (NaCl) has been studied by means of circular dichroism and electronic absorption spectroscopies. In the microemulsive medium, both polynucleotides show temperature-induced modifications that markedly vary with both Ni(II) concentration and ionic strength. An increase of temperature causes denaturation of the polyAT duplex at low nickel concentrations, while more complex CD spectral modifications are observed at higher nickel concentrations and ionic strengths. By contrast, thermal denaturation is never observed for polyGC. At low Ni(II) concentrations, the increase of temperature induces conformational transitions from B-DNA to Z-DNA form, or, more precisely, to left-handed helical structures. In some cases, at higher nickel concentrations, the CD spectra suggest the presence of Z'-type forms of the polynucleotide.
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Affiliation(s)
- Marta Airoldi
- Dipartimento di Chimica Inorganica e Analitica Stanislao Cannizzaro, Università di Palermo, 90128 Palermo, Italy
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Whan RM, Messerle BA, Hambley TW. Binding of [Pt(1C3)(dien)](2+) to the duplex DNA oligonucleotide 5'-d(TGGCCA)-3': the effect of an appended positive charge on the orientation and location of anthraquinone intercalation. Dalton Trans 2008:932-9. [PMID: 19173075 DOI: 10.1039/b814604g] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The binding of a platinum intercalator complex [Pt(1C3)(dien)](2+) (1C3 = 1-[(3-aminopropyl)amino]-anthracene-9,10-dione, dien = 3-azapentane-1,5-diamine) to DNA and to the self-complementary oligonucleotide 5'-d(TGGCCA)-3' has been investigated by UV-visible spectrophotometry and 2D NMR spectroscopy, respectively. The uncomplexed anthraquinone, 1C3, has an apparent DNA binding constant of 1.4 x 10(4), similar to that of ethidium bromide. Addition of the coordinatively saturated {Pt(dien)} moiety increases the binding constant to 3.7 x 10(5) M(-1), showing the effect of the increased positive charge introduced by this moiety. Multiple binding modes are evident from the lack of isosbestic points in the titration spectra and the non-linear nature of the half-reciprocal plot used to calculate the binding constant. [Pt(1C3)(dien)](2+) forms a 2 : 1 adduct with 5'-d(TGGCCA)-3' and is shown by 2D NMR to intercalate primarily in the TG:CA base pairs at the ends of the oligonucleotide with the side chain and {Pt(dien)} situated in the minor groove.
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Affiliation(s)
- Renee M Whan
- School of Chemistry, The University of Sydney, NSW, 2006, Australia
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