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Khalid S, Rodger P. Molecular Dynamics Simulations of Dna and Its Complexes. PROGRESS IN REACTION KINETICS AND MECHANISM 2019. [DOI: 10.3184/007967404777726232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA–ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands—including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.
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Affiliation(s)
- Syma Khalid
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Current address: Laboratory of Molecular Biophysics, University of Oxford, South Parks Rd, Oxford, OX1 3QU, UK
| | - P.Mark Rodger
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
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Arias-Gonzalez JR. Single-molecule portrait of DNA and RNA double helices. Integr Biol (Camb) 2015; 6:904-25. [PMID: 25174412 DOI: 10.1039/c4ib00163j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The composition and geometry of the genetic information carriers were described as double-stranded right helices sixty years ago. The flexibility of their sugar-phosphate backbones and the chemistry of their nucleotide subunits, which give rise to the RNA and DNA polymers, were soon reported to generate two main structural duplex states with biological relevance: the so-called A and B forms. Double-stranded (ds) RNA adopts the former whereas dsDNA is stable in the latter. The presence of flexural and torsional stresses in combination with environmental conditions in the cell or in the event of specific sequences in the genome can, however, stabilize other conformations. Single-molecule manipulation, besides affording the investigation of the elastic response of these polymers, can test the stability of their structural states and transition models. This approach is uniquely suited to understanding the basic features of protein binding molecules, the dynamics of molecular motors and to shedding more light on the biological relevance of the information blocks of life. Here, we provide a comprehensive single-molecule analysis of DNA and RNA double helices in the context of their structural polymorphism to set a rigorous interpretation of their material response both inside and outside the cell. From early knowledge of static structures to current dynamic investigations, we review their phase transitions and mechanochemical behaviour and harness this fundamental knowledge not only through biological sciences, but also for Nanotechnology and Nanomedicine.
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Affiliation(s)
- J Ricardo Arias-Gonzalez
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), Calle Faraday no. 9, Cantoblanco, 28049 Madrid, Spain.
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Wen LN, Xie MX. Evidence of different G-quadruplex DNA binding with biogenic polyamines probed by electrospray ionization-quadrupole time of flight mass spectrometry, circular dichroism and atomic force microscopy. Biochimie 2013; 95:1185-95. [PMID: 23352964 DOI: 10.1016/j.biochi.2013.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/14/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Li-Na Wen
- Analytical & Testing Center of Beijing Normal University, Xinjiekouwaidajie No. 19, Beijing 100875, People's Republic of China
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Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint. Biochem J 2013; 451:439-51. [DOI: 10.1042/bj20121761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hammerhead ribozyme is a versatile tool for down-regulation of gene expression in vivo. Owing to its small size and high activity, it is used as a model for RNA structure–function relationship studies. In the present paper we describe a new extended hammerhead ribozyme HH-2 with a tertiary stabilizing motif constructed on the basis of the tetraloop receptor sequence. This ribozyme is very active in living cells, but shows low activity in vitro. To understand it, we analysed tertiary structure models of substrate–ribozyme complexes. We calculated six unique catalytic core geometry parameters as distances and angles between particular atoms that we call the ribozyme fingerprint. A flanking sequence and tertiary motif change the geometry of the general base, general acid, nucleophile and leaving group. We found almost complete correlation between these parameters and the decrease of target gene expression in the cells. The tertiary structure model calculations allow us to predict ribozyme intracellular activity. Our approach could be widely adapted to characterize catalytic properties of other RNAs.
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Pavan GM, Kostiainen MA, Danani A. Computational Approach for Understanding the Interactions of UV-Degradable Dendrons with DNA and siRNA. J Phys Chem B 2010; 114:5686-93. [DOI: 10.1021/jp911439q] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Giovanni M. Pavan
- Mathematical and Physical Sciences Research Unit (SMF), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| | - Mauri A. Kostiainen
- Mathematical and Physical Sciences Research Unit (SMF), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
| | - Andrea Danani
- Mathematical and Physical Sciences Research Unit (SMF), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Institute for Molecules and Materials, Radboud University Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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Ziebarth J, Wang Y. Molecular dynamics simulations of DNA-polycation complex formation. Biophys J 2009; 97:1971-83. [PMID: 19804728 DOI: 10.1016/j.bpj.2009.03.069] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 03/06/2009] [Accepted: 03/30/2009] [Indexed: 10/20/2022] Open
Abstract
Complexes formed from DNA and polycations are of interest because of their potential use in gene therapy; however, there remains a lack of understanding of the structure and formation of DNA-polycation complexes at atomic scale. In this work, molecular dynamics simulations of the DNA duplex d(CGCGAATTCGCG) in the presence of polycation chains are carried out to shed light on the specific atomic interaction that result in complex formation. The structures of complexes formed from DNA with polyethylenimine, which is considered one of the most promising DNA vector candidates, and a second polycation, poly-L-lysine, are compared. After an initial separation of approximately 50 A, the DNA and polycation come together and form a stable complex within 10 ns. The DNA does not undergo any major structural changes on complexation and remains in the B-form. In the formed complex, the charged amine groups of the polycation mainly interact with DNA phosphate groups, with polycation intrusion into the major and minor grooves dependent on the identity and charge state of the polycation. The ability of the polycation to effectively neutralize the charge of the DNA phosphate groups and the resulting influence on the DNA helix interaction are discussed.
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Affiliation(s)
- Jesse Ziebarth
- Department of Chemistry, The University of Memphis, Memphis, Tennessee, USA
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Pavan GM, Danani A, Pricl S, Smith DK. Modeling the Multivalent Recognition between Dendritic Molecules and DNA: Understanding How Ligand “Sacrifice” and Screening Can Enhance Binding. J Am Chem Soc 2009; 131:9686-94. [DOI: 10.1021/ja901174k] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Giovanni M. Pavan
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - Andrea Danani
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - Sabrina Pricl
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
| | - David K. Smith
- Molecular Simulations Engineering (MOSE) Laboratory, Department of Chemical Engineering (DICAMP), University of Trieste, Piazzale Europa 1, 34127 Trieste, Italy, Institute of Computer Integrated Manufacturing for Sustainable Innovation (ICIMSI), University for Applied Sciences of Southern Switzerland (SUPSI), Centro Galleria 2, Manno, CH-6928, Switzerland, and Department of Chemistry, University of York, Heslington, York, YO10 5DD, U.K
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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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Chapter 6 Molecular Modeling and Atomistic Simulation of Nucleic Acids. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/s1574-1400(05)01006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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Ouameur AA, Tajmir-Riahi HA. Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis. J Biol Chem 2004; 279:42041-54. [PMID: 15284235 DOI: 10.1074/jbc.m406053200] [Citation(s) in RCA: 232] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Biogenic polyamines, such as putrescine, spermidine, and spermine are small organic polycations involved in numerous diverse biological processes. These compounds play an important role in nucleic acid function due to their binding to DNA and RNA. It has been shown that biogenic polyamines cause DNA condensation and aggregation similar to that of inorganic cobalt(III)hexamine cation, which has the ability to induce DNA conformational changes. However, the nature of the polyamine.DNA binding at the molecular level is not clearly established and is the subject of much controversy. In the present study the effects of spermine, spermidine, putrescine, and cobalt(III)hexamine on the solution structure of calf-thymus DNA were investigated using affinity capillary electrophoresis, Fourier transform infrared, and circular dichroism spectroscopic methods. At low polycation concentrations, putrescine binds preferentially through the minor and major grooves of double strand DNA, whereas spermine, spermidine, and cobalt(III)hexamine bind to the major groove. At high polycation concentrations, putrescine interaction with the bases is weak, whereas strong base binding occurred for spermidine in the major and minor grooves of DNA duplex. However, major groove binding is preferred by spermine and cobalt(III)hexamine cations. Electrostatic attractions between polycation and the backbone phosphate group were also observed. No major alterations of B-DNA were observed for biogenic polyamines, whereas cobalt(III)hexamine induced a partial B --> A transition. DNA condensation was also observed for cobalt(III)hexamine cation, whereas organic polyamines induced duplex stabilization. The binding constants calculated for biogenic polyamines are K(Spm) = 2.3 x 10(5) M(-1), K(Spd) = 1.4 x 10(5) M(-1), and K(Put) = 1.02 x 10(5) M(-1). Two binding constants have been found for cobalt(III)hexamine with K(1) = 1.8 x 10(5) M(-1) and K(2) = 9.2 x 10(4) M(-1). The Hill coefficients indicate a positive cooperativity binding for biogenic polyamines and a negative cooperativity for cobalt(III)hexamine.
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Affiliation(s)
- Amin Ahmed Ouameur
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
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Abstract
In moving towards the simulation of larger nucleic acid assemblies over longer timescales that include more accurate representations of the environment, we are nearing the end of an era characterized by single nanosecond molecular dynamics simulation of nucleic acids. We are excited by the promise and predictability of the modeling methods, yet remain prudently cautious of sampling and force field limitations. Highlights include the accurate representation of subtle drug-DNA interactions, the detailed study of modified and unusual nucleic acid structures, insight into the influence of dynamics on the structure of DNA, and exploration of the interaction of solvent and ions with nucleic acids.
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Affiliation(s)
- Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah, 2000 East, 30 South, Skaggs Hall 201, Salt Lake City, Utah 84112, USA.
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