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Veclani D, Tolazzi M, Cerón-Carrasco JP, Melchior A. Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action. J Chem Inf Model 2021; 61:4391-4399. [PMID: 34156233 PMCID: PMC8479807 DOI: 10.1021/acs.jcim.1c00430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Phenanthriplatin
(PtPPH) is a monovalent platinum(II)-based complex
with a large cytotoxicity against cancer cells. Although the aqua-activated
drug has been assumed to be the precursor for DNA damage, it is still
under debate whether the way in which that metallodrug attacks to
DNA is dominated by a direct binding to a guanine base or rather by
an intercalated intermediate product. Aiming to capture the mechanism
of action of PtPPH, the present contribution used theoretical tools
to systematically assess the sequence of all possible mechanisms on
drug activation and reactivity, for example, hydrolysis, intercalation,
and covalent damage to DNA. Ab initio quantum mechanical
(QM) methods, hybrid QM/QM′ schemes, and independent gradient
model approaches are implemented in an unbiased protocol. The performed
simulations show that the cascade of reactions is articulated in three
well-defined stages: (i) an early and fast intercalation of the complex
between the DNA bases, (ii) a subsequent hydrolysis reaction that
leads to the aqua-activated form, and (iii) a final formation of the
covalent bond between PtPPH and DNA at a guanine site. The permanent
damage to DNA is consequently driven by that latter bond to DNA but
with a simultaneous π–π intercalation of the phenanthridine
into nucleobases. The impact of the DNA sequence and the lateral backbone
was also discussed to provide a more complete picture of the forces
that anchor the drug into the double helix.
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Affiliation(s)
- Daniele Veclani
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - Marilena Tolazzi
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - José P Cerón-Carrasco
- Reconocimiento y Encapsulación Molecular, Universidad Católica San Antonio de Murcia (UCAM). Campus de los Jerónimos, 30107 Murcia, Spain
| | - Andrea Melchior
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
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2
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Stacking of nucleic acid bases: optimization of the computational approach—the case of adenine dimers. Struct Chem 2018. [DOI: 10.1007/s11224-018-1253-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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3
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Zabardasti A, Abbasi Tyula Y, Goudarziafshar H. Theoretical investigation of molecular interactions between sulfur ylide and hypohalous acids (HOX, X═F, Cl, Br, and I). J Sulphur Chem 2016. [DOI: 10.1080/17415993.2016.1246551] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - Hamid Goudarziafshar
- Department of Chemistry, Faculty of Science Sayyed Jamaleddinasadabadi University, Asadabad, Iran
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4
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Cysewski P, Oliński R. Structural, electronic and energetic consequences of epigenetic cytosine modifications. Phys Chem Chem Phys 2015; 17:19616-24. [PMID: 26151626 DOI: 10.1039/c5cp02188j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen bonding patterns of cytosine and its seven C5-modifed analogues paired with canonical guanine were studied using the first principle approach. Both global minima and biologically relevant conformations were studied. The former resulted from full gradient geometry optimizations of hydrogen bonded pairs, while the latter were obtained based on 125 d(GpC) dinucleotides found in the PDB database. The obtained energetic, electronic and structural data lead to the conclusion that the epigenetically relevant modification of cytosine may have serious consequences on hydrogen bonding with guanine. First of all, the significant substituent effects were observed for such trends as charges on sites involved in hydrogen bonding, the total intermolecular interaction energy or electron densities at bond critical points. Moreover, the molecular orbital polarization contribution resulting from energy decomposition expressed in terms of absolutely localized molecular orbitals exhibited an inverse linear correlation with frozen density contributions. A substituent effect on the amount of charge transfer from pyrimidine toward guanine was also observed. The increase of intermolecular interactions of guanine with modified cytosine is associated with the increase of the electro-donating character of the C5-substituent. However, only pairs involving 5-methylcytosine are more stable than those formed by canonical cytosine. Furthermore, the energy differences observed for global minima also remain important for a broad range of displacement and angular parameters defining pair conformations in model d(GpC) dinucleotides. Due to the sensitivities of intermolecular interactions to mutual arrangements of monomers the modification of cytosine at the C5 site can significantly alter the actual energy profiles. Consequently, it may be anticipated that the modified dinucleotides will adopt different conformations than a standard G-C pair in a B-DNA double helix.
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Affiliation(s)
- P Cysewski
- Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Physical Chemistry Department, Kurpińskiego 5, Bydgoszcz, Poland.
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5
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Aakeröy CB, Wijethunga TK, Haj MA, Desper J, Moore C. The structural landscape of heteroaryl-2-imidazoles: competing halogen- and hydrogen-bond interactions. CrystEngComm 2014. [DOI: 10.1039/c4ce00803k] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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Misiaszek T, Czyżnikowska Ż. The nature of interactions in nicotinamide crystal. J Mol Graph Model 2014; 51:73-8. [PMID: 24863341 DOI: 10.1016/j.jmgm.2014.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 11/27/2022]
Abstract
In this study, we analyze the nature of intermolecular interactions in nicotinamide complexes appearing in conformations found in the crystal structure, including many-body effects. In doing so, we employ symmetry-adapted perturbation theory based on density functional theory description of monomers, and we perform the many-body variational-perturbational interaction energy decomposition. The principal finding of this study is that the stability of nicotinamide complexes is a complicated interplay of four (large in magnitude) interaction-energy components, i.e. induction, dispersion, electrostatic and exchange repulsion. However, the last two contributions cancel each other out to a large extent. In the case of considered three-body complexes, the nonadditivity effects are found to be not important. Based on the results of topological analysis of charge densities we characterized also the properties of short H ⋯ H contact and identified it as a weak noncovalent closed shell interaction.
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Affiliation(s)
- Tomasz Misiaszek
- Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Żaneta Czyżnikowska
- Department of Inorganic Chemistry, Wrocław Medical University, Borowska 211, 50-556 Wrocław, Poland.
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7
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Competition between hydrogen bonds and halogen bonds in complexes of formamidine and hypohalous acids. J Mol Model 2013; 19:4529-35. [DOI: 10.1007/s00894-013-1969-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/30/2013] [Indexed: 01/28/2023]
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8
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Villani G. Theoretical investigation of the coupling between hydrogen-atom transfer and stacking interaction in adenine-thymine dimers. Chemphyschem 2013; 14:1256-63. [PMID: 23494877 DOI: 10.1002/cphc.201200971] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/07/2013] [Indexed: 12/13/2022]
Abstract
Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM-UOS Pisa, Area della Ricerca del CNR, Via G. Moruzzi 1, 56124 Pisa, Italy.
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9
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Theoretical study of molecular interactions of sulfur ylide with HSX (X = F, Cl, and Br) molecules. Struct Chem 2013. [DOI: 10.1007/s11224-013-0200-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Villani G. Theoretical investigation of the coupling between hydrogen atoms transfer and stacking interaction in guanine–cytosine dimers. Phys Chem Chem Phys 2013; 15:19242-52. [DOI: 10.1039/c3cp52855c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Banáš P, Mládek A, Otyepka M, Zgarbová M, Jurečka P, Svozil D, Lankaš F, Šponer J. Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics. J Chem Theory Comput 2012; 8:2448-60. [PMID: 26588974 DOI: 10.1021/ct3001238] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sequence-dependent local variations of helical parameters, structure, and flexibility are crucial for molecular recognition processes involving B-DNA. A-tracts, i.e., stretches of several consecutive adenines in one strand that are in phase with the DNA helical repeat, mediate significant DNA bending. During the past few decades, there have been intense efforts to understand the sequence dependence of helical parameters in DNA. Molecular dynamics (MD) simulations can provide valuable insights into the molecular mechanism behind the relationship between sequence and structure. However, although recent improvements in empirical force fields have helped to capture many sequence-dependent B-DNA properties, several problems remain, such as underestimation of the helical twist and suspected underestimation of the propeller twist in A-tracts. Here, we employ reference quantum mechanical (QM) calculations, explicit solvent MD, and bioinformatics to analyze the underestimation of propeller twisting of A-tracts in simulations. Although we did not identify a straightforward explanation, we discovered two imbalances in the empirical force fields. The first was overestimation of stacking interactions accompanied by underestimation of base-pairing energy, which we attribute to anisotropic polarizabilities that are not reflected by the isotropic force fields. This may lead to overstacking with potentially important consequences for MD simulations of nucleic acids. The second observed imbalance was steric clash between A(N1) and T(N3) nitrogens of AT base pairs in force-field descriptions, resulting in overestimation of the AT pair stretch in MD simulations. We also substantially extend the available set of benchmark estimated CCSD(T)/CBS data for B-DNA base stacking and provide a code that allows the generation of diverse base-stacking geometries suitable for QM computations with predefined intra- and interbase pair parameters.
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Affiliation(s)
- Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Daniel Svozil
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.,Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technicka 5, 166 28 Prague, Czech Republic
| | - Filip Lankaš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 6, 166 10 Prague, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, 625 00 Brno, Czech Republic
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Zabaradsti A, Kakanejadifard A, Ghasemian M. Theoretical study of molecular interactions of phosphorus ylide with hypohalous acids HOF, HOCl and HOBr. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Zabardasti A, Kakanejadifard A, Ghasemian M, Solimannejad M. Theoretical study of molecular interactions of phosphorus ylide with HF, HCN, and HN3. Struct Chem 2012. [DOI: 10.1007/s11224-011-9939-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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16
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Dailidonis VV, Danilov VI, Früchtl HA, van Mourik T. The nature of base stacking: a Monte Carlo study. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1046-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Maia FF, Freire VN, Caetano EWS, Azevedo DL, Sales FAM, Albuquerque EL. Anhydrous crystals of DNA bases are wide gap semiconductors. J Chem Phys 2011; 134:175101. [DOI: 10.1063/1.3584680] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Competition and cooperativity between hydrogen bond and halogen bond in HNC⋯(HOBr)n and (HNC)n⋯HOBr (n=1 and 2) systems. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.11.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Czyżnikowska Ż, Góra RW, Zaleśny R, Lipkowski P, Jarzembska KN, Dominiak PM, Leszczynski J. Structural Variability and the Nature of Intermolecular Interactions in Watson−Crick B-DNA Base Pairs. J Phys Chem B 2010; 114:9629-44. [DOI: 10.1021/jp101258q] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ż. Czyżnikowska
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - R. W. Góra
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - R. Zaleśny
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - P. Lipkowski
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - K. N. Jarzembska
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - P. M. Dominiak
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
| | - J. Leszczynski
- Theoretical Chemistry Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland; Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Jackson State University, 1400 J. R. Lynch St., Jackson, Mississippi 39217; and Department of Chemistry, Warsaw University, Pasteura 1, 02-093 Warsaw, Poland
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20
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Jing B, Li Q, Gong B, Cheng J, Li W, Liu Z. A theoretical analysis of the weakly bound complexes HM ··· HXY (M=O and S; XY=CN and NC): comparison with H2M ··· HXY complexes. Mol Phys 2010. [DOI: 10.1080/00268976.2010.489518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Svozil D, Hobza P, Sponer J. Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations? J Phys Chem B 2010; 114:1191-203. [PMID: 20000584 DOI: 10.1021/jp910788e] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
High level ab initio methods have been used to study stacking interactions in ten unique base pair steps both in A-RNA and in B-DNA duplexes. The protocol for selection of geometries based on molecular dynamics (MD) simulations is proposed, and its suitability is demonstrated by comparison with stacking in steps at fiber diffraction geometries. It is shown that fiber diffraction geometries are not sufficiently accurate for interaction energy calculations. In addition, the protocol for selection of geometries based on MD simulations allows for the evaluation of the variability of the intrinsic stacking energies along the MD trajectories. The uncertainty in stacking energies (difference between the most and least stable geometry) due to the dynamical nature of systems can be, in some cases, as large as 3.0 kcal x mol(-1), which is almost 50% of the actual sequence dependence of base stacking energies (the energy difference between the most and least stable sequences). Thus, assessing the relative magnitude of the gas phase stacking energy using a single geometry for each sequence is insufficient to obtain an unambiguous order of gas phase stacking energies in canonical double helices. Though the ordering of ten unique dinucleotide steps cannot be definitive, some general conclusions were drawn. The stacking energies of base pair steps in A-RNA are more evenly separated compared to B-DNA, and their ordering is less sensitive to the dynamics of the system compared to be B-DNA. The most stable step both in B-DNA and A-RNA is the GC/GC [corrected] step that is well separated from the second most stable step CG/CG. [corrected] Also the least stable step (the CC/GG step) is well separated from the rest of the structures. The calculations further show that B-DNA stacking is favorable only marginally (on average by 1.14 kcal x mol(-1) per base pair step) over A-RNA stacking, and this difference vanishes after subtracting the stabilizing van der Waals effect of the thymine 5-methyl group that is absent in RNA. Basically, no correlation between the sequence dependence of gas phase stacking energies and the sequence dependence of DeltaG degrees(37) free energies used in nearest-neighbor models was found either for B-DNA or for A-RNA. This reflects the complexity of the balance of forces that are responsible for the sequence dependence of thermodynamics stability of nucleic acids, which masks the effect of the intrinsic interactions between the stacked base pairs.
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Affiliation(s)
- Daniel Svozil
- Faculty of Chemical Technology, Laboratory of Informatics and Chemistry, Institute of Chemical Technology, Technická 3, 166 28, Prague 6, Czech Republic.
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Czyznikowska Z. How does modification of adenine by hydroxyl radical influence the stability and the nature of stacking interactions in adenine-cytosine complex? J Mol Model 2009; 15:615-22. [PMID: 19198902 DOI: 10.1007/s00894-008-0447-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Accepted: 12/16/2008] [Indexed: 11/28/2022]
Abstract
This study reports on ab initio calculations of adenine-cytosine complexes in two different context alignments appearing in B-DNA. The influence of adenine modification by hydroxyl radical on the stability of the complexes is also discussed. The analysis was performed on over 40 crystallographic structures for each of the sequence contexts. In most cases, modification of adenine by hydroxyl radical leads to less negative intermolecular interaction energies. The issue of the influence of alteration of structural base step parameters on the stability of modified and unmodified adenine-cytosine complexes is also addressed. Analysis of the dependence of intermolecular interaction energy on base step parameters reveals that for twist and shift modification of adenine by hydroxyl radical leads to quite different interaction energy profiles in comparison with unmodified complexes. In order to elucidate the physical origins of this phenomenon, i.e. to analyze how the modification of adenine by hydroxyl radical is reflected in the change of intermolecular interaction energy components, a variational-perturbational decomposition scheme was applied at the MP2/aug-cc-pVDZ level of theory.
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Affiliation(s)
- Zaneta Czyznikowska
- Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Jagiellonska 13-15, 85-067 Bydgoszcz, Poland.
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Czyznikowska Z, Zaleśny R. Theoretical insights into the nature of intermolecular interactions in cytosine dimer. Biophys Chem 2008; 139:137-43. [PMID: 19038487 DOI: 10.1016/j.bpc.2008.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 11/03/2008] [Accepted: 11/04/2008] [Indexed: 10/21/2022]
Abstract
In this study we discuss stacking interactions in cytosine dimer in conformations appearing in B-DNA crystals. The variational-perturbational scheme was applied for decomposition of the intermolecular interaction energy at the MP2 level of theory. The significant influence of the mutual orientation of cytosine monomers was observed not only on the total intermolecular interaction energy but also on its components: Different components of intermolecular interaction energy depend in different manner on parameters describing mutual orientation of cytosine monomers.
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Affiliation(s)
- Zaneta Czyznikowska
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, 11635 Athens, Greece
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