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Cisplatin GG-crosslinks within single-stranded DNA: origin of the preference for left-handed helicity. J Inorg Biochem 2012; 115:106-12. [PMID: 22947917 DOI: 10.1016/j.jinorgbio.2012.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/27/2012] [Accepted: 05/29/2012] [Indexed: 11/21/2022]
Abstract
Molecular dynamics (MD) simulations of the single-stranded DNA trinucleotide TG*G*, with the G* guanines crosslinked by the antitumor drug cisplatin, were performed with explicit representation of the water as solvent. The purpose of the simulations was to explain previous NMR observations indicating that in single-stranded cisplatin-DNA adducts, the crosslinked guanines adopt a left-handed helical orientation, whereas in duplexes, the orientation is right-handed. The analysis of the MD trajectory of TG*G* has ascribed a crucial role to hydrogen-bonding (direct or through-water) interactions of the 5'-oriented NH(3) ligand of platinum with acceptor groups at the 5'-side of the crosslink, namely the TpG* phosphate and the terminal 5'-OH group. These interactions bring about some strain into the trinucleotide which is slightly but significantly (1-1.5 kcal.mol(-1)) higher for the right-handed orientation than for the left-handed one. During the unconstrained, 3 ns long MD simulation, left-handed conformations were ~15 times more abundant than the right-handed ones. This sampling difference agrees roughly with the calculated energy difference in strain energy. Overall, these results show that the Pt-GG crosslink within single-stranded DNA is malleable and can access different conformations at a moderate energy cost. This malleability could be of importance in interactions between the platinated DNA and cellular proteins, in which the DNA is locally unwound.
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Over D, Bertho G, Elizondo-Riojas MA, Kozelka J. Fixing the conformations of diamineplatinum(II)-GpG chelates: NMR and CD signatures of individual rotamers. J Biol Inorg Chem 2006; 11:139-52. [PMID: 16429316 DOI: 10.1007/s00775-005-0058-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Accepted: 11/01/2005] [Indexed: 10/25/2022]
Abstract
The bulky, asymmetric analog of the antitumor drug cisplatin, [PtCl(2)(tmen)] (tmen = N,N,N'-trimethylethylenediamine), was used to produce crosslinks with the dinucleotide d(GpG), modeling the most frequent lesions that cisplatin and its analogs cause to DNA. The ligand tmen was chosen because it is expected to constrain the guanine cis to the NMe(2) group in the adduct [Pt(tmen){d(GpG)}](+) to an orientation perpendicular to the coordination plane and to stabilize the other guanine in an oblique orientation, thus maintaining a head-to-head geometry typical of cisplatin-d(GpG) crosslinks within single- and double-stranded DNA. Of the four possible combinations of tmen chirality (R or S symmetry of the coordinated NHMe group) and crosslink direction (5'-G bound cis to the secondary or the tertiary amino group of tmen), two isomers were preponderantly formed, [Pt(R-tmen){d(GpG)}](+) with 5'-G bound cis to NMe(2) and [Pt(S-tmen){d(GpG)}](+) with 5'-G bound cis to NHMe. The former was shown to have a right-handed R2 orientation of guanines similar to that found in duplex DNA, whereas the latter had a left-handed L1 orientation that modeled cisplatin-d(GpG) adducts within single-stranded DNA. The R2 rotamer was found to be in an equilibrium (as observed using EXSY spectroscopy) with a minor fraction (< or =4%) of a Delta-HT rotamer related to R2 by rotation of the 3'-G about the Pt-N7 bond. The major rotamers R2 and L1 were isolated using reverse-phase HPLC, and their NMR and CD signatures were compared to those of the corresponding rotamers of the less hindered adduct [Pt(dmen)(GpG)](+) (dmen = N,N-dimethylethylenediamine). From this and other comparisons with previously reported platinum dinucleotide complexes, and from molecular modeling, it could be concluded that both steric repulsion between guanine and substituents of the cis amino group and N-H...O6 hydrogen bonding are significant effects favoring the oblique orientation of one guanine base typical of the HH rotamers of [Pt(diamine){d(GpG)}](+) and [Pt(diamine)(GpG)](+) complexes.
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Affiliation(s)
- Diana Over
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université René Descartes, UMR 8601 CNRS, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
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Erxleben A, Metzger S, Britten JF, Lock CJ, Albinati A, Lippert B. Model of the most abundant DNA interstrand cross-link of Transplatin: X-ray structures of two modifications and H bonding behavior in the solid state and in solution of trans-[Pt(NH3)2(1-MeC-N3)(9-EtGH-N7)](ClO4)2·nH2O (1-MeC=1-methylcytosine; 9-EtGH=9-ethylguanine). Inorganica Chim Acta 2002. [DOI: 10.1016/s0020-1693(02)00955-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Šponer JE, Glahé F, Leszczynski J, Lippert B, Šponer J. How Nucleobases Rotate When Bonded to a Metal Ion: Detailed View from an Ab Initio Quantum Chemical Study of a Cytosine Complex of trans-a2PtII. J Phys Chem B 2001. [DOI: 10.1021/jp012795h] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Judit E. Šponer
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Frank Glahé
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Bernhard Lippert
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
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