The influence of a sugar-phosphate backbone on the cisplatin-bridged BpB? models of DNA purine bases. Quantum chemical calculations of Pt(ii) bonding characteristics

Zeizinger, Michal; Burda, Jaroslav V.; Leszczyński, Jerzy

doi:10.1039/b317052g

Cited by 46 publications

(27 citation statements)

References 50 publications

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“…2 + (B = guanine or adenine) [38] and found excellent agreement between B3LYP and experimental structures. Carloni et al [39] used Car-Parrinello molecular dynamics (MD) to investigate DNA-cisplatin interactions, and found close agreement between DFT and experiment, for example, in thermodynamic aspects of cisplatin hydrolysis.…”

Section: Cis-diamminodichloroplatinum(ii) (Cis-[ptcl 2 a C H T U N G mentioning

confidence: 50%

A QM/MM Study of Cisplatin–DNA Oligonucleotides: From Simple Models to Realistic Systems

Robertazzi

Platts

2006

Chemistry A European J

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QM/MM calculations were employed to investigate the role of hydrogen bonding and pi stacking in several single- and double-stranded cisplatin-DNA structures. Computed geometrical parameters reproduce experimental structures of cisplatin and its complex with guanine-phosphate-guanine. Following QM/MM optimisation, single-point DFT calculations allowed estimation of intermolecular forces through atoms in molecules (AIM) analysis. Binding energies of platinated single-strand DNA qualitatively agree with myriad experimental and theoretical studies showing that complexes of guanine are stronger than those of adenine. The topology of all studied complexes confirms that platination strongly affects the stability of both single- and double-stranded DNAs: Pt-N-H...X (X = N or O) interactions are ubiquitous in these complexes and account for over 70 % of all H-bonding interactions. The pi stacking is greatly reduced by both mono- and bifunctional complexation: the former causes a loss of about 3-4 kcal mol(-1), whereas the latter leads to more drastic disruption. The effect of platination on Watson-Crick GC is similar to that found in previous studies: major redistribution of energy occurs, but the overall stability is barely affected. The BH&H/AMBER/AIM approach was also used to study platination of a double-stranded DNA octamer d(CCTG*G*TCC)d(GGACCAGG), for which an experimental structure is available. Comparison between theory and experiment is satisfactory, and also reproduces previous DFT-based studies of analogous structures. The effect of platination is similar to that seen in model systems, although the effect on GC pairing was more pronounced. These calculations also reveal weaker, secondary interactions of the form Pt...O and Pt...N, detected in several single- and double-stranded DNA.

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Section: Cis-diamminodichloroplatinum(ii) (Cis-[ptcl 2 a C H T U N G mentioning

confidence: 50%

A QM/MM Study of Cisplatin–DNA Oligonucleotides: From Simple Models to Realistic Systems

Robertazzi

Platts

2006

Chemistry A European J

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“…This work can be considered as an extension of our previous studies on platinum activation [17,18,69,70] and platinum interaction with DNA bases and base pairs [71][72][73][74][75].…”

Section: Introductionmentioning

confidence: 96%

Cisplatin interaction with cysteine and methionine, a theoretical DFT study

Zimmermann

Zeizinger

Burda

2005

Journal of Inorganic Biochemistry

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“…This points to some kind of saturation of the electron donation to the vacant orbitals of the transition metal. We also saw this effect in some other calculations, which involved platinum [34,40], ruthenium [43], and copper [44] complexes. Also, the lower coordination energy of adenine in the diadenine complex in comparison with the mixed AG complex can be explained on the same basis.…”

Section: Energy Relations and Thermodynamicsmentioning

confidence: 84%

“…Contrary to cisplatin or the recently reported ''pianostool'' Ru(II) complexes [13,15,37,38], where only N7 coordination can occur, here two different sites (N7 and X6) are involved in the metal-base interaction. Thus not only the different polarizability or dipole moment can be used for the characterization of the differences between metal-base bondings [34,[39][40][41][42]. The stronger interaction of adenine can be explained by the stronger Rh-N6 dative bond in comparison with the Rh-O6 bond in guanine.…”

Section: Energy Relations and Thermodynamicsmentioning

confidence: 98%

The influence of a sugar-phosphate backbone on the cisplatin-bridged BpB? models of DNA purine bases. Quantum chemical calculations of Pt(ii) bonding characteristics

Cited by 46 publications

References 50 publications

A QM/MM Study of Cisplatin–DNA Oligonucleotides: From Simple Models to Realistic Systems

A QM/MM Study of Cisplatin–DNA Oligonucleotides: From Simple Models to Realistic Systems

Cisplatin interaction with cysteine and methionine, a theoretical DFT study

A computational study on DNA bases interactions with dinuclear tetraacetato-diaqua-dirhodium(II,II) complex

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