cis-[Pt(NH3)2]2+ coordination to the N7 and O6 sites of a guanine–cytosine pair: disruption of the Watson–Crick H-bonding pattern

Pelmenschikov, Alexander; Zilberberg, Igor L.; Leszczyński, Jerzy; Famulari, Antonino; Sironi, Maurizio; Raimondi, Mario

doi:10.1016/s0009-2614(99)01156-2

Cited by 47 publications

(31 citation statements)

References 24 publications

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“…[ 40,67,68] The trinucleotides show a similar trend, but here the difference in binding energy between cisGpGpG bi and cisGpApG bi is only 2 kcal mol À1 . To rationalise these differences, we turn to AIM analysis for decomposition into covalent bonding, H-bonding and p-stacking effects.…”

Section: Resultsmentioning

confidence: 78%

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: Resultsmentioning

confidence: 78%

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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“…Distortion of a proper DNA structure is also induced by stabilization of rare guanine tautomers caused by metal cations [13,14] and formation of non-Watson-Crick base pairs [15,16]. Metal ions can also weaken [17,18], and in some cases even disrupt [19], one or more hydrogen bonds in the base pairs and stabilize non-canonical structures of nucleic acids [20]. Such interactions between metal cations and nucleobases can be direct or solvent-mediated [21].…”

Section: Introductionmentioning

confidence: 99%

Aromaticity of H-bonded and metal complexes of guanine tautomers

2015

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) on structural and p-electron delocalization changes in four most stable guanine tautomers and their structural subunits has been studied in the gas phase using the B3LYP/6-311??G(2d,2p) computational level. In both cases, i.e., H-bonding and metal complexation, the strongest interactions are found in bifurcated complexes of the keto guanine tautomers. Interactions in which the functional groups participate (NH 2 or C=O) regularly lead to the greatest geometric and aromaticity changes. As a consequence, aromaticity of substituted six-membered rings is decisive for aromaticity of whole ring system in guanine tautomers. Aromaticity of guanine tautomers and their structural subunits changes in the same way (increase or decrease) depending on particular type of interactions. Graphical Abstract

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“…Cisplatin has attracted interest in recent years mainly due to its novel chemical behavior and potential applications. Numerous experimental [7][8][9][10] and theoretical [11][12][13][14] investigations on the molecular properties and the mechanism of action of cisplatin have been reported.…”

Section: Introductionmentioning

confidence: 99%

Density functional theory calculations on the molecular structures and vibration spectra of platinum(II) antitumor drugs

Gao

Xia

Chang-jiang

et al. 2011

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

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cis-[Pt(NH3)2]2+ coordination to the N7 and O6 sites of a guanine–cytosine pair: disruption of the Watson–Crick H-bonding pattern

Cited by 47 publications

References 24 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

Aromaticity of H-bonded and metal complexes of guanine tautomers

Density functional theory calculations on the molecular structures and vibration spectra of platinum(II) antitumor drugs

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