Molecular modeling study on the binding mode of polypyridyl transition Ru metal complexes with B-DNA

Han, Daxiong; Wang, Haiyan; Ren, Nailin

doi:10.1016/j.theochem.2004.10.004

Cited by 12 publications

(5 citation statements)

References 20 publications

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“…The melting temperature corresponded to 47 8C and was increased by 2 8C in the presence of 1.5 mm of complex 1 (see Supporting Information). The T4 polynucleotide kinase was purchased from Pharmacia Biotech and the [g- 2 + complex, the non-Ru-labelled strand of the duplex was 32 P-labelled at the 5' extremity.…”

Section: Resultsmentioning

confidence: 99%

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A Rigid Dinuclear Ruthenium(II) Complex as an Efficient Photoactive Agent for Bridging Two Guanine Bases of a Duplex or Quadruplex Oligonucleotide

Rickling

Ghisdavu

Pierard

et al. 2010

Chemistry A European J

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The rigid dinuclear [(tap)(2)Ru(tpac)Ru(tap)(2)](4+) complex (1) (TAP=1,4,5,8-tetraazaphenanthrene, TPAC=tetrapyridoacridine) is shown to be much more efficient than the mononuclear bis-TAP complexes at photodamaging oligodeoxyribonucleotides (ODNs) containing guanine (G). This is particularly striking with the G-rich telomeric sequence d(T(2)AG(3))(4). Complex 1, which interacts strongly with the ODNs as determined by surface plasmon resonance (SPR) and emission anisotropy experiments, gives rise under illumination to the formation of covalent adducts with the G units of the ODNs. The yield of photocrosslinking of the two strands of duplexes by 1 is the highest when the G bases of each strand are separated by three to four base pairs. This corresponds with each Ru(tap)(2) moiety of complex 1 forming an adduct with the G base. This separation distance of the G units of a duplex could be determined thanks to the rigidity of complex 1. On the basis of results of gel electrophoresis, mass spectrometry, and molecular modelling, it is suggested that such photocrosslinking can also occur intramolecularly in the human telomeric quadruplex d(T(2)AG(3))(4).

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Section: Resultsmentioning

confidence: 99%

“…[32] Geometry optimisation was carried out by using the adopted basis Newton-Raphson algorithm with an RMS distance criterion of 10 À2 kcal mol À1 . Molecular dynamics (MD) simulations were performed in the canonical ensemble (N,V,T) with a time step of 1 fs.…”

Section: Molecular Mechanics and Molecular Dynamicsmentioning

confidence: 99%

A Rigid Dinuclear Ruthenium(II) Complex as an Efficient Photoactive Agent for Bridging Two Guanine Bases of a Duplex or Quadruplex Oligonucleotide

Rickling

Ghisdavu

Pierard

et al. 2010

Chemistry A European J

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“…For all of the simulations, the water solvent was implicitly taken into account via the use of the generalized Born model with a simple smoothing function . Several geometries and distances between the complexes and DNA were tested (similarly to the docking approach), and the evolution of the total energy was followed as a function of the distance . For energy minimization, the adopted basis Newton−Raphson algorithm was used with a rms distance of 10 −2 kcal/mol Å.…”

Section: Methodsmentioning

confidence: 99%

Oxidizing Ru(II) Complexes as Irreversible and Specific Photo-Cross-Linking Agents of Oligonucleotide Duplexes

et al. 2009

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Oxidizing polyazaaromatic Ru(II) complexes containing two TAP ligands (TAP = 1,4,5,8-tetraazaphenanthrene) are able under illumination to cross-link irreversibly the two strands of an oligonucleotide (ODN) duplex by covalent bond formation. The cross-linking proceeds by two successive absorptions of a photon. An adduct of the metallic complex on a guanine (G) base of one ODN strand is first photoproduced, followed by a second photoaddition of the same Ru species to a G base of the complementary strand, provided that the two G moieties are separated by 0 or 1 base pair. These two processes lead to the cross-linking of the two strands. Such a photo-cross-linking is easily detected with [Ru(TAP)(2)(phen)](2+) (1; phen = 1,10-phenanthroline) and [Ru(HAT)(2)(phen)](2+) (2; HAT = 1,4,5,8,9,12-hexaazatriphenylene), whereas it is not observed with [Ru(TAP)(2)TPAC](2+) (3; TPAC = tetrapyridoacridine) at the same level of loading of the duplex by 3. With a concentration of 3 similar to that of 1 and 2, when the loading of the duplex by 3 is much more important than with 1 and 2, the photo-cross-linking with 3 can thus also be observed. As 3 intercalates its TPAC ligand into the base pairs stack, its mobility is restricted in the duplex. In contrast, 1 and 2 can adopt different geometries of interaction, which probably facilitate the photo-cross-linking.

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“…Despite the large number of experimental studies reported on these complexes over the past 10 years, few theoretical studies have been performed. These studies have often focused either on structural or binding mode aspects [21,22] or on the nature and position of the lowlying triplet excited states. The spectroscopic calculations, based essentially on semi-empirical [22,23] or time-dependent density functional theory TD-DFT [24][25][26] approaches show that the low-lying MLCT states delocalized over the three ligands in the free complex are slightly red shifted and re-localize on the ancillary and dppz ligands upon binding to DNA.…”

Section: Introductionmentioning

confidence: 99%

A theoretical study of Ru(II) polypyridyl DNA intercalators

Ambrosek

Loos

Assfeld

et al. 2010

Journal of Inorganic Biochemistry

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Molecular modeling study on the binding mode of polypyridyl transition Ru metal complexes with B-DNA

Cited by 12 publications

References 20 publications

A Rigid Dinuclear Ruthenium(II) Complex as an Efficient Photoactive Agent for Bridging Two Guanine Bases of a Duplex or Quadruplex Oligonucleotide

A Rigid Dinuclear Ruthenium(II) Complex as an Efficient Photoactive Agent for Bridging Two Guanine Bases of a Duplex or Quadruplex Oligonucleotide

Oxidizing Ru(II) Complexes as Irreversible and Specific Photo-Cross-Linking Agents of Oligonucleotide Duplexes

A theoretical study of Ru(II) polypyridyl DNA intercalators

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