Gas phase interaction of zinc ion with purine and pyrimidine DNA and RNA bases

Marino, Tiziana; Mazzuca, Donatella; Toscano, Marirosa; Russo, Nino; Grand, André

doi:10.1002/qua.21194

Cited by 21 publications

(15 citation statements)

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“…Zinc is one of the most abundant transition metals which is found in cytoplasm, and has a role in regulating genes 29. 30 Marino et al31 studied the interaction of zinc ion with purine and pyrimidine bases in the gas phase using DFT calculations. In the thymine and uracil cases, the lowest‐energy complexes are again bicoordinate rather than monocoordinate, and Zn 2+ is ligated by deprotonated N3 and the adjacent oxygen atom O4.…”

Section: Introductionmentioning

confidence: 93%

Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]⁺ Complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): Loss of Uracil versus HNCO

2012

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Complexes formed between metal dications, the conjugate base of uracil, and uracil are investigated by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) in a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Positive-ion electrospray spectra show that [M(Ura-H)(Ura)](+) (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd, Mg, Ca, Sr, Ba, or Pb) is the most abundant ion even at low concentrations of uracil. SORI-CID experiments show that the main primary decomposition pathway for all [M(Ura-H)(Ura)](+) , except where M=Ca, Sr, Ba, or Pb, is the loss of HNCO. Under the same SORI-CID conditions, when M is Ca, Sr, Ba, or Pb, [M(Ura-H)(Ura)](+) are shown to lose a molecule of uracil. Similar results were observed under infrared multiple-photon dissociation excitation conditions, except that [Ca(Ura-H)(Ura)](+) was found to lose HNCO as the primary fragmentation product. The binding energies between neutral uracil and [M(Ura-H)](+) (M=Zn, Cu, Ni, Fe, Cd, Pd ,Mg, Ca, Sr Ba, or Pb) are calculated by means of electronic-structure calculations. The differences in the uracil binding energies between complexes which lose uracil and those which lose HNCO are consistent with the experimentally observed differences in fragmentation pathways. A size dependence in the binding energies suggests that the interaction between uracil and [M(Ura-H)](+) is ion-dipole complexation and the experimental evidence presented supports this.

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Section: Introductionmentioning

confidence: 93%

Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]⁺ Complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): Loss of Uracil versus HNCO

2012

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“…Location shift (N1, O2, N3, and O4) for a hydrogen (H1 or H2) of T1 can create different rare tautomers (such as T3o4l, T3o4r, and T1o41 in Scheme ), which may cause base mispairing and spontaneous point mutations. The relative stability for T1 and its rare tautomers are influenced by the surrounding environment, such as solvent solution and interaction with metal ions, which received extensive attentions theoretically and experimentally. For example, Russo et al .…”

Section: Introductionmentioning

confidence: 99%

A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

Chen

Zhao

et al. 2011

J of Physical Organic Chem

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Stability orderings of 150 stable complexes formed by metal ions (Na+, K+, Ca2+, Mg2+, and Zn2+) and 13 stable thymine tautomers in both solvent and gas phases are obtained, and the optimal binding site for a metal ion in a specific thymine tautomer is identified. Results indicate that the complex with the canonical thymine tautomer (T1) is more stable than those with the rare ones, and the monodentate complex M–T1o4(o2) are their ground‐state form in the solvent phase. The ground‐state thymine complexes bound by Ca2+, Mg2+, or Zn2+ become bidentate M–T3o4lo2,n3, which is derived from a rare thymine tautomer T3o4l, whereas those bound by Na+ and K+ are still monodentate complexes M–T1o4(o2), however, in the gas phase. The differences in stability are discussed in detail from the binding strength of metal ions, relative energy of the corresponding thymine tautomers, and solution effect. Copyright © 2011 John Wiley & Sons, Ltd.

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“…Our purpose in this paper is not to analyze the small interactions, but to point out their noticeable weaknesses in these complexes. In fact, when two basic centers are near the metal, its association is favored as bi‐coordinate fashion as was found in zinc interactions with guanine, cytosine, and adenine 32. In the case of oxazolidine, the lone pairs of oxygen at position 1 are in resonance with the carbonyl group attached to position 2′ which markedly decreases its interaction with the incoming metal.…”

Section: Resultsmentioning

confidence: 93%

A theoretical density functional study of association of Zn²⁺ with oxazolidine and its thio derivatives in the gas phase

Safi

Lamsabhi

2010

J of Physical Organic Chem

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We have performed density functional theory (DFT) calculations in order to study the gas‐phase interaction of oxo‐ and thio‐oxazolidine derivatives with Zn2+. The calculations were performed at B3LYP/6‐311+(2df,2p) level of theory. It has been found, in all cases, that the direct association of Zn2+ with the carbonyl and thiocarbonyl groups takes place at the heteroatom attached to position 2 irrespective of its nature. This preference has been attributed to the resonance effects caused by the nearest heteroatoms (oxygen and nitrogen). The most stable complexes correspond to structures with Zn2+ bridging between the heteroatom at position 2 or 4 of the 4‐ or 2‐enol (or the 4‐ or 2‐enethiol) tautomer and the dehydrogenated ring nitrogen atom, N3. Zn2+ association has a clear catalytic effect on the tautomerization processes which connect the oxo–thione forms with the enol–enethiol tautomers. Hence, although the enol–enethiol tautomers of oxazolidine and its thio derivatives should not be observed in the gas phase, the corresponding Zn2+ complexes are the most stable species and should be accessible, because the tautomerization barriers are smaller than the Zn2+ binding energies. Copyright © 2010 John Wiley & Sons, Ltd.

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Gas phase interaction of zinc ion with purine and pyrimidine DNA and RNA bases

Cited by 21 publications

References 39 publications

Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]⁺ Complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): Loss of Uracil versus HNCO

Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]⁺ Complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): Loss of Uracil versus HNCO

A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

A theoretical density functional study of association of Zn²⁺ with oxazolidine and its thio derivatives in the gas phase

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Gas phase interaction of zinc ion with purine and pyrimidine DNA and RNA bases

Cited by 21 publications

References 39 publications

Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]+ Complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): Loss of Uracil versus HNCO

Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]+ Complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): Loss of Uracil versus HNCO

A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

A theoretical density functional study of association of Zn2+ with oxazolidine and its thio derivatives in the gas phase

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Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]⁺ Complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): Loss of Uracil versus HNCO

Primary Fragmentation Pathways of Gas Phase [M(Uracil−H)(Uracil)]⁺ Complexes (M=Zn, Cu, Ni, Co, Fe, Mn, Cd, Pd , Mg, Ca, Sr, Ba, and Pb): Loss of Uracil versus HNCO

A theoretical density functional study of association of Zn²⁺ with oxazolidine and its thio derivatives in the gas phase