Matias Berdakin

Gas Phase Structure of Metal Mediated (Cytosine)2Ag+ Mimics the Hemiprotonated (Cytosine)2H+ Dimer in i-Motif Folding

The study of metal ion-DNA interaction aiming to understand the stabilization of artificial base pairing and a number of noncanonical motifs is of current interest, due to their potential exploitation in developing new technological devices and expanding the genetic code. A successful strategy has been the synthesis of metal-mediated base pairs, in which a coordinative bond to a central metal cation replaces a H-bond in a natural pair. In this work, we characterized, for the first time, the gas phase structure of the cytosine···Ag+···cytosine (C-Ag+-C) complex by means of InfraRed-MultiPhoton-Dissociation (IR-MPD) spectroscopy and theoretical calculation. The IR-spectrum was confidently assigned to one structure with the Ag+ acting as a bridge between the heteronitrogen atoms in each cytosine (both in the keto-amino form). This structure is biologically relevant since it mimics the structure of the hemiprotonated C-H+-C dimer responsible for the stabilization of the i-motif structure in DNA, with the replacement of the NH···N bond by a stronger N···Ag+···N bond. Moreover, since the structure of the C-Ag+-C complex is planar, it allows an optimum intercalation between pairs of the two antiparallel strand duplex in the DNA i-motif structure.

Effect of Ag+ on the Excited-State Properties of a Gas-Phase (Cytosine)2Ag+ Complex: Electronic Transition and Estimated Lifetime

Recently, DNA molecules have received great attention because of their potential applications in material science. One interesting example is the production of highly fluorescent and tunable DNA-Agn clusters with cytosine (C)-rich DNA strands. Here, we report the UV photofragmentation spectra of gas-phase cytosine···Ag(+)···cytosine (C2Ag(+)) and cytosine···H(+)···cytosine (C2H(+)) complexes together with theoretical calculations. In both cases, the excitation energy does not differ significantly from that of isolated cytosine or protonated cytosine, indicating that the excitation takes place on the DNA base. However, the excited-state lifetime of the C2H(+) (τ = 85 fs), estimated from the bandwidth of the spectrum, is at least 2 orders of magnitude shorter than that of the C2Ag(+) (τ > 5000 fs). The increased excited-state lifetime upon silver complexation is quite unexpected, and it clearly opens the question about what factors are controlling the nonradiative decay in pyrimidine DNA bases. This is an important result for the expanding field of metal-mediated base pairing and may also be important to the photophysical properties of DNA-templated fluorescent silver clusters.

Excited States of Proton-Bound DNA/RNA Base Homodimers: Pyrimidines

We are presenting the electronic photofragment spectra of the protonated pyrimidine DNA base homodimers. Only the thymine dimer exhibits a well structured vibrational progression, while the protonated monomer shows broad vibrational bands. This shows that proton bonding can block some nonradiative processes present in the monomer.

Communication: UV photoionization of cytosine catalyzed by Ag+

The photo-induced damages of DNA in interaction with metal cations, which are found in various environments, still remain to be characterized. In this paper, we show how the complexation of a DNA base (cytosine (Cyt)) with a metal cation (Ag(+)) changes its electronic properties. By means of UV photofragment spectroscopy of cold ions, it was found that the photoexcitation of the CytAg(+) complex at low energy (315-282) nm efficiently leads to ionized cytosine (Cyt(+)) as the single product. This occurs through a charge transfer state in which an electron from the p orbital of Cyt is promoted to Ag(+), as confirmed by ab initio calculations at the TD-DFT/B3LYP and RI-ADC(2) theory level using the SV(P) basis set. The low ionization energy of Cyt in the presence of Ag(+) could have important implications as point mutation of DNA upon sunlight exposition.

Solvation of barium atoms and singly charged cations in acetonitrile clusters

The size distributions of neutral and cationic Ba x (CH3CN) n (x = 0, +1; n ≤ 7) clusters, as produced by a standard laser vaporization-supersonic expansion pick-up source, were determined from molecular beam experiments. The size distribution for cations is in the range of n = 1-7, whereas only the n = 1 complex is observed for neutral clusters, and these two features are unaffected by the variables controlling the performance of the cluster source. The distinct behavior is compatible with the expected charge-dipole interactions in the ionic species, which are stronger than the dipole induced-dipole interactions at play in neutral clusters, and it is corroborated by the relative magnitude of the theoretical successive binding energies (SBEs) for the lowest-lying isomers of cationic and neutral clusters with n = 1-5, as computed at the density functional theory level. The theoretical results also allow for the rationalization of the bimodal Ba+(CH3CN)1-7 size distribution, featuring an apparent minimum at n = 3, in terms of chiefly 6s-5d σ hybridization of the Ba+ ions, which ultimately leads to a relatively small third SBE for the Ba+(CH3CN)3 complex, as compared to those for n = 1, 2, and 4. Additional Born-Oppenheimer molecular dynamics simulations on the Ba+(CH3CN)2-4 clusters suggest that all of the ligands are coordinated to the Ba+ ion and prevent considering completion of the first solvent shell as responsible for the bimodal size distribution.