Matias Berdakin | Universidad Nacional de Córdoba (original) (raw)

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Papers by Matias Berdakin

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

The Journal of Physical Chemistry A, 2014

The study of metal ion-DNA interaction aiming to understand the stabilization of artificial base ... more 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.

Research paper thumbnail of On the Ag + –cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory

Phys. Chem. Chem. Phys., 2015

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

The Journal of Physical Chemistry B, 2015

We are presenting the electronic photofragment spectra of the protonated pyrimidine DNA base homo... more 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.

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

The Journal of Physical Chemistry Letters, 2014

Recently, DNA molecules have received great attention because of their potential applications in ... more 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−Ag n clusters with cytosine (C)-rich DNA strands. Here, we report the UV photofragmentation spectra of gas-phase cytosine···Ag + ···cytosine (C 2 Ag + ) and cytosine···H + ···cytosine (C 2 H + ) 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 C 2 H + (τ = 85 fs), estimated from the bandwidth of the spectrum, is at least 2 orders of magnitude shorter than that of the C 2 Ag + (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.

Research paper thumbnail of Excited states of protonated DNA/RNA bases

Physical Chemistry Chemical Physics, 2014

The very fast relaxation of the excited states to the ground state in DNA/RNA bases is a necessar... more The very fast relaxation of the excited states to the ground state in DNA/RNA bases is a necessary process to ensure the photostability of DNA and its rate is highly sensitive to the tautomeric form of the bases. Protonation of the bases plays a crucial role in many biochemical and mutagenic processes and it can result in alternative tautomeric structures, thus making important the knowledge of the properties of protonated DNA/RNA bases. We report here the photofragmentation spectra of the five protonated DNA/RNA bases. In most of the cases, the spectra exhibit well resolved vibrational structures, with broad bands associated with very short excited state lifetimes. The similarity between the electronic properties, e.g. excitation energy and very short excited state lifetimes for the canonical tautomers of protonated and neutral DNA bases, suggests that the former could also play an important role in the photostability mechanism of DNA. . ‡ We also confirmed recently the identification of different tautomers of protonated uracil with a new UV-UV hole-burning spectroscopy. 39

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

The Journal of Physical Chemistry A, 2014

The study of metal ion-DNA interaction aiming to understand the stabilization of artificial base ... more 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.

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

The Journal of Physical Chemistry A, 2014

The study of metal ion-DNA interaction aiming to understand the stabilization of artificial base ... more 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.

Research paper thumbnail of On the Ag + –cytosine interaction: the effect of microhydration probed by IR optical spectroscopy and density functional theory

Phys. Chem. Chem. Phys., 2015

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

The Journal of Physical Chemistry B, 2015

We are presenting the electronic photofragment spectra of the protonated pyrimidine DNA base homo... more 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.

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

The Journal of Physical Chemistry Letters, 2014

Recently, DNA molecules have received great attention because of their potential applications in ... more 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−Ag n clusters with cytosine (C)-rich DNA strands. Here, we report the UV photofragmentation spectra of gas-phase cytosine···Ag + ···cytosine (C 2 Ag + ) and cytosine···H + ···cytosine (C 2 H + ) 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 C 2 H + (τ = 85 fs), estimated from the bandwidth of the spectrum, is at least 2 orders of magnitude shorter than that of the C 2 Ag + (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.

Research paper thumbnail of Excited states of protonated DNA/RNA bases

Physical Chemistry Chemical Physics, 2014

The very fast relaxation of the excited states to the ground state in DNA/RNA bases is a necessar... more The very fast relaxation of the excited states to the ground state in DNA/RNA bases is a necessary process to ensure the photostability of DNA and its rate is highly sensitive to the tautomeric form of the bases. Protonation of the bases plays a crucial role in many biochemical and mutagenic processes and it can result in alternative tautomeric structures, thus making important the knowledge of the properties of protonated DNA/RNA bases. We report here the photofragmentation spectra of the five protonated DNA/RNA bases. In most of the cases, the spectra exhibit well resolved vibrational structures, with broad bands associated with very short excited state lifetimes. The similarity between the electronic properties, e.g. excitation energy and very short excited state lifetimes for the canonical tautomers of protonated and neutral DNA bases, suggests that the former could also play an important role in the photostability mechanism of DNA. . ‡ We also confirmed recently the identification of different tautomers of protonated uracil with a new UV-UV hole-burning spectroscopy. 39

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

The Journal of Physical Chemistry A, 2014

The study of metal ion-DNA interaction aiming to understand the stabilization of artificial base ... more 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.