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Resonant Infrared Multiple Photon Dissociation Spectroscopy of Anionic Nucleotide Monophosphate Clusters

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    0446133 - ÚOCHB 2016 RIV US eng J - Journal Article
    Ligare, M. R. - Rijs, A. M. - Berden, G. - Kabeláč, M. - Nachtigallová, Dana - Oomens, J. - de Vries, M. S.
    Resonant Infrared Multiple Photon Dissociation Spectroscopy of Anionic Nucleotide Monophosphate Clusters.
    Journal of Physical Chemistry B. Roč. 119, č. 25 (2015), s. 7894-7901. ISSN 1520-6106
    R&D Projects: GA ČR GAP208/12/1318
    Institutional support: RVO:61388963
    Keywords : DNA polymerase beta * gas-phase conformations * excited-state dynamics
    Subject RIV: CF - Physical ; Theoretical Chemistry
    Impact factor: 3.187, year: 2015

    We report mid-infrared spectra and potential energy surfaces of four anionic, 2'-deoxynucleotide-5'-monophosphates (dNMPs) and the ionic DNA pairs [dGMP-dCMP-H](1-), [dAMP-dTMP-H](1-) with a total charge of the complex equal to -1. We recorded IR action Spectra by resonant IR multiple-photon dissociation (IRMPD) using the FELIX free electron laser. The potential energy surface study employed an on-the-fly molecular dynamics quenching method (MD/Q), using a semiempirical AM1 method, followed by an optimization of the most stable structures using density functional theory. By employing infrared multiple-photon dissociation (IRMPD) spectroscopy in combination with high-level computational methods, we aim at a better understanding of the hydrogen bonding competition between the phosphate, moieties and the nucleobases. We find that, unlike in multimer double stranded DNA structures, the hydrogen bonds in these isolated nucleotide pairs are predominantly formed between the phosphate groups. This intermolecular interaction appears to exceed the stabilization energy resulting from base pairing and directs the overall cluster structure and alignment.
    Permanent Link: http://hdl.handle.net/11104/0248128