Photon induced charge and structural dynamics in gas-phase DNA

Xin Wang

Research output: ThesisThesis fully internal (DIV)

165 Downloads (Pure)

Abstract

In this thesis, the response of DNA upon absorption of energetic photons have been systematically investigated, with a home-built tandem mass spectrometer that combines an electrospray ion source with a Paul trap. The thesis includes three studies: (a) a near-edge soft X-ray absorption mass spectrometry (NEXAMS) experiment at nitrogen K-edge has been performed on a singly-protonated trinucleotide dFUAG. With the time-dependent density functional theory (TD-DFT) calculations, we have analyzed the protonation effect on electronic structures and have determined the protonation site. (b) By using NEXAMS on dFUAG at K-edges of carbon, nitrogen, oxygen and fluorine, the hydrogen transfer from the DNA backbone towards the nucleobase is found to be a fundamental phenomenon occuring during the base loss process during DNA fragmentation, which can also be induced by resonant soft X-ray absorptions. The TD-DFT calculations show great agreement with the experiments. The non-covalent interaction (NCI) maps give the most obvious intramolecular hydrogen bonds between the base and backbone suggesting the most possible hydrogen acceptors and donors during the hydrogen transfer process. (c) A serials of ultrafast NIR and VUV fragmentation experiments for DNA G-quadruplexes and their counter- monomers have been conducted and allowed us to successfully find the best candidate system for the study of G4 ultrafast unfolding process. With this system, a clear time effect on G4 unfolding has been observed in the following VUV-pump NIR-probe experiments.
Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • University of Groningen
Supervisors/Advisors
  • Hoekstra, Ronnie, Supervisor
  • Schlathölter, Thomas, Co-supervisor
Award date13-Sept-2022
Place of Publication[Groningen]
Publisher
DOIs
Publication statusPublished - 2022

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