Site-selective soft X-ray absorption as a tool to study protonation and electronic structure of gas-phase DNA
Open Access
- 10 May 2021
- journal article
- research article
- Published by Royal Society of Chemistry (RSC) in Physical Chemistry Chemical Physics
- Vol. 23 (20), 11900-11906
- https://doi.org/10.1039/d1cp01014j
Abstract
The conformation and the electronic structure of gas-phase oligonucleotides depends strongly on the protonation site. 5′-d(FUAG) can either be protonated at the A-N1 or at the G-N7 position. We have stored protonated 5′-d(FUAG) cations in a cryogenic ion trap held at about 20 K. To identify the protonation site and the corresponding electronic structure, we have employed soft X-ray absorption spectroscopy at the nitrogen K-edge. The obtained spectra were interpreted by comparison to time-dependent density functional theory calculations using a short-range exchange correlation functional. Despite the fact that guanine has a significantly higher proton affinity than adenine, the agreement between experiment and theory is better for the A-N1 protonated system. Furthermore, an inverse site sensitivity is observed in which the yield of the nucleobase fragments that contain the absorption site appears substantially reduced, which could be explained by non-statistical fragmentation processes, localized on the photoabsorbing nucleobase.Funding Information
- European Cooperation in Science and Technology (MD-GAS (CA18212))
- China Scholarship Council (Wen Li, Xin Wang)
- Bundesministerium für Bildung und Forschung (05K16VF1)
- Horizon 2020 Framework Programme (CALIPSOplus, Grant Agreement 730872)
This publication has 29 references indexed in Scilit:
- Protonation of Nucleobases in Single‐ and Double‐Stranded DNAChemBioChem, 2018
- Separating and probing tautomers of protonated nucleobases using differential mobility spectrometryInternational Journal of Mass Spectrometry, 2018
- Soft X-ray Spectroscopy as a Probe for Gas-Phase Protein Structure: Electron Impact Ionization from WithinChemistry – A European Journal, 2018
- Native Mass Spectrometry: What is in the Name?Journal of the American Society for Mass Spectrometry, 2016
- K-Shell Excitation and Ionization of a Gas-Phase Protein: Interplay between Electronic Structure and Protein FoldingThe Journal of Physical Chemistry Letters, 2015
- Gas-Phase Conformations and Energetics of Protonated 2′-Deoxyadenosine and Adenosine: IRMPD Action Spectroscopy and Theoretical StudiesThe Journal of Physical Chemistry B, 2015
- Circular dichroism and conformational polymorphism of DNANucleic Acids Research, 2009
- Thermal difference spectra: a specific signature for nucleic acid structuresNucleic Acids Research, 2005
- Site-Selective Photochemistry of Core Excited Molecules: Role of the Internal EnergyPhysical Review Letters, 1998
- Electrospray Collision-induced Dissociation Mass Spectra of Positively Charged OligonucleotidesRapid Communications in Mass Spectrometry, 1997