Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides

Abstract

Understanding how charge and energy, as well as protons and hydrogen atoms, are transferred in molecular systems as a result of an electronic excitation is fundamental for understanding the interaction between ionizing radiation and biological matter on the molecular level. To localize the excitation at the atomic scale, it was chosen to target phosphorus atoms in the backbone of gas-phase oligonucleotide anions and cations, by means of resonant photoabsorption at the L-and K-edges. The ionic photoproducts of the excitation process were studied by a combination of mass spectrometry and X-ray spectroscopy. The combination of absorption site selectivity and photoproduct sensitivity allowed the identification of X-ray spectral signatures of specific processes. Moreover, charge and/or energy as well as H transfer from the backbone to nucleobases has been directly observed. Although the probability of one versus two H transfer following valence ionization depends on the nucleobase, ionization of sugar or phosphate groups at the carbon K-edge or the phosphorus L-edge mainly leads to single H transfer to protonated adenine. Moreover, our results indicate a surprising proton-transfer process to specifically form protonated guanine after excitation or ionization of P 2p electrons.

Radiation‐Induced Transfer of Charge, Atoms, and Energy within Isolated Biomolecular Systems

“…These results are in line with transfer of H from the initial site of single ionization, and the mechanisms proposed by the authors are shown in Scheme 3. We have obtained consistent results for the same molecular ion upon photoabsorption around the P L‐edge: since P atoms are located only in the backbone, it confirms that H transfer to nucleobases is triggered by photoabsorption at the backbone [133] . In the same article, we have provided experimental mass spectra of negative as well as positive ionic products of a deprotonated oligonucleotide after X‐ray photoabsorption around the P K‐edge energy, showing that specific absorption indeed occurs, and that abundant nucleobase cations (protonated and radical) are produced.…”

“…We have obtained consistent results for the same molecular ion upon photoabsorption around the P Ledge: since P atoms are located only in the backbone, it confirms that H transfer to nucleobases is triggered by photoabsorption at the backbone. [133] In the same article, we have provided experimental mass spectra of negative as well as positive ionic products of a deprotonated oligonucleotide after X-ray photo- [48] absorption around the P K-edge energy, showing that specific absorption indeed occurs, and that abundant nucleobase cations (protonated and radical) are produced. Since the oligonucleotide is initially deprotonated at the backbone, the positive charge on the nucleobase fragments means that charge and/or energy has been transferred from the backbone to the nucleobases.…”

Radiation‐Induced Molecular Processes in DNA: A Perspective on Gas‐Phase Interaction Studies

“…After exposure to the beam, the product ions are extracted into a high‐resolution reflectron time‐of‐flight mass spectrometer. Over the last years, we have used this technique to study VUV, soft X‐ray and ion induced dynamics in both protonated and deprotonated oligonucleotides [13,16,25–28] …”

“…Here, protonation of a nucleobase N‐site transforms an imine‐group into an amine‐group and the resulting N 1s shift leads to a shifted X‐ray absorption resonance that can be selectively adressed. Site‐selective photoionization of complex gas‐phase biomolecules currently is a rapidly growing field [14–17] …”

“…Site-selective photoionization of complex gas-phase biomolecules currently is a rapidly growing field. [14][15][16][17] The oligonucleotide conformation can in principle be determined and selected prior to the interaction process, using established techniques such as for instance ion-mobility spectrometry (IMS), where the drift velocity of a molecular ion through a gas is related to its geometric cross section and thus to its conformation. Even though this technology is routinely applied in the field of mass spectrometry, its use for e. g. soft Xray interaction studies with biomolecular ions is far from being straightforward, for instance because conformer selection further reduces the already low ESI signal.…”