Posts Tagged ‘radiation damage’

STSM by Violaine VIZCAINO, CIMAP, Caen (FR) withThomas Schlatholter, Zernike Institute for Advanced Materials (NL)VVIZ_logos
On September 26, 2015 (10 days)

Radiation damage to human type II collagen fragments on the single molecule level

The purpose of the STSM was to study the radiation-induced molecular degradation of human type II collagen. We looked at the photo-fragmentation induced by both soft X-ray and XUV of two peptides: PK26-P [PGGPPGPKGNSGEPGAPGSKGDTGAK] which is made of a repetition of the amino acids sequence X-Y-Gly specific to collagen protein, and PK26-HyP [PGGP-HyP-GPKGNSGE-HyP-GA-HyP-GSKGDTGAK] which contains the unnatural hydroxyproline (HyP) residue.

Fragmentation of both peptides, in two different protonated states (M+3H)3+ and (M+4H)4+, were measured at different photon energies in order to highlight the main fragmentation channels, their threshold and the influence of hydroxyproline (HyP) residue in these processes. Figure 1 shows typical fragmentation spectra of (PK26-Hyp +4H)4+ at three different energies (14, 18 and 21 eV).

We expect to submit our results in a peer-reviewed scientific journal at the beginning of 2016. Moreover, this STSM has also allowed strengthening the collaboration between the CIMAP (Caen, France) and the University of Groningen (Netherlands).


Figure 1 : Fragmentation spectra of (PK26-Hyp +4H)4+. All spectra are normalized to the parent depletion.

STSM by Sylvain Maclot, CIMAP, Caen (FR) with Paola Bolognesi, CNR, IMIP (IT)
On March 26th, 2014 (12 days)


Study of stability of nucleosides and their radiosensitising analogues after interaction with X-Rays

This work is part of a combined effort of the groups at CIMAP in Caen and CNR/IMIP in Rome aiming to study the radiation damage of biomolecules at the molecular scale using X-ray absorption and multiply-charged ion impact.

The aim of the experiments performed in Elettra Synchrotron was to investigate the basic processes at molecular level occurring in nucleosides after interaction with X-Rays. Nucleosides are building blocks of DNA/RNA and are composed of a sugar and a nucleic base. This study was mainly focused on valence photoionization using photoemission spectroscopy (PES) and photo-electron-photo-ion coincidence (PEPICO) measurements in order to probe the fragmentation dynamics of ionised molecules. We obtained results for nucleosides 2’-deoxythymidine and 2’-deoxycytidine.

This work should lead to publication and especially marks the consolidation of collaboration between the two teams on nucleoside studies in the gas phase.


STSM by Janina Kopyra, Siedlce University, Siedlce (PL), with Alicja Domaracka, CIMAP-GANIL, Caen (FR)
On April 6th, 2014 (8 days)JAKOP-logo

Fragmentation dynamics of N-methyl substituted glycine

The purpose of the STSM was to study the fragmentation dynamics of methyl derivatives of amino acid, namely N,N,N-trimethylglycine (glycine-betaine) and its fully deuterated analogue, with respect to low-energy ion collisions. The molecule exists in the zwitterionic form thus carry two opposite formal charges located at the clearly separated molecular sites. Since in a real biological environment amino acids exist as zwitterionic (twin-ion molecules) therefore the investigation of the glycine-betaine is of particular interest in order to understand the physico-chemical stage of radiation damage.

The experiments were performed by using COLIMACON set-up within ARIBE facility. Briefly, we obtain molecules in the gas phase by evaporation of powders in the ovens. The collimated molecular beam interacts with a pulsed ion beam of O6+. The cationic products are analysed by linear TOF mass spectrometer.

We have performed the experiments with isolated molecules of glycine-betaine and its labelled analogue, which allow us to precisely determine from which side of the molecule a projectile captures the electrons.

The most abundant ionic fragment is observed at m/z 44 and can unambiguously be assigned to COO+. This type of fragmentation has been previously reported from canonical amino acids, however, the fragment has been attributed to N-containing cationic species. Further prominent fragments appear at m/z 58 and 59 from non-labelled molecule and at m/z 66 and 68 from its deuterated analogue. These observations indicate that the fragments are generated from the cleavage of the Ca-Cb bond with the charge localised at the N-terminal group. In addition we observe that for zwitterionic amino acid the probability of nondissociative ionization is negligible (see Figure). The future experiments are planned as a continuation of this project, which will concern the different projectiles and different charge states.


Figure: Mass spectrum of product ions from 48 keV O6+ collisions with fully deuterated N,N,N-trimethylglycine.