Ion beam processing of DNA origami nanostructures.

DNA origami nanostructures are emerging as a bottom-up nanopatterning approach. Direct combination of this approach with top-down nanotechnology, such as ion beams, has not been considered because of the soft nature of the DNA material. Here we demonstrate that the shape of 2D DNA origami nanostructures deposited on Si substrates is well preserved upon irradiation by ion beams, modeling ion implantation, lithography, and sputtering conditions. Structural changes in 2D DNA origami nanostructures deposited on Si are analyzed using AFM imaging. The observed effects on DNA origami include structure height decrease or increase upon fast heavy ion irradiation in vacuum and in air, respectively. Slow- and medium-energy heavy ion irradiation results in the cutting of the nanostructures or crater formation with ion-induced damage in the 10 nm range around the primary ion track. In all these cases, the designed shape of the 2D origami nanostructure remains unperturbed. Present stability and nature of damages on DNA origami nanostructures enable fusion of DNA origami advantages such as shape and positioning control into novel ion beam nanofabrication approaches.

Mass Spectral Signatures of Complex Post-Translational Modifications in Proteins: A Proof-of-Principle Based on X-ray Irradiated Vancomycin.

Characterizing post-translational modifications (PTM) of proteins is of key relevance for the understanding of many biological processes, as these covalent modifications strongly influence or even determine protein function. Among the different analytical techniques available, mass spectrometry is attracting growing attention because recent instrumental and computational improvements have led to a massive rise of the number of PTM sites that can be identified and quantified. However, multiple PTM occurring at adjacent amino acid residues can lead to complex and dense chemical patterns that are a challenge to characterize. By means of X-ray synchrotron radiation coupled to mass spectrometry, and through the test-case of the glycopeptide antibiotic vancomycin, we show that such a pattern has a unique and robust signature in terms of photon energy and molecular environment. This highlights the potential of this technique in proteomics and its value as a tool to understand the biological roles of PTM.

Photoinduced Processes within Noncovalent Complexes Involved in Molecular Recognition.

Investigating the intrinsic properties of molecular complexes is crucial for understanding the influence of noncovalent interactions on fundamental chemical reactions. Moreover, specific molecular recognition between a ligand and its receptor is a highly important biological process, but little is known about the effects of ionizing radiation on ligand-receptor complexes. The processes triggered by VUV photoabsorption on isolated noncovalent complexes between the glycopeptide antibiotic vancomycin and a mimic of its receptor have been probed by means of mass spectrometry and synchrotron radiation. In the case of protonated species, the glycosidic bond of vancomycin was cleaved with low activation energy, regardless of the molecular environment. In sharp contrast, for deprotonated species, electron photodetachment from carboxylate groups only triggered CO2 loss, whereas the glycosidic bond remained intact. Importantly, the noncovalent complex was also found to survive VUV photoabsorption only when the native structure is conserved in the gas phase.

Direct Radiation Effects on the Structure and Stability of Collagen and Other Proteins.

In this review, recent progress in understanding the direct effects of radiation on the structure and stability of collagen, the most abundant protein in the human body, and other proteins is surveyed. Special emphasis is placed on the triple-helical structure of collagen, as studied by means of collagen mimetic peptides. The emerging patterns are the dose dependence of radiation processes and their abundance, the crucial role of radicals in covalent-bond formation (crosslinking) or cleavage, and the influence of the radiation energy and nature. Future research should allow fundamental questions, such as charge transfer and fragmentation dynamics triggered by ionization, to be answered, as well as developing applications such as protein-based biomaterials, notably with properties controlled by irradiation.

A tandem mass spectrometer for crossed-beam irradiation of mass-selected molecular systems by keV atomic ions.

In the present paper, we describe a new home-built crossed-beam apparatus devoted to ion-induced ionization and fragmentation of isolated biologically relevant molecular systems. The biomolecular ions are produced by an electrospray ionization source, mass-over-charge selected, accumulated in a 3D ion trap, and then guided to the extraction region of an orthogonal time-of-flight mass spectrometer. Here, the target molecular ions interact with a keV atomic ion beam produced by an electron cyclotron resonance ion source. Cationic products from the collision are detected on a position sensitive detector and analyzed by time-of-flight mass spectrometry. A detailed description of the operation of the setup is given, and early results from irradiation of a protonated pentapeptide (leucine-enkephalin) by a 7 keV He+ ion beam are presented as a proof-of-principle.

High-energy collision-induced dissociation of histidine ions [His + H]+ and [His - H]- and histidine dimer [His2 + H].

RATIONALE: Histidine (His) is an essential amino acid, whose side group consists of an aromatic imidazole moiety that can bind a proton or metal cation and act as a donor in intermolecular interactions in many biological processes. While the dissociation of His monomer ions is well known, information on the kinetic energy released in the dissociation is missing. METHODS: Using a new home-built electrospray ionization (ESI) source adapted to a double-focusing mass spectrometer of BE geometry, we investigated the fragmentation reactions of protonated and deprotonated His, [His + H]+ and [His - H]- , and the protonated His dimer [His2  + H]+ , accelerated to 6 keV in a high-energy collision with helium gas. We evaluated the kinetic energy release (KER) for the observed dissociation channels. RESULTS: ESI of His solution in positive mode led to the formation of His clusters [Hisn + H]+ , n = 1-6, with notably enhanced stability of the tetramer. [His + H]+ dissociates predominantly by loss of (H2 O + CO) with a KER of 278 meV, while the dominant dissociation channel of [His - H]- involves loss of NH3 with a high KER of 769 meV. Dissociation of [His2 + H]+ is dominated by loss of the monomer but smaller losses are also observed. CONCLUSIONS: The KER for HCOOH loss from both [His + H]+ and [His - H]- is similar at 278 and 249 meV, respectively, which suggests that the collision-induced dissociation takes place via a similar mechanism. The loss of COOH and C2 H5 NO2 from the dimer suggests that the dimer of His binds through a shared proton between the imidazole moieties.

Radical-driven processes within a peptidic sequence of type I collagen upon single-photon ionisation in the gas phase.

We report on an experimental single-photon absorption study on gas-phase protonated collagen peptides employing a combination of mass spectrometry and synchrotron radiation. Partial ion yields for the main photoabsorption products vary steadily with photon energy over the range from 14 to 545 eV. At low energy, non-dissociative photoionisation competes with neutral molecule loss from the precursor ion, whereas fragmentation of the peptide backbone dominates at soft X-ray energies. Neutral molecule losses from the ionised peptide are found to have low energy barriers and most likely involve amino-acid residue side-chains with radical character, in particular aspartic acid. A particularly interesting finding is photoinduced loss of proline hydroxylation. The loss of this typical collagen post-translational modification might play a destabilizing role in the collagen structure.

Single-photon absorption of isolated collagen mimetic peptides and triple-helix models in the VUV-X energy range.

Cartilage and tendons owe their special mechanical properties to the fibrous collagen structure. These strong fibrils are aggregates of a sub-unit consisting of three collagen proteins wound around each other in a triple helix. Even though collagen is the most abundant protein in the human body, the response of this protein complex to ionizing radiation has never been studied. In this work, we probe the direct effects of VUV and soft X-ray photons on isolated models of the collagen triple helix, by coupling a tandem mass spectrometer to a synchrotron beamline. Single-photon absorption is found to induce electronic excitation, ionization and conversion into internal energy leading to inter- and intra-molecular fragmentation, mainly due to Gly-Pro peptide bond cleavages. Our results indicate that increasing the photon energy from 14 to 22 eV reduces fragmentation. We explain this surprising behavior by a smooth transition from excitation to ionization occurring with increasing photon energy. Moreover, our data support the assumption of a stabilization of the triple helix models by proline hydroxylation via intra-complex stereoelectronic effects, instead of the influence of solvent.

Formation and Fragmentation of Protonated Molecules after Ionization of Amino Acid and Lactic Acid Clusters by Collision with Ions in the Gas Phase.

Collisions between O(3+) ions and neutral clusters of amino acids (alanine, valine and glycine) as well as lactic acid are performed in the gas phase, in order to investigate the effect of ionizing radiation on these biologically relevant molecular systems. All monomers and dimers are found to be predominantly protonated, and ab initio quantum-chemical calculations on model systems indicate that for amino acids, this is due to proton transfer within the clusters after ionization. For lactic acid, which has a lower proton affinity than amino acids, a significant non-negligible amount of the radical cation monomer is observed. New fragment-ion channels observed from clusters, as opposed to isolated molecules, are assigned to the statistical dissociation of protonated molecules formed upon ionization of the clusters. These new dissociation channels exhibit strong delayed fragmentation on the microsecond time scale, especially after multiple ionization.

Electron attachment to CO2 embedded in superfluid He droplets.

Electron attachment to CO2 embedded in superfluid He droplets leads to ionic complexes of the form (CO2)n(-) and (CO2)nO(-) and, at much lower intensities, He containing ions of the form Hem(CO2)nO(-). At low energies (<5 eV), predominantly the non-decomposed complexes (CO2)n(-) are formed via two resonance contributions, similar to electron attachment to pristine CO2 clusters. The significantly different shapes and relative resonance positions, however, indicate particular quenching and mediation processes in CO2@He. A series of further resonances in the energy range up to 67 eV can be assigned to electronic excitation of He and capture of the inelastically scattered electron generating (CO2)n(-) and two additional processes where an intermediately formed He* leads to the nonstoichiometric anions (CO2)nO(-).

Electron attachment to the dipeptide dialanine: influence of methylation on site selective dissociation reactions.

Gas phase dissociative electron attachment (DEA) measurements with methyl-dialanine, C(7)H(14)N(2)O(3), are performed in a crossed electron-molecular beam experiment at high energy resolution (∼120 meV). Anion efficiency yields as a function of the incident electron energy are obtained for the most abundant fragments up to electron energies of ∼15 eV. There is no evidence of molecular anion formation whereas the dehydrogenated closed shell anion (M-H)(-) is one of the most dominant reaction products. Quantum chemical calculations are performed to investigate the electron attachment process and to elucidate site selective bond cleavage in the (M-H)(-) DEA-channel. Previous DEA studies on dialanine have shown that (M-H)(-) formation proceeds through abstraction of a hydrogen atom from the carboxyl and amide groups, contributing to two distinct resonances at 0.81 and 1.17 eV, respectively [D. Gschliesser, V. Vizcaino, M. Probst, P. Scheier and S. Denifl, Chem.-Eur. J., 2012, 18, 4613-4619]. Here we show that by methylation of the carboxyl group, all (calculated) thresholds for H-loss from the different sites in the dialanine molecule are shifted up to a maximum of 1.4 eV. The lowest lying resonance observed experimentally for (M-H)(-) remains operative from the amide group at the electron energy of 2.4 eV due to the methylation. We further study methylation-induced effects on the unimolecular dissociation leading to a variety of negatively charged DEA products.

Formation and decay of the dehydrogenated parent anion upon electron attachment to dialanine.

The dehydrogenated parent anion [M-H](-) is one of the most dominant anions formed in dissociative electron attachment to various small biomolecules like nucleobases and single amino acids. In the present study, we investigate the [M-H](-) channel for the dipeptide dialanine by utilizing an electron monochromator and a two-sector-field mass spectrometer. At electron energies below 2 eV, the measured high-resolution ion-efficiency curve has a different shape to that for the single amino acid alanine, which is explained by the altered threshold energies for formation of [M-H](-) determined in quantum chemical calculations. Moreover, the structure of the formed [M-H](-) anion is further studied by investigating the unimolecular and collision-induced decay of this anion. Trajectory calculations have been carried out to aid the interpretation of the experimentally observed fragmentation patterns.

Dissociative electron attachment to ß-alanine.

A detailed study on dissociative electron attachment (DEA) to ß-alanine (ßA) in the gas phase is presented. Ion yields as a function of the incident electron energy from about 0 to 15 eV have been measured for most of the fragments. As for all α-amino acids, the main reaction corresponds to the loss of a hydrogen atom, although many other fragments have been observed that involved more complex bond cleavages. Threshold energies have been calculated by using the G4(MP2) method for various decomposition reactions. Fragmentation pathways were also investigated to measure metastable decays of the intermediate fragment anion (ßA-H)(-) by using the mass-analyzed ion kinetic energy (MIKE) scan technique. Comparisons with α-alanine and other amino acids are made when relevant.

Bond dissociation of the dipeptide dialanine and its derivative alanine anhydride induced by low energy electrons.

Dissociative electron attachment to dialanine and alanine anhydride has been studied in the gas phase utilizing a double focusing two sector field mass spectrometer. We show that low-energy electrons (i.e., electrons with kinetic energies from near zero up to 13 eV) attach to these molecules and subsequently dissociate to form a number of anionic fragments. Anion efficiency curves are recorded for the most abundant anions by measuring the ion yield as a function of the incident electron energy. The present experiments show that as for single amino acids (M), e.g., glycine, alanine, valine, and proline, the dehydrogenated closed shell anion (M-H)(-) is the most dominant reaction product. The interpretation of the experiments is aided by quantum chemical calculations based on density functional theory, by which the electrostatic potential and molecular orbitals are calculated and the initial electron attachment process prior to dissociation is investigated.

Low energy (0-4 eV) electron impact to N(2)O clusters: Dissociative electron attachment, ion-molecule reactions, and vibrational Feshbach resonances.

Electron attachment to clusters of N(2)O in the energy range of 0-4 eV yields the ionic complexes [(N(2)O)(n)O](-), [(N(2)O)(n)NO](-), and (N(2)O)(n) (-) . The shape of the ion yields of the three homologous series differs substantially reflecting the different formation mechanisms. While the generation of [(N(2)O)(n)O](-) can be assigned to dissociative electron attachment (DEA) of an individual N(2)O molecule in the target cluster, the formation of [(N(2)O)(n)NO](-) is interpreted via a sequence of ion molecule reactions involving the formation of O(-) via DEA in the first step. The nondecomposed complexes (N(2)O)(n) (-) are preferentially formed at very low energies (below 0.5 eV) as a result of intramolecular stabilization of a diffuse molecular anion at low energy. The ion yields of [(N(2)O)(n)O](-) and (N(2)O)(n) (-) versus electron energy show sharp peaks at the threshold region, which can be assigned to vibrational Feshbach resonances mediated by the diffuse anion state as already observed in an ultrahigh resolution electron attachment study of N(2)O clusters [E. Leber, S. Barsotti, J. Bömmels, J. M. Weber, I. I. Fabrikant, M.-W. Ruf, and H. Hotop, Chem. Phys. Lett. 325, 345 (2000)].

High resolution electron attachment to CO2 clusters.

Electron attachment to CO2 clusters performed at high energy resolution (0.1 eV) is studied for the first time in the extended electron energy range from threshold (0 eV) to about 10 eV. Dissociative electron attachment (DEA) to single molecules yields O(-) as the only fragment ion arising from the well known (2)Π(u) shape resonance (ion yield centered at 4.4 eV) and a core excited resonance (at 8.2 eV). On proceeding to CO2 clusters, non-dissociated complexes of the form (CO2)(n)(-) including the monomer CO2(-) are generated as well as solvated fragment ions of the form (CO2)(n)O(-). The non-decomposed complexes appear already within a resonant feature near threshold (0 eV) and also within a broad contribution between 1 and 4 eV which is composed of two resonances observed for example for (CO2)(4)(-) at 2.2 eV and 3.1 eV (peak maxima). While the complexes observed around 3.1 eV are generated via the (2)Π(u) resonance as precursor with subsequent intracluster relaxation, the contribution around 2.2 eV can be associated with a resonant scattering feature, recently discovered in single CO2 in the selective excitation of the higher energy member of the well known Fermi dyad [M. Allan, Phys. Rev. Lett., 2001, 87, 0332012]. Formation of (CO2)(n)(-) in the threshold region involves vibrational Feshbach resonances (VFRs) as previously discovered via an ultrahigh resolution (1 meV) laser photoelectron attachment method [E. Leber, S. Barsotti, I. I. Fabrikant, J. M. Weber, M.-W. Ruf and H. Hotop, Eur. Phys. J. D, 2000, 12, 125]. The complexes (CO2)(n)O(-) clearly arise from DEA at an individual molecule within the cluster involving both the (2)Π(u) and the core excited resonance.

Very low energy electrons transform the cyclobutane-pyrimidine dimer into a highly reactive intermediate.

Electrons with virtually no kinetic energy (close to 0 eV) trigger the decomposition of cytotoxic cyclobutane-pyrimidine dimer (CPD) into a surprisingly large variety of fragment ions plus their neutral counterparts. The response of CPD to low energy electrons is thus comparable to that of explosives like trinitrotoluene (TNT). The dominant unimolecular reaction is the splitting into two thymine like units, which can be considered as the essential molecular step in the photolyase of CPD. We find that CPD is significantly more sensitive towards low energy electrons than its thymine building blocks. It is proposed that electron attachment at very low energy proceeds via dipole bound states, supported by the large dipole moment of the molecule (6.2 D). These states act as effective doorways to dissociative electron attachment (DEA).