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.

An electrostatic in-line charge-state purification system for multicharged ions in the kiloelectronvolt energy range.

The performance of a newly built omega type electrostatic analyzer designed to act as an in-line charge-state purification system for ions in the kiloelectronvolt energy range is reported. The analyzer consists of a set of four consecutive electrostatic 140° concentric cylindrical electrodes enclosed by Matsuda electrodes. This setup was recently tested and validated using O5+, Ar9+, and Xe20+ ion beams at an energy of 14 qkeV at the ARIBE facility. A resolving power of 10.5 and a transmission of 100% of the desired charge state are measured allowing a good purification of incoming ion beams with charge states up to 10+ and a fairly good purification for charge states at least up to 20+. In comparison with other in-line solutions such as the Wien filter, our system has the advantage of being purely electrostatic and therefore lacking common drawbacks as, for example, hysteresis.

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.

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.

A multicoincidence study of fragmentation dynamics in collision of γ-aminobutyric acid with low-energy ions.

Fragmentation of the γ-aminobutyric acid molecule (GABA, NH(2)(CH(2))(3)COOH) following collisions with slow O(6+) ions (v≈0.3 a.u.) was studied in the gas phase by a combined experimental and theoretical approach. In the experiments, a multicoincidence detection method was used to deduce the charge state of the GABA molecule before fragmentation. This is essential to unambiguously unravel the different fragmentation pathways. It was found that the molecular cations resulting from the collisions hardly survive the interaction and that the main dissociation channels correspond to formation of NH(2)CH(2)(+), HCNH(+), CH(2)CH(2)(+), and COOH(+) fragments. State-of-the-art quantum chemistry calculations allow different fragmentation mechanisms to be proposed from analysis of the relevant minima and transition states on the computed potential-energy surface. For example, the weak contribution at [M-18](+), where M is the mass of the parent ion, can be interpreted as resulting from H(2)O loss that follows molecular folding of the long carbon chain of the amino acid.

Ion-induced fragmentation of amino acids: effect of the environment.

In general, radiation-induced fragmentation of small amino acids is governed by the cleavage of the C-C(α) bond. We present results obtained with 300 keV Xe(20+) ions that allow molecules (glycine and valine) to be ionised at large distances without appreciable energy transfer. Also in the present case, the C-C(α) bond turns out to be the weakest link and hence its scission is the dominant fragmentation channel. Intact ionised molecules are observed with very low intensities. When the molecules are embedded in a cluster of amino acids, a protective effect of the environment is observed. The fragmentation pattern changes: the C-C(α) bond becomes more protected and stable amino acid cations are observed as fragments of the molecular clusters. Evidently, the molecular cluster acts as a "buffer" for the excess energy, capable of rapidly redistributing excess energy and charge.