# Ion Beam Nanopatterning of Biomaterial Surfaces
## 3 Ion Beam-Nanopatterned Surfaces in Contact with Biomolecules and Cells
### Biomolecular Adsorption
#### 3.1.2 Dna  
While less relevant in the context of medical implants, DNA adsorption at various technologically relevant surfaces is an important issue in bioanalysis and biosensing [110; 111; 112]. The adsorption of plasmid DNA at ion beam-nanopatterned TiO\({}_{2}\) surfaces was investigated by [PERSON] et al. [113]. The authors irradiated TiO\({}_{2}\) single crystal surfaces with 3 keV Ar\({}^{+}\) ions at slightly off-normal incidence, which resulted in the formation of randomly distributed nanodots, the size of which increased with ion fluence. At the irradiated surfaces, adsorbed plasmid DNA films displayed some morphological differences, which were attributed, however, not primarily to the nanoscale surface topography but to an increased hydrophilicity due to ion bombardment. In a more detailed study by [PERSON] et al., the adsorption of DNA origami nanotubes at nanorippled SiO\({}_{\rm x}\)/Si surfaces with varying periodicities was investigated [114]. Ordered nanoscale ripple patterns with periodicities of about 20 and 30 nm were fabricated by oblique Ar\({}^{+}\) irradiation of Si wafers at ion energies of 300 and 500 eV, respectively, whereas larger ripple patterns with about 50 nm periodicity were obtained by 5 keV Xe\({}^{+}\) irradiation. Adsorption of negatively charged DNA origami nanotubes with a diameter and length of 6 and 412 nm, respectively, at the like-charged SiO\({}_{\rm x}\)/Si surfaces was facilitated by Mg\({}^{2+}\) ions in the buffer solution. For all three nanopatterned SiO\({}_{\rm x}\)/Si surfaces, the nanotubes were showing preferential alignment along the ripple patterns (see Figure 5). However, the pattern with 30 nm periodicity displayed by far the largest alignment yield with more than 70% of the DNA origami nanotubes adsorbed in the ripple valleys, where they perfectly followed the pattern. Based on finite element simulations and further experiments with different Mg\({}^{2+}\) concentrations, it was concluded that nanotube alignment results from an inhomogeneous electrostatic field distribution along the nanorippled SiO\({}_{\rm x}\)/Si surface with the obtained degree of alignment depending on the dimensions of the nanopatterns, the dimensions of the nanotubes, and the Debye length of the adsorption buffer. This interpretation was further supported by a follow-up study, which attempted to decorate the pre-aligned DNA origami nanotubes with gold nanoparticles at a lower Mg\({}^{2+}\) concentration [115]. Under such conditions, the DNA origami nanotubes were displaced from the ripple valleys, resulting in reduced alignment. This is in agreement with Mg\({}^{2+}\) ions being released from the DNA-SiO\({}_{\rm x}\) interface, which leads to weaker binding of the DNA origami nanotubes and, therefore, a stronger propensity for them to move along the surface, in particularly during washing of the sample surface. Even though only a handful of studies so far have examined biomolecular adsorption at nanopatterned surfaces fabricated by ion beam irradiation, the examples discussed in this section clearly demonstrate that ion beam nanopatterning may be used to control the behavior of adsorbing biomolecules on several levels. In particular, the preferential alignment of different proteins as well as DNA nanotubes on nanoscale ripple patterns was observed [98; 106; 114]. This, however, is not too surprising, since such surfaces are frequently used as templates for the alignment of various nanostructures [57; 58; 59; 61; 116; 117; 118; 119; 120; 121]. More intriguingly, it was also shown that the presence of such nanopatterns sometimes hinders or even completely suppresses protein adsorption [98; 106]. Ion beam nanopatterning may, therefore, turn into a valuable tool in the fabrication of antifouling surfaces [122]. Furthermore, nanorippled surfaces were also found to affect the conformation of adsorbed proteins [98; 106], which may be a beneficial feature in applications that require controlled protein unfolding, for instance, to expose cell-binding RGD domains [123].