Modification of block copolymer lithography masks by O2/Ar plasma treatment: insights from lift-off experiments, nanopore etching and free membranes.

Block copolymer lithography allows for the large-area patterning of surfaces with self-assembled nanoscale features. The created nanostructured polymer films can be applied as masks in common lithography processing steps, such as lift-off and etching for pattern replication and transfer. In this work, we discuss an approach to improve the pattern replication efficiency by modification of the polymer mask prior to lithographical use by means of an O2/Ar plasma treatment. We present a much better quality of pattern replication without loss of features, along with a precise tunability of feature sizes, that can be achieved by short mask treatment. We point out a correlation between nanopore position within the ordered arrays, expressed by its coordination number, the nanopore shape and the replication efficiency. Our experimental strategy to explain these correlations combines the indirect investigation of patterns replicated from the modified polymer masks and direct investigation of the mask top and bottom. Pattern replication is performed either in the form of gold nanodot arrays created via lift-off or nanopores transferred into a SiO2 substrate by reactive ion etching. The direct analysis of free polymer membranes released from the substrate reveals the nanopore shape at the mask top and bottom surfaces.

O6-2'-Deoxyguanosine-butylene-O6-2'-deoxyguanosine DNA Interstrand Cross-Links Are Replication-Blocking and Mutagenic DNA Lesions.

DNA interstrand cross-links (ICLs) are cytotoxic DNA lesions derived from reactions of DNA with a number of anti-cancer reagents as well as endogenous bifunctional electrophiles. Deciphering the DNA repair mechanisms of ICLs is important for understanding the toxicity of DNA cross-linking agents and for developing effective chemotherapies. Previous research has focused on ICLs cross-linked with the N7 and N2 atoms of guanine as well as those formed at the N6 atom of adenine; however, little is known about the mutagenicity of O6-dG-derived ICLs. Although less abundant, O6-alkylated guanine DNA lesions are chemically stable and highly mutagenic. Here, O6-2'-deoxyguanosine-butylene-O6-2'-deoxyguanosine (O6-dG-C4-O6-dG) is designed as a chemically stable ICL, which can be induced by the action of bifunctional alkylating agents. We investigate the DNA replication-blocking and mutagenic properties of O6-dG-C4-O6-dG ICLs during an important step in ICL repair, translesion DNA synthesis (TLS). The model replicative DNA polymerase (pol) Sulfolobus solfataricus P2 DNA polymerase B1 (Dpo1) is able to incorporate a correct nucleotide opposite the cross-linked template guanine of ICLs with low efficiency and fidelity but cannot extend beyond the ICLs. Translesion synthesis by human pol κ is completely inhibited by O6-dG-C4-O6-dG ICLs. Moderate bypass activities are observed for human pol Î· and S. solfataricus P2 DNA polymerase IV (Dpo4). Among the pols tested, pol Î· exhibits the highest bypass activity; however, 70% of the bypass products are mutagenic containing substitutions or deletions. The increase in the size of unhooked repair intermediates elevates the frequency of deletion mutation. Lastly, the importance of pol Î· in O6-dG-derived ICL bypass is demonstrated using whole cell extracts of Xeroderma pigmentosum variant patient cells and those complemented with pol Î·. Together, this study provides the first set of biochemical evidence for the mutagenicity of O6-dG-derived ICLs.

Mass spectrometric real-time monitoring of an enzymatic phosphorylation assay using internal standards and data-handling freeware.

RATIONALE: Continuous-flow reaction detection systems (monitoring enzymatic reactions with mass spectrometry (MS)) lack quantitative values so far. Therefore, two independent internal standards (IS) are implemented in a way that the online system stability can be observed, quantitative conversion values for substrate and product can be obtained and they can be used as mass calibration standards for high MS accuracy. METHODS: An application previously developed for the MS detection of peptide phosphorylation by cAMP-dependent protein kinase A (PKA) (De Boer et al., Anal. Bioanal. Chem. 2005, 381, 647-655) was transferred to a continuous-flow reaction detection system. This enzymatic reaction, involving enzyme activation as well as the transfer of a phosphate group from ATP to a peptide substrate, was used to prove the compatibility of a quantitative enzymatic assay in a continuous-flow real-time system (connected to MS). RESULTS: Moreover (using internal standards), the critical parameter reaction temperature (including solution density variations depending on temperature) was studied in the continuous-flow mixing system. Furthermore, two substrates (malantide and kemptide), two enzyme types (catalytic subunit of PKA and complete PKA) and one inhibitor were tested to determine system robustness and long-term availability. Even spraying solutions that contained significant amount of MS contaminants (e.g. the polluted catalytic subunit) resulted in quantifiable MS signal intensities. Subsequent recalculations using the internal standards led to results representing the power of this application. CONCLUSIONS: The presented methodology and the data evaluation with available Achroma freeware enable the direct coupling of biochemical assays with quantitative MS detection. Monitoring changes such as temperature, reaction time, inhibition, or compound concentrations can be observed quantitatively and thus enzymatic activity can be calculated.

Characterisation of the PS-PMMA Interfaces in Microphase Separated Block Copolymer Thin Films by Analytical (S)TEM.

Block copolymer (BCP) self-assembly is a promising tool for next generation lithography as microphase separated polymer domains in thin films can act as templates for surface nanopatterning with sub-20 nm features. The replicated patterns can, however, only be as precise as their templates. Thus, the investigation of the morphology of polymer domains is of great importance. Commonly used analytical techniques (neutron scattering, scanning force microscopy) either lack spatial information or nanoscale resolution. Using advanced analytical (scanning) transmission electron microscopy ((S)TEM), we provide real space information on polymer domain morphology and interfaces between polystyrene (PS) and polymethylmethacrylate (PMMA) in cylinder- and lamellae-forming BCPs at highest resolution. This allows us to correlate the internal structure of polymer domains with line edge roughnesses, interface widths and domain sizes. STEM is employed for high-resolution imaging, electron energy loss spectroscopy and energy filtered TEM (EFTEM) spectroscopic imaging for material identification and EFTEM thickness mapping for visualisation of material densities at defects. The volume fraction of non-phase separated polymer species can be analysed by EFTEM. These methods give new insights into the morphology of polymer domains the exact knowledge of which will allow to improve pattern quality for nanolithography.

Hierarchical nanopores formed by block copolymer lithography on the surfaces of different materials pre-patterned by nanosphere lithography.

Bottom-up patterning techniques allow for the creation of surfaces with ordered arrays of nanoscale features on large areas. Two bottom-up techniques suitable for the formation of regular nanopatterns on different length scales are nanosphere lithography (NSL) and block copolymer (BCP) lithography. In this paper it is shown that NSL and BCP lithography can be combined to easily design hierarchically nanopatterned surfaces of different materials. Nanosphere lithography is used for the pre-patterning of surfaces with antidots, i.e. hexagonally arranged cylindrical holes in thin films of Au, Pt and TiO2 on SiO2, providing a periodic chemical and topographical contrast on the surface suitable for templating in subsequent BCP lithography. PS-b-PMMA BCP is used in the second self-assembly step to form hexagonally arranged nanopores with sub-20 nm diameter within the antidots upon microphase separation. To achieve this the microphase separation of BCP on planar surfaces is studied, too, and it is demonstrated for the first time that vertical BCP nanopores can be formed on TiO2, Au and Pt films without using any neutralization layers. To explain this the influence of surface energy, polarity and roughness on the microphase separation is investigated and discussed along with the wetting state of BCP on NSL-pre-patterned surfaces. The presented novel route for the creation of advanced hierarchical nanopatterns is easily applicable on large-area surfaces of different materials. This flexibility makes it suitable for a broad range of applications, from the morphological design of biocompatible surfaces for life science to complex pre-patterns for nanoparticle placement in semiconductor technology.