Determination of the Mechanical Properties of Model Lipid Bilayers Using Atomic Force Microscopy Indentation.

By conducting a systematic study of model lipid membranes using the atomic force microscopy (AFM) indentation, we demonstrate the importance of an experimental protocol on the determination of their mechanical parameters. We refine the experimental approach by analyzing the influence of the contact mechanics models used to process the data, substrate preparation, and indenter geometry. We show that both bending rigidity and area compressibility can be determined from a single AFM indentation measurement.

Photografting and Patterning of Poly(ethylene glycol) Methacrylate Hydrogel on Glass for Biochip Applications.

An efficient procedure for chemical initiator-free, in situ synthesis of a functional polyethylene glycol methacrylate (PEG MA) hydrogel on regular glass substrates is reported. It is demonstrated that self-initiated photografting and photopolymerization driven by UV irradiation can yield tens of nanometer-thick coatings of carboxy-functionalized PEG MA on the aldehyde-terminated borosilicate glass surface. The most efficient formulation for hydrogel synthesis contained methyl methacrylic acid (MAA), 2-hydroxyethyl methacrylate (HEMA), and PEG methacrylate (PEG10MA) monomers (1:1:1). The resulting HEMA/PEG10MA/MAA (HPMAA) coatings had a defined thickness in the range from 11 to 50 nm. The physicochemical properties of the synthesized HPMAA coatings were analyzed by combining water contact angle measurements, stylus profilometry, imaging null ellipsometry, and atomic force microscopy (AFM). The latter technique was employed in the quantitative imaging mode not only for direct probing of the surface topography but also for swelling behavior characterization in the pH range from 4.5 to 8.0. The estimated high swelling ratios of the HPMAA hydrogel (up to 3.2) together with its good stability and resistance to nonspecific protein binding were advantageous in extracellular matrix mimetics via patterning of fibronectin (FN) at a resolution close to 200 nm. It was shown that the fabricated FN micropatterns on HPMAA were equally suitable for single-cell arraying, as well as controlled cell culture lasting at least for 96 h.

Scanning Probe-Directed Assembly and Rapid Chemical Writing Using Nanoscopic Flow of Phospholipids.

Nanofluidic systems offer a huge potential for discovery of new molecular transport and chemical phenomena that can be employed for future technologies. Herein, we report on the transport behavior of surface-reactive compounds in a nanometer-scale flow of phospholipids from a scanning probe. We have investigated microscopic deposit formation on polycrystalline gold by lithographic printing and writing of 1,2-dioleoyl-sn-glycero-3-phosphocholine and eicosanethiol mixtures, with the latter compound being a model case for self-assembled monolayers (SAMs). By analyzing the ink transport rates, we found that the transfer of thiols was fully controlled by the fluid lipid matrix allowing to achieve a certain jetting regime, i.e., transport rates previously not reported in dip-pen nanolithography (DPN) studies on surface-reactive, SAM-forming molecules. Such a transport behavior deviated significantly from the so-called molecular diffusion models, and it was most obvious at the high writing speeds, close to 100 µm s-1. Moreover, the combined data from imaging ellipsometry, scanning electron microscopy, atomic force microscopy (AFM), and spectroscopy revealed a rapid and efficient ink phase separation occurring in the AFM tip-gold contact zone. The force curve analysis indicated formation of a mixed ink meniscus behaving as a self-organizing liquid. Based on our data, it has to be considered as one of the co-acting mechanisms driving the surface reactions and self-assembly under such highly nonequilibrium, crowded environment conditions. The results of the present study significantly extend the capabilities of DPN using standard AFM instrumentation: in the writing regime, the patterning speed was already comparable to that achievable by using electron beam systems. We demonstrate that lipid flow-controlled chemical patterning process is directly applicable for rapid prototyping of solid-state devices having mesoscopic features as well as for biomolecular architectures.

Fixed DNA Molecule Arrays for High-Throughput Single DNA-Protein Interaction Studies.

The DNA Curtains assay is a recently developed experimental platform for protein-DNA interaction studies at the single-molecule level that is based on anchoring and alignment of DNA fragments. The DNA Curtains so far have been made by using chromium barriers and fluid lipid bilayer membranes, which makes such a specialized assay technically challenging and relatively unstable. Herein, we report on an alternative strategy for DNA arraying for analysis of individual DNA-protein interactions. It relies on stable DNA tethering onto nanopatterned protein templates via high affinity molecular recognition. We describe fabrication of streptavidin templates (line features as narrow as 200 nm) onto modified glass coverslips by combining surface chemistry, atomic force microscopy (AFM), and soft lithography techniques with affinity-driven assembly. We have employed such chips for arraying single- and double-tethered DNA strands, and we characterized the obtained molecular architecture: we evaluated the structural characteristics and specific versus nonspecific binding of fluorescence-labeled DNA using AFM and total internal reflection fluorescence microscopy. We demonstrate the feasibility of our DNA molecule arrays for short single-tethered as well as for lambda single- and double-tethered DNA. The latter type of arrays proved very suitable for localization of single DNA-protein interactions employing restriction endonucleases. The presented molecular architecture and facile method of fabrication of our nanoscale platform does not require clean room equipment, and it offers advanced functional studies of DNA machineries and the development of future nanodevices.

Mixed Self-Assembled Monolayers with Terminal Deuterated Anchors: Characterization and Probing of Model Lipid Membrane Formation.

We describe herein a series of self-assembled monolayers (SAMs) on gold designed for adjustable tethering of model lipid membrane phases. The SAMs consist of deuterated aliphatic anchors, HS(CH2)15CONH(CH2CH2O)6CH2CONH-X, where X is either -(CD2)7CD3 or -(CD2)15CD3, dispersed in a stable matrix of protein-repellent molecules, HS(CH2)15CONHCH2CH2OH. The mixed SAMs with variable surface densities of the anchors are thoroughly characterized before and after adsorption of phospholipids by means of ellipsometry, contact angle goniometry, and infrared reflection-absorption spectroscopy (IRRAS). In all cases, the bottom portions of the mixed SAMs (i.e., the h-alkyl thiol segments of the molecules) are arranged in a highly ordered all-trans conformation stabilized by a network of lateral hydrogen bonds. The terminal portions of the anchors (the oligo(ethylene glycol) spacer and deuterated alkyl segments, respectively), however, possess less ordered conformations in the mixed composition regime. For the SAMs containing the longer anchors (-(CD2)15CD3), the contact angle and infrared data point toward partial phase segregation. These findings are in excellent agreement with molecular dynamics simulations by Schulze and Stein. Upon analysis in air, the IRRAS data also indicate strong interaction between the adsorbed phospholipid molecules and the d-alkyl tails of the mixed SAM constituents. In such assemblies are the alkyl tails of the phospholipids aligned perpendicularly with respect to the supporting substrate, regardless of the anchor length. We also probed the in situ formation of a tethered bilayer lipid membrane (tBLM) via fusion of small unilamellar vesicles (SUVs) on the characterized SAMs using a quartz crystal microbalance with dissipation monitoring. Our experiments show that SUVs fuse efficiently of the two mixed SAMs with and without a pre-adsorbed lipid layer. Owing to the defined molecular composition and phase behavior, our SAM platform is attractive for detailed studies of tBLM formation and cell mimetic applications.

Cup-Shaped Nanoantenna Arrays for Zeptoliter Volume Biochemistry and Plasmonic Sensing in the Visible Wavelength Range.

Although three-dimensional shaping of metallic nanostructures is an important strategy for control and manipulation of localized surface plasmon resonance (LSPR), its implementation in high-throughput, on-chip fabrication of plasmonic devices remains challenging. Here, we demonstrate nanocontact-based large-area fabrication of a novel, LSPR-active Au architecture consisting of periodic arrays of reduced-symmetry nanoantennas having sub-50 nm, out-of-plane features. Namely, by combining nanosphere and molecular self-assembly processes, we have patterned evaporated polycrystalline Au films for chemical etching of nanocups with controlled aspect ratios (outer diameter d = 100 nm and void volumes = 18 or 39 zL). The resulting nanoantennas were highly ordered, forming a hexagonal lattice structure over centimeter-sized glass substrates, and they displayed characteristic LSPR absorption in the visible/near-infrared spectral range. Theoretical simulations indicated electric field confinement and enhancement patterns located not only around the rims but also inside the nanocups. We also explored how these patterns and the overall spectral characteristics depended on the nanocup aspect ratio as well as on electric field coupling in the arrays. We have successfully tested the fabricated architecture for detection of stepwise immobilization and interactions of proteins, thus demonstrating its potential for both nanoscopic scaffolding and sensing of biomolecular assemblies.