Molecular Crowding Effects on Microgel-Tethered Oligonucleotide Probes

Microgel tethering is a nontraditional method with which to bind oligonucleotide hybridization probes to a solid surface. Microgel-tethering physically positions the probes away from the underlying hard substrate and maintains them in a highly waterlike environment. This paper addresses the question of whether molecular crowding affects the performance of microgel-tethered molecular beacon probes. The density of probe-tethering sites is controlled experimentally using thin-film blends of biotin-terminated [PEG-B] and hydroxyl-terminated [PEG-OH] poly(ethylene glycol) from which microgels are synthesized and patterned by electron beam lithography. Fluorescence measurements indicate that the number of streptavidins, linear DNA probes, hairpin probes, and molecular beacon probes bound to the microgels increases linearly with increasing PEG-B/PEG-OH ratio. For a given tethering-site concentration, more linear probes can bind than structured probes. Crowding effects emerge during the hybridization of microgel-tethered molecular beacons but not during the hybridization of linear probes, as the tethering density increases. Crowding during hybridization is associated with conformational constraints imposed by the close proximity of closed and hybridized structured probes. The signal-to-background ratio (SBR) of hybridized beacons is highest and roughly constant for low tethering densities and decreases at the highest tethering densities. Despite differences between microgel tethering and traditional oligonucleotide surface-immobilization approaches, these results show that crowding defines an optimum tethering density for molecular beacon probes that is less than the maximum possible, which is consistent with previous studies involving various linear and structured oligonucleotide probes.

High sensitive and direct fluorescence detection of single viral DNA sequences by integration of double strand probes onto microgels particles

A novel class of probes for fluorescence detection was developed and combined to microgel particles for a high sensitive fluorescence detection of nucleic acids.

Ultra-large scale AFM of lipid droplet arrays: investigating the ink transfer volume in dip pen nanolithography

There are only few quantitative studies commenting on the writing process in dip-pen nanolithography with lipids. Lipids are important carrier ink molecules for the delivery of bio-functional patters in bio-nanotechnology. In order to better understand and control the writing process, more information on the transfer of lipid material from the tip to the substrate is needed. The dependence of the transferred ink volume on the dwell time of the tip on the substrate was investigated by topography measurements with an atomic force microscope (AFM) that is characterized by an ultra-large scan range of 800 × 800 μm(2). For this purpose arrays of dots of the phospholipid1,2-dioleoyl-sn-glycero-3-phosphocholine were written onto planar glass substrates and the resulting pattern was imaged by large scan area AFM. Two writing regimes were identified, characterized of either a steady decline or a constant ink volume transfer per dot feature. For the steady state ink transfer, a linear relationship between the dwell time and the dot volume was determined, which is characterized by a flow rate of about 16 femtoliters per second. A dependence of the ink transport from the length of pauses before and in between writing the structures was observed and should be taken into account during pattern design when aiming at best writing homogeneity. The ultra-large scan range of the utilized AFM allowed for a simultaneous study of the entire preparation area of almost 1 mm(2), yielding good statistic results.

Macrophage phagocytic activity toward adhering staphylococci on cationic and patterned hydrogel coatings versus common biomaterials

Biomaterial-associated-infection causes failure of biomaterial implants. Many new biomaterials have been evaluated for their ability to inhibit bacterial colonization and stimulate tissue-cell-integration, but neglect the role of immune cells. This paper compares macrophage phagocytosis of adhering Staphylococcus aureus on cationic-coatings and patterned poly(ethylene)glycol-hydrogels versus common biomaterials and stainless steel in order to identify surface conditions that promote clearance of adhering bacteria. Staphylococci were allowed to adhere and grow on the materials in a parallel-plate-flow-chamber, after which murine macrophages were introduced. From the decrease in the number of adhering staphylococci, phagocytosis-rates were calculated, and total macrophage displacements during an experiment determined. Hydrophilic surfaces had the lowest phagocytosis-rates, while common biomaterials had intermediate phagocytosis-rates. Patterning of poly(ethylene)glycol-hydrogel coatings increased phagocytosis-rates to the level of common biomaterials, while on cationic-coatings phagocytosis-rates remained relatively low. Likely, phagocytosis-rates on cationic coatings are hampered relative to common biomaterials through strong electrostatic binding of negatively-charged macrophages and staphylococci. On polymeric biomaterials and glass, phagocytosis-rates increased with macrophage displacement, while both parameters increased with biomaterial surface hydrophobicity. Thus hydrophobicity is a necessary surface condition for effective phagocytosis. Concluding, next-generation biomaterials should account for surface effects on phagocytosis in order to enhance the ability of these materials to resist biomaterial-associated-infection.