Katrin Günther

Mechanical and structural properties of YOYO-1 complexed DNA

YOYO-1 is a fluorescent dye widely used for probing the statistical–mechanical properties of DNA. However, currently contradicting data exist how YOYO-1 binding alters the DNA structure and rigidity. Here, we systematically address this problem using magnetic tweezers. Remarkably, we find that the persistence length of DNA remains constant independent of the amount of bound YOYO-1, which contrasts previous assumptions. While the ionic conditions can considerably alter the stability of YOYO-1 binding, the DNA bending rigidity seems not to be affected. We furthermore determine important structural parameters such as the binding site size, the elongation, as well as the untwisting angle per bound YOYO-1 molecule. We expect that our assay, in which all the parameters are determined within a single experiment, will be beneficial for a large range of other DNA binding drugs.

Single Molecules Trapped by Dynamic Inhomogeneous Temperature Fields.

We demonstrate a single molecule trapping concept that modulates the actual driving force of Brownian motion--the temperature. By spatially and temporally varying the temperature at a plasmonic nanostructure, thermodiffusive drifts are induced that are used to trap single nano-objects. A feedback controlled switching of local temperature fields allows us to confine the motion of a single DNA molecule for minutes and tailoring complex effective trapping potentials. This new type of thermophoretic microbeaker even provides control over a well-defined number of single molecules and is scalable to large arrays of trapping structures.

Thermo-Osmotic Flow in Thin Films

We report on the first microscale observation of the velocity field imposed by a nonuniform heat content along the solid-liquid boundary. We determine both radial and vertical velocity components of this thermo-osmotic flow field by tracking single tracer nanoparticles. The measured flow profiles are compared to an approximate analytical theory and to numerical calculations. From the measured slip velocity we deduce the thermo-osmotic coefficient for both bare glass and Pluronic F-127 covered surfaces. The value for Pluronic F-127 agrees well with Soret data for polyethylene glycol, whereas that for glass differs from literature values and indicates the complex boundary layer thermodynamics of glass-water interfaces.

Analysis of the fluctuations of a single-tethered, quantum-dot labeled DNA molecule in shear flow

A novel technique for analyzing the conformational fluctuations of a single, surface-tethered DNA molecule by fluorescence microscopy is reported. Attaching a nanometer-sized fluorescent quantum dot to the free end of a λ-phage DNA molecule allows us to study the fluctuations of a native DNA molecule without the mechanical properties being altered by fluorescent dye staining. We report on the investigation of single-tethered DNA in both the unperturbed and the shear flow induced stretched state. The dependence of the observed fractional extension and the magnitude of fluctuations on the shear rate can be qualitatively interpreted by Brochards stem-and-flower model. The cyclic dynamics of a DNA molecule is directly observed in the shear flow experiment.

Noncovalent Sidewall Functionalization of Carbon Nanotubes by Biomolecules: Single‐stranded DNA and Hydrophobin

Single‐stranded DNA (ssDNA) is known to disperse individual carbon nanotubes (CNT) into aqueous suspensions. But other biomolecules are able to do so as well. We demonstrate a protein‐assisted CNT dispersion by using hydrophobin. The yields of the suspensions are monitored by optical absorption spectroscopy (OAS). We perform atomic force microscopy (AFM) studies of DNA‐ and hydrophobin‐functionalized CNT with a resolution that allows us to identify individual molecules attached to isolated CNT. We control the density of DNA on the nanotubes by the DNA:CNT ratio, and observe stable suspensions of CNT with surprisingly low surface coverages.

Universal lab-on-a-chip platform for complex, perfused 3D cell cultures

The miniaturization, rapid prototyping and automation of lab-on-a-chip technology play nowadays a very important role. Lab-on-a-chip technology is successfully implemented not only for environmental analysis and medical diagnostics, but also as replacement of animals used for the testing of substances in the pharmaceutical and cosmetics industries. For that purpose the Fraunhofer IWS and partners developed a lab-on-a-chip platform for perfused cell-based assays in the last years, which includes different micropumps, valves, channels, reservoirs and customized cell culture modules. This technology is already implemented for the characterization of different human cell cultures and organoids, like skin, liver, endothelium, hair follicle and nephron. The advanced universal lab-on-a-chip platform for complex, perfused 3D cell cultures is divided into a multilayer basic chip with integrated micropump and application-specific 3D printed cell culture modules. Moreover a technology for surface modification of the printed cell culture modules by laser micro structuring and a complex and flexibly programmable controlling device based on an embedded Linux system was developed. A universal lab-on-a-chip platform with an optional oxygenator and a cell culture module for cubic scaffolds as well as first cell culture experiments within the cell culture device will be presented. The module is designed for direct interaction with robotic dispenser systems. This offers the opportunity to combine direct organ printing of cells and scaffolds with the microfluidic cell culture module. The characterization of the developed system was done by means of Micro-Particle Image Velocimetry (μPIV) and an optical oxygen measuring system.

Thermophoretic trapping and manipulation of single molecules

We demonstrate the long time trapping of single DNA molecules in liquids by feedback driven dynamic temperature fields. By spatially and temporally varying the temperature at a plasmonic nanostructure, thermophoretic drifts are induced that are used to trap single nano-objects. A feedback controlled switching of local temperature fields allows us to confine the motion of a single DNA molecule for minutes. The DNA conformation and conformation dynamics are analyzed in terms of a principle component analysis. Current results are in agreement with previous measurements in thermal equilibrium and suggest only a weak influence of the inhomogeneous temperature rise on the structure and dynamics in the trap.