How occasional backstepping can speed up a processive motor protein

Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the amount of free energy that ATP hydrolysis makes available. This is puzzling as more than a billion years of natural selection should have optimized the motor protein for its speed and efficiency. But more backstepping allows for the production of more entropy. Such entropy production will make free energy available. With this additional free energy, the catalytic cycle of the kinesin can be speeded up. We show how measured backstep percentages represent an optimum at which maximal net forward speed is achieved.Comment: LaTeX, 5 pages, 3 figure

Immobilization of different biomolecules by atomic force microscopy

<p>Abstract</p> <p>Background</p> <p>Micrometer resolution placement and immobilization of probe molecules is an important step in the preparation of biochips and a wide range of lab-on-chip systems. Most known methods for such a deposition of several different substances are costly and only suitable for a limited number of probes. In this article we present a flexible procedure for simultaneous spatially controlled immobilization of functional biomolecules by molecular ink lithography.</p> <p>Results</p> <p>For the bottom-up fabrication of surface bound nanostructures a universal method is presented that allows the immobilization of different types of biomolecules with micrometer resolution. A supporting surface is biotinylated and streptavidin molecules are deposited with an AFM (atomic force microscope) tip at distinct positions. Subsequent incubation with a biotinylated molecule species leads to binding only at these positions. After washing streptavidin is deposited a second time with the same AFM tip and then a second biotinylated molecule species is coupled by incubation. This procedure can be repeated several times. Here we show how to immobilize different types of biomolecules in an arbitrary arrangement whereas most common methods can deposit only one type of molecules. The presented method works on transparent as well as on opaque substrates. The spatial resolution is better than 400 nm and is limited only by the AFM's positional accuracy after repeated z-cycles since all steps are performed in situ without moving the supporting surface. The principle is demonstrated by hybridization to different immobilized DNA oligomers and was validated by fluorescence microscopy.</p> <p>Conclusions</p> <p>The immobilization of different types of biomolecules in high-density microarrays is a challenging task for biotechnology. The method presented here not only allows for the deposition of DNA at submicrometer resolution but also for proteins and other molecules of biological relevance that can be coupled to biotin.</p

Information and maximum power in a feedback controlled Brownian ratchet

Closed-loop or feedback controlled ratchets are Brownian motors that operate using information about the state of the system. For these ratchets, we compute the power output and we investigate its relation with the information used in the feedback control. We get analytical expressions for one-particle and few-particle flashing ratchets, and we find that the maximum power output has an upper bound proportional to the information. In addition, we show that the increase of the power output that results from changing the optimal open-loop ratchet to a closed-loop ratchet also has an upper bound that is linear in the information.Comment: LaTeX, 6 pages, 4 figures, improved version to appear in Eur. Phys. J.

Construction of an artificial cell membrane anchor using DARC as a fitting for artificial extracellular functionalities of eukaryotic cells

The need to functionalize cell membranes in a directed way for specific applications as single cell arrays or to force close cell-to-cell contact for artificial intercellular interaction and/or induction concerning stem cell manipulation or in general to have a tool for membrane and cell surface-associated processes, we envisaged a neutral inactive membrane anchor for extracellular entities to facillitate the above mentioned functionalities

Label-free electrical quantification of the dielectrophoretic response of DNA

A purely electrical sensing scheme is presented that determines the concentration of macromolecules in solution by measuring the capacitance between planar microelectrodes. Concentrations of DNA in the ng/mL range have been used in samples of 1 microL volume. The method has been applied to the characterisation of the dielectrophoretic response of DNA without the need for any chemical modifications. The influence of electrical parameters like duty cycle, voltage and frequency has been investigated. The results are in good agreement with data from dielectrophoretic studies on fluorescently labelled DNA. Extension of the method down to the single molecule level appears feasible.Comment: 12 pages, 7 figure

Stability of additive-free water-in-oil emulsions

We calculate ion distributions near a planar oil-water interface within non-linear Poisson-Boltzmann theory, taking into account the Born self-energy of the ions in the two media. For unequal self-energies of cations and anions, a spontaneous charge separation is found such that the water and oil phase become oppositely charged, in slabs with a typical thickness of the Debye screening length in the two media. From the analytical solutions, the corresponding interfacial charge density and the contribution to the interfacial tension is derived, together with an estimate for the Yukawa-potential between two spherical water droplets in oil. The parameter regime is explored where the plasma coupling parameter exceeds the crystallization threshold, i.e. where the droplets are expected to form crystalline structures due to a strong Yukawa repulsion, as recently observed experimentally. Extensions of the theory that we discuss briefly include numerical calculations on spherical water droplets in oil, and analytical calculations of the linear PB-equation for a finite oil-water interfacial width.Comment: 9 pages, 4 figures, accepted by JPCM for proceedings of LMC

DNA-nanostructure-assembly by sequential spotting

<p>Abstract</p> <p>Background</p> <p>The ability to create nanostructures with biomolecules is one of the key elements in nanobiotechnology. One of the problems is the expensive and mostly custom made equipment which is needed for their development. We intended to reduce material costs and aimed at miniaturization of the necessary tools that are essential for nanofabrication. Thus we combined the capabilities of molecular ink lithography with DNA-self-assembling capabilities to arrange DNA in an independent array which allows addressing molecules in nanoscale dimensions.</p> <p>Results</p> <p>For the construction of DNA based nanostructures a method is presented that allows an arrangement of DNA strands in such a way that they can form a grid that only depends on the spotted pattern of the anchor molecules. An atomic force microscope (AFM) has been used for molecular ink lithography to generate small spots. The sequential spotting process allows the immobilization of several different functional biomolecules with a single AFM-tip. This grid which delivers specific addresses for the prepared DNA-strand serves as a two-dimensional anchor to arrange the sequence according to the pattern. Once the DNA-nanoarray has been formed, it can be functionalized by PNA (peptide nucleic acid) to incorporate advanced structures.</p> <p>Conclusions</p> <p>The production of DNA-nanoarrays is a promising task for nanobiotechnology. The described method allows convenient and low cost preparation of nanoarrays. PNA can be used for complex functionalization purposes as well as a structural element.</p

Dielectrophoretic immobilisation of antibodies on microelectrode arrays

A silicon based chip device with a regular array of more than 100 000 cylindrical sub-microelectrodes has been developed for the dielectrophoretic (DEP) manipulation of nanoparticles and molecules in solution. It was fabricated by a standard CMOS (complementary metal oxide semiconductor) compatible process. The distribution of the electrical field gradient was calculated to predict the applicability of the setup. Heating due to field application was determined microscopically using a temperature sensitive fluorescent dye. Depending on voltage and frequency, temperature increase was found to be compatible with protein function. Successful field controlled immobilisation of biomolecules from solution was demonstrated with the autofluorescent protein R-phycoerythrin (RPE) and with fluorescently labelled IgG antibodies. Biological activity after DEP application was proven by immobilisation of an anti-RPE antibody and subsequent binding of RPE. These results demonstrate that the developed chip system allows the directed immobilisation of proteins onto microelectrodes by dielectrophoresis without the need for any chemical modification and that protein function is preserved. Being based on standard lithographical methods, further miniaturisation and on-chip integration of electronics towards a multiparameter single cell analysis system appear near at hand

Origin of attraction between likely charged hydrophobic and hydrophilic walls confining near-critical binary aquaeous mixture with ions

Effect of ionic solute on a near-critical binary aqueous mixture confined between charged walls with different adsorption preferences is considered within a simple density functional theory. For the near-critical system containing small amount of ions a Landau-type functional is derived based on the assumption that the correlation, $\xi$, and the Debye screening length, $\kappa^{-1}$, are both much larger than the molecular size. The corresponding approximate Euler-Lagrange equations aresolved analytically for ions insoluble in the organic solvent. Nontrivial concentration profile of the solvent is found near the charged hydrophobic wall as a result of the competition between the short-range attraction of the organic solvent and the electrostatic attraction of the hydrated ions. Excess of water may be present near the hydrophobic surface for some range of the surface charge and $\xi\kappa$. As a result, the effective potential between the hydrophilic and the hydrophobic surface can be repulsive far from the critical point, then attractive and again repulsive when the critical temperature is approached, in agreement with the recent experiment [Nellen at.al., Soft Matter {\bf 7}, 5360 (2011)]

Dielectrophoretic immobilisation of antibodies on microelectrode arrays

A silicon based chip device with a regular array of more than 100 000 cylindrical sub-microelectrodes has been developed for the dielectrophoretic (DEP) manipulation of nanoparticles and molecules in solution. It was fabricated by a standard CMOS (complementary metal oxide semiconductor) compatible process. The distribution of the electrical field gradient was calculated to predict the applicability of the setup. Heating due to field application was determined microscopically using a temperature sensitive fluorescent dye. Depending on voltage and frequency, temperature increase was found to be compatible with protein function. Successful field controlled immobilisation of biomolecules from solution was demonstrated with the autofluorescent protein R-phycoerythrin (RPE) and with fluorescently labelled IgG antibodies. Biological activity after DEP application was proven by immobilisation of an anti-RPE antibody and subsequent binding of RPE. These results demonstrate that the developed chip system allows the directed immobilisation of proteins onto microelectrodes by dielectrophoresis without the need for any chemical modification and that protein function is preserved. Being based on standard lithographical methods, further miniaturisation and on-chip integration of electronics towards a multiparameter single cell analysis system appear near at hand