Differential Cyclic Voltammetry - a Novel Technique for Selective and Simultaneous Detection using Redox Cycling Based Sensors

Redox cycling (RC) is an effect that is used to amplify electrochemical signals. However, traditional techniques such as cyclic voltammetry (CV) do not provide clear insight for a mixture of multiple redox couples while RC is applied. Thus, we have developed a new measurement technique which delivers electrochemical spectra of all reversible redox couples present based on concentrations and standard potentials. This technique has been named differential cyclic voltammetry (DCV). We have fabricated micrometer-sized interdigitated electrode (IDE) sensors to conduct DCV measurements in mixtures of 1mM catechol and 4mM [Ru(NH3)6]Cl3. To simulate the electrochemical behavior of these sensors we have also developed a finite element model (FEM) in Comsol®. The\ud experimental data corresponds to the calculated spectra obtained from simulations. Additionally, the measured spectra can be used to easily derive standard potentials and concentrations simultaneously and selectively.\u

Scaling theory of DNA confined in nanochannels and nanoslits

A scaling analysis is presented of the statistics of long DNA confined in nanochannels and nanoslits. It is argued that there are several regimes in between the de Gennes and Odijk limits introduced long ago. The DNA chain folds back on itself giving rise to a global persistence length which may be very large owing to entropic deflection. Moreover, there is an orientational excluded-volume effect between the DNA segments imposed solely by the nanoconfinement. These two effects cause the chain statistics to be intricate leading to nontrivial power laws for the chain extension in the intermediate regimes. It is stressed that DNA confinement within nanochannels differs from that in nanoslits because the respective orientational excluded-volume effects are not the same.Comment: 5 pages, 1 figure Several corrections, some minor changes in the text and replacement of one referenc

Forces During Bacteriophage DNA Packaging and Ejection

The conjunction of insights from structural biology, solution biochemistry, genetics and single molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a beneficiary of these experimental techniques is the study of viruses. In this paper we describe how the insights obtained from such experiments can be utilized to construct physical models of processes in the viral life cycle. We focus on dsDNA bacteriophages and show that the bending elasticity of DNA and its electrostatics in solution can be combined to determine the forces experienced during packaging and ejection of the viral genome. Furthermore, we quantitatively analyze the effect of fluid viscosity and capsid expansion on the forces experienced during packaging. Finally, we present a model for DNA ejection from bacteriophages based on the hypothesis that the energy stored in the tightly packed genome within the capsid leads to its forceful ejection. The predictions of our model can be tested through experiments in vitro where DNA ejection is inhibited by the application of external osmotic pressure

A closed form for the electrostatic interaction between two rod-like charged objects

We have calculated the electrostatic interaction between two rod-like charged objects with arbitrary orientations in three dimensions. we obtained a closed form formula expressing the interaction energy in terms of the separation distance between the centers of the two rod-like objects, $r$, their lengths (denoted by $2l_1$ and $2l_2$), and their relative orientations (indicated by $\theta$ and $\phi$). When the objects have the same length ($2l_1=2l_2=l$), for particular values of separations, i.e for $r\leq0.8 l$, two types of minimum are appeared in the interaction energy with respect to $\theta$. By employing the closed form formula and introducing a scaled temperature $t$, we have also studied the thermodynamic properties of a one dimensional system of rod-like charged objects. For different separation distances, the dependence of the specific heat of the system to the scaled temperature has been studied. It is found that for $r<0.8 l$, the specific heat has a maximum.Comment: 10 pages, 9 figures, 1 table, Accepted by J. Phys.: Condens. Matte

Buckling instability for a charged and fluctuating semiflexible polymer

In this article we address the problem of Euler's buckling instability in a charged semi-flexible polymer that is under the action of a compressive force. We consider this instability as a phase transition and investigate the role of thermal fluctuations in the buckling critical force. By performing molecular dynamic simulations, we show that the critical force decreases when the temperature increases. Repulsive electrostatic interaction in the finite temperature is in competition with thermal fluctuations to increase the buckling threshold

Dynamics of DNA Ejection From Bacteriophage

The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is diffusion, but in the case of phage ejection a significant driving force derives from the high degree of stress to which the DNA is subjected in the viral capsid. The translocation is further sped up by the ratcheting and entropic forces associated with proteins that bind to the viral DNA in the host cell cytoplasm. We formulate a generalized diffusion equation that includes these various pushing and pulling effects and make estimates of the corresponding speed-ups in the overall translocation process. Stress in the capsid is the dominant factor throughout early ejection, with the pull due to binding particles taking over at later stages. Confinement effects are also investigated, in the case where the phage injects its DNA into a volume comparable to the capsid size. Our results suggest a series of in vitro experiments involving the ejection of DNA into vesicles filled with varying amounts of binding proteins from phage whose state of stress is controlled by ambient salt conditions or by tuning genome length.Comment: 17 pages, 5 figure