Jakub Dvořák

Interaction of DNA with echinomycin at the mercury electrode surface as detected by impedance and chronopotentiometric measurements.

The capacitance measurement (dependence of the differential capacitance C of the electrode double layer on potential E, C-E curves), electrochemical impedance spectroscopy (frequency response of the impedance Z of the electrode double layer-EIS) and constant current chronopotentiometry (dependence of dt/dE on potential at constant current, chronopotentiometric stripping analysis-CPSA) have been used for electrochemical study of echinomycin and its interaction with single-stranded (ss) and double-stranded (ds) DNA at the hanging mercury drop electrode (HMDE). The capacitance measurement showed that echinomycin gives a pseudocapacitance redox peak strongly dependent on the a.c. voltage frequency at the potential of -0.53 V. This peak is observed with dsDNA-echinomycin complex as well, but not with ssDNA treated by echinomycin. Similar results were obtained using CPSA measurements. Thus capacitance measurements and CPSA can distinguish with the aid of the bis-intercalator echinomycin the single-stranded and double helical form of DNA adsorbed at the mercury electrode surface. Impedance measurement in connection with adsorptive transfer technique can find the differences between ssDNA and dsDNA, which promise to use this technique for detection of dsDNA in hybridisation reactions.

Electrochemical impedance spectroscopy of polynucleotide adsorption.

The dependence of the impedance of the electrode double layer of mercury electrode on frequency around the potentials of the tensammetric peaks of single-stranded and double-helical polynucleotides and DNA was studied. From the frequency dependence of the impedance of the electrode double layer represented in a complex plane impedance plot, the electric equivalent circuit of the electrode covered with adsorbed DNA layer was determined. It was concluded that the desorption of denatured ssDNA is accompanied by higher dielectric losses than the desorption of native dsDNA. This can be explained by the higher flexibility of ssDNA compared to the dsDNA. The capacitance peak of single-stranded polyadenylic acid (poly A) observed at pH 8 around -1.3 V splits at low frequencies in two peaks.

Impedance Analysis of DNA and DNA-Drug Interactions on Thin Mercury Film Electrodes

In this review we briefly summarize the results of impedance measurements (dependence of the differential capacitance C and/or impedance Z of the electrode double layer on potential E, C-E curves) or on frequency (Electrochemical Impedance Spectroscopy-EIS) of nucleic acids at mercury film electrode (MFE). Mercury film was plated either on a glassy carbon electrode (GCE) or pyrolytic graphite electrode (PGE). The dependence of the pseudocapacitance redox peak of echinomycin on concentration and on the ac voltage frequency was measured in bulk solution. Interaction of single- and double-stranded DNA with bis-intercalator echinomycin at nucleic acid-modified surface was studied using EIS with adsorptive transfer method.

Nucleic acid sensing by impedance measurements

Abstract The adsorption of cytosine, 5-bromocytosine and native and denatured DNA was followed by measurement of the impedance of the electrode double layer. The two-dimensional condensation of both cytosine and 5-Br-cytosine and the formation of a self-assembled compact layer at the electrode surface was observed resulting in a capacitance pit on the C–E curves. The pit of 5-Br-cytosine occurs around the potential of electrocapillary maximum (ECM), the pit of cytosine around −1.4 V. The electrode impedance is affected by the conformation of nucleic acid.

Softening Splits in Decision Trees Using Simulated Annealing

Predictions computed by a classification tree are usually constant on axis-parallel hyperrectangles corresponding to the leaves and have strict jumps on their boundaries. Frequently a better approximation may be expected, if the prediction function of the original tree is replaced by a continuous approximation. The approximation is constructed using the same training data on which the original tree was grown and the structure of the tree is preserved. The current paper uses the model of trees with soft splits suggested by Quinlan and implemented in C4.5, however, the training algorithm is substantially different. The method uses simulated annealing, so it is quite computationally expensive. However, numerical test with data derived from an experiment in particle physics shows that besides the expected better approximation of the training data, also smaller generalization error is achieved.