Effect of Bubbling on the Potential of Reference Electrode

The method for the examination of gas/water interface electrokinetic behavior is developed. "Bubbling potential", i.e. the difference in the potential of the indicator electrode in the absence and presence of gas bubbles was measured. The indicator electrode is a reference electrode with the porous plug exposed to gas bubbles. The charged bubble in contact with the porous plug would affect the potential of the indicator electrode. However, electrodes, whose potential depends on the reversible interfacial reaction, would be relaxed due to the interfacial ionic equilibration and their potential will not be affected by the presence of bubbles. Measured Bubbling potentials are directly related to electrokinetic - potentials. The proposed method is fast, accurate and reproducible so that it can be used for the examination of gas/water interfaces in different conditions. The isoelectric point of argon bubbles in the aqueous NaCl solution was obtained as pHiep = 3.9 and pHiep = 3.4 at ionic strength of 10–3 and 10–2 mol dm–3, respectively. (doi: 10.5562/cca2235

High Resistance Compensation Method for Surface Potential Measurement

The High Resistance Compensation Method (HRCM) was developed to measure the electrode potentials of high resistance electrodes. It is essentially similar to the classical Poggendorff compensation method, but instead of an ampere-meter, the pH-meter was introduced as an indicator of complete compensation. The method was applied to measurements of the electrode potentials of a single crystal rutile (TiO2) electrode. Electrode potentials were converted to surface potentials, and the dependency of the surface potential on pH in aqueous medium was determined

Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands

Interactions of an array of nucleic acid structures with a small series of benzothiazole ligands (bis-benzothiazolyl-pyridines—group 1, 2- thienyl/2-benzothienyl-substituted 6-(2- imidazolinyl) benzothiazoles—group 2, and three 2- aryl/heteroaryl-substituted 6-(2- imidazolinyl)benzothiazoles—group 3) were screened by competition dialysis. Due to the involvement of DNA:RNA hybrids and triplex helices in many essential functions in cells, this study’s main aim is to detect benzothiazole based moieties with selective binding or spectroscopic response to these nucleic structures compared to regular (non- hybrid) DNA and RNA duplexes and single-stranded forms. Complexes of nucleic acids and benzothiazoles, selected by this method, were characterized by UV/Vis, fluorescence and circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and molecular modeling. Two compounds (1 and 6) from groups 1 and 2 demonstrated the highest affinities against 13 nucleic acid structures, while another compound (5) from group 2, despite lower affinities, yielded higher selectivity among studied compounds. Compound 1 significantly inhibited RNase H. Compound 6 could differentiate between B- (binding of 6 dimers inside minor groove) and A- type (intercalation) helices by an induced CD signal, while both 5 and 6 selectively stabilized ATT triplex in regard to AT duplex. Compound 3 induced strong condensation-like changes in CD spectra of AT-rich DNA sequences

Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives

Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as psi-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis- derivative compounds (enthalpy driven) and that of spermine and of their monomeric counterparts (entropy driven). Atomic force microscopy confirmed GC-DNA compaction by the bis-derivatives and the formation of toroid- and rod-like structures responsible for the psi-type pattern in the CD spectra

Bis-phenanthridinium–adenine conjugates as fluorescent and CD reporters for fine structural differences in ds-DNA/RNA and ss-RNA structures

<p>Two structurally similar bis-phenanthridinium–adenine conjugates (equipped with one or two adenines, respectively), exhibiting strong ds-DNA/RNA groove binding, revealed ratiometric fluorescent recognition of alternating AT-DNA with respect to other ds-DNA/RNA and ss-RNA. Further, CD spectra pattern of adenine–bis-phenanthridinium conjugate/polynucleotide complexes strongly depended on polynucleotide secondary structure. Attached adenine was essential for spectrophotometric recognition response, ds-DNA stabilisation and orientation of compounds regarding chiral DNA helix.</p

Effect of Bubbling on the Potential of Reference Electrode

The method for the examination of gas/water interface electrokinetic behavior is developed. "Bubbling potential", i.e. the difference in the potential of the indicator electrode in the absence and presence of gas bubbles was measured. The indicator electrode is a reference electrode with the porous plug exposed to gas bubbles. The charged bubble in contact with the porous plug would affect the potential of the indicator electrode. However, electrodes, whose potential depends on the reversible interfacial reaction, would be relaxed due to the interfacial ionic equilibration and their potential will not be affected by the presence of bubbles. Measured Bubbling potentials are directly related to electrokinetic - potentials. The proposed method is fast, accurate and reproducible so that it can be used for the examination of gas/water interfaces in different conditions. The isoelectric point of argon bubbles in the aqueous NaCl solution was obtained as pHiep = 3.9 and pHiep = 3.4 at ionic strength of 10–3 and 10–2 mol dm–3, respectively. (doi: 10.5562/cca2235

Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III

Dipeptidyl peptidase III (DPP III, EC 3.4.14.4) is a monozinc metalloexopeptidase that hydrolyzes dipeptides from the N-terminus of peptides consisting of three or more amino acids. Recently, DPP III has attracted great interest from scientists, and numerous studies have been conducted showing that it is involved in the regulation of various physiological processes. Since it is the only metalloenzyme among the dipeptidyl peptidases, we considered it important to study the process of binding and exchange of physiologically relevant metal dications in DPP III. Using fluorimetry, we measured the Kd values for the binding of Zn2+, Cu2+, and Co2+ to the catalytic site, and using isothermal titration calorimetry (ITC), we measured the Kd values for the binding of these metals to an additional binding site. The structure of the catalytic metal’s binding site is known from previous studies, and in this work, the affinities for this site were calculated for Zn2+, Cu2+, Co2+, and Mn2+ using the QM approach. The structures of the additional binding sites for the Zn2+ and Cu2+ were also identified, and MD simulations showed that two Cu2+ ions bound to the catalytic and inhibitory sites exchanged less frequently than the Zn2+ ions bound to these sites