Ideal‐filter capillary electrophoresis: A highly efficient partitioning method for selection of protein binders from oligonucleotide libraries

Selection of affinity ligands for protein targets from oligonucleotide libraries currently involves multiple rounds of alternating steps of partitioning of protein‐bound oligonucleotides (binders) from protein‐unbound oligonucleotides (nonbinders). We have recently introduced ideal‐filter capillary electrophoresis (IFCE) for binder selection in a single step of partitioning. In IFCE, protein‐binder complexes and nonbinders move inside the capillary in the opposite directions, and the efficiency of their partitioning reaches 10⁹, i.e., only one of a billion molecules of nonbinders leaks through IFCE while all binders pass through. The condition of IFCE can be satisfied when the magnitude of the mobility of EOF is smaller than that of the protein‐binder complexes and larger than that of nonbinders. The efficiency of partitioning in IFCE is 10 million times higher than those of solid‐phase‐based methods of partitioning typically used in selection of affinity ligands for protein targets from oligonucleotide libraries. Here, we provide additional details on our justification for IFCE development. We elaborate on electrophoretic aspects of the method and define the theoretical range of EOF mobilities that support IFCE. Based on these theoretical results, we identify an experimental range of background electrolyte's ionic strength that supports IFCE. We also extend our interpretation of the results and discuss in‐depth IFCE's prospective in practical applications and fundamental studies.     

New DNA-sensor based on thiacalix[4]arene-modified polydiacetylene particles

Russian Chemical Bulletin - New p-tert-butyl thiacalix[4]arene derivative in the 1,3-alternate stereoisomeric form containing two diethylenetriamine groups and pentacosa-10,12-diynoic moieties on...     

Thermal and electrical properties of Ca5Mg4−xZnx(VO4)6 (0 ≤ x ≤ 4)

Calcium vanadates Ca₅Mg_4−xZn_x(VO₄)₆ (0 ≤ x ≤ 4) have been studied for the first time using a set of high-temperature methods of analysis. The onset of melting process determined from differential scanning calorimetry decreases from 1158 to 881 °C (± 1.5 °C) with increasing of x (dopant’s content). CTE temperature dependence is found to show a hysteresis. Electrical transport properties measured by impedance spectroscopy in air of different humidity are also discussed. The value of electrical conductivity does not depend on air humidity. It is found to equal to 1.5 × 10⁻⁶ S cm⁻¹ at 720 °C for Ca₅Mg₄(VO₄)₆ which is specific for garnet-related crystals.

     

Ferrocene‐modified thiopyrimidines: synthesis,enantiomeric resolution,antitumor activity

Ferrocenylalkyl thiopyrimidines ( 6a–d to 9a–d ) were prepared via the reaction of the α‐(hydroxy)alkyl ferrocenes, FcCHR(OH) ( 1a–d ; Fc = ferrocenyl; R = H, Me, Et, Ph), with 2‐thiopyrimidines ( 2 – 5 ) in acetone at room temperature in the presence of TFA, yielding 50–95%. The resulting enantiomers were resolved using HPLC on modified cellulose as chiral selector. The antitumor activities of S‐ferrocenylethyl 2‐thiopyrimidine ( 6b ) against two murine solid tumor models, carcinoma 755 (Ca755) and Lewis lung carcinoma (LLC) were evaluated in vivo. The strong antitumor effect of compound 6b on Ca755 and LLC was demonstrated. The index of tumor growth inhibition on Ca755 equaled 95% in comparison with control. Copyright © 2010 John Wiley & Sons, Ltd.     

Dependence of Total p-Electron Energy on the Number of Non-Bonding Molecular Orbitals

In recent work [Gutman et al. (2004) Chem Phys Lett 383: 171] a method was developed by means of which the influence of non-bonding molecular orbitals (NBMOs) on the value of total -electron energy (E) can be separated from the multitude of other molecular-structure-dependent effects. We now extend this method and establish the relation between E and the number n ₀ of NBMOs. It is shown that E (when computed within the HMO approximation, and expressed in the units of the HMO resonance integral ) is a decreasing function of n ₀, and that the dependence of E on n ₀ is almost perfectly linear.     

Observation of an unprecedented Cu Bis-His site: crystal structure of the H129V mutant of nitrite reductase

Copper nitrite reductases contain both an electron-transfer type 1 Cu site and a catalytic type 2 Cu site. We have mutated one of the type 2 copper ligating histidines to observe the effect on catalytic turnover. This mutation has created a unique site where Cu is ligated by 2 His Nepsilon2 atoms alone.     

Computational analysis of native and modified oligofructosides

This paper presents a quantum chemical calculation of native (2–7 fructoside residues) and chemically modified (2–4 fructoside residues) levan molecule models. A levan modification was carried out by oxidation and the following reduction or hyrdazonation of the fructoside rings. The conformational particularity and reaction ability was studied for the native and for the modified levan molecules.     

Platinum metallodrug-protein binding studies by capillary electrophoresis-inductively coupled plasma-mass spectrometry: characterization of interactions between Pt(II) complexes and human serum albumin

Characterizing how platinum metallocomplexes bind to human serum albumin (HSA) is essential in evaluating anticancer drug candidates. Using cisplatin as a reference complex, the application of capillary electrophoresis (CE) to reliably assess drug/HSA interactions was validated. Since this complex is small compared to the size of the protein, the binding response could only be recognized when applying CE coupled to a (platinum) metal-specific mode of detection, namely inductively coupled plasma-mass spectrometry (ICP-MS). This coupling allowed for confirmation of a specific affinity of cisplatin and novel Pt complexes to HSA, measurement of the kinetics of binding reactions, and determination of the number of drug molecules attached to the protein. As the cisplatin/HSA molar ratio increased, the reaction rate became faster with a maximum on the kinetic curve appearing at about 50 h of incubation at 20 times excess of cisplatin. The reaction was characterized as a pseudo-first order reaction with the rate constant k = 0.003 min(-1) at 37 degrees C. When incubated with a 20-fold excess of cisplatin, HSA bound up to 10 mol of Pt per mol of the protein. This is indicative for a strong metal-protein coordination occurring at several HSA sites other than the only protein cysteine residue. Structural analogs of cisplatin, bearing aminoalcohol ligands, showed comparable protein binding reactivity and stoichiometry but a common equilibrium was not reached even after one week of incubation. Also apparent was a two-step mechanism of the binding reaction. Results demonstrated the suitability of CE-ICP-MS as a rapid assay for high-throughput studying of drug/HSA interactions.