Capillary gel electrophoresis of single-stranded DNA fragments with UV detection

Capillary gel electrophoresis has proven to be a powerful tool in biomedical research. We report our investigation of some of the critical parameters affecting separations of single-stranded DNA fragments as monitored by ultraviolet (UV) absorbance detection. Although not as sensitive as laser-induced fluorescence (LIF), UV absorbance detection allows one to calculate quite accurately, and inexpensively, the molarity of each separated DNA fragment and, moreover, the signal “fading” effect normally observed with LIF detection can be, in many cases, substituted for fluorescence to detect the many different single-stranded DNAs, as well as for detection of sequencing reactions.     

Paenibacillus polymyxa PKB1 produces variants of polymyxin B-type antibiotics

Polymyxins are cationic lipopeptide antibiotics active against many species of Gram-negative bacteria. We sequenced the gene cluster for polymyxin biosynthesis from Paenibacillus polymyxa PKB1. The 40.8 kb gene cluster comprises three nonribosomal peptide synthetase-encoding genes and two ABC transporter-like genes. Disruption of a peptide synthetase gene abolished all antibiotic production, whereas deletion of one or both transporter genes only reduced antibiotic production. Computational analysis of the peptide synthetase modules suggested that the enzyme system produces variant forms of polymyxin B (1 and 2), with D-2,4-diaminobutyrate instead of L-2,4-diaminobutyrate in amino acid position 3. Two antibacterial metabolites were resolved by HPLC and identified by high-resolution mass spectrometry and MS/MS sequencing as the expected variants 3 and 4 of polymyxin B₁ (1) and B₂ (2). Stereochemical analysis confirmed the presence of both D-2,4-diaminobutyrate and L-2,4-diaminobutyrate residues.     

Adsorption of anionic and cationic dyes by activated carbons, PVA hydrogels, and PVA/AC composite

The textural and adsorption characteristics of a series of activated carbons (ACs), porous poly(vinyl alcohol) (PVA) gels, and PVA/AC composites were studied using scanning electron microscopy, mercury porosimetry, adsorption of nitrogen (at 77.4 K), cationic methylene blue (MB), anionic methyl orange (MO), and Congo red (CR) from the aqueous solutions. Dye-PVA-AC-water interactions were modeled using the semiempirical quantum chemical method PM6. The percentage of dye removed (C(rem)) by the ACs was close to 100% at an equilibrium concentration (C(eq)) of less than 0.1 mM but decreased with increasing dye concentration. This decrease was stronger at C(eq) of less than 1 mM, and C(rem) was less than 50% at a C(eq) of 10-20 mM. For PVA and the PVA/AC composite containing C-7, the C(rem) values were minimal (<75%). The free energy distribution functions (f(ΔG)) for dye adsorption include one to three peaks in the -ΔG range of 1-60 kJ/mol, depending on the dye concentration range used and the spatial, charge symmetry of the hydrated dye ions and the structural characteristics of the adsorbents. The f(ΔG) shape is most complex for MO with the most asymmetrical geometry and charge distribution and adsorbed at concentrations over a large C(eq) range. For symmetrical CR ions, adsorbed over a narrow C(eq) range, the f(ΔG) plot includes mainly one narrow peak. MB has a minimal molecular size at a planar geometry (especially important for effective adsorption in slit-shaped pores) which explains its greater adsorptive capacity over that of MO or CR. Dye adsorption was greatest for ACs with the largest surface area but as molecular size increases adsorption depends to a greater extent on the pore size distribution in addition to total and nanopore surface areas and pore volume.     

Amino-acid-dependent shift in tRNA synthetase editing mechanisms

Many aminoacyl-tRNA synthetases prevent mistranslation by relying upon proofreading activities at multiple stages of the aminoacylation reaction. In leucyl-tRNA synthetase (LeuRS), editing activities that precede or are subsequent to tRNA charging have been identified. Although both are operational, either the pre- or post-transfer editing activity can predominate. Yeast cytoplasmic LeuRS (ycLeuRS) misactivates structurally similar noncognate amino acids including isoleucine and methionine. We show that ycLeuRS has a robust post-transfer editing activity that efficiently clears tRNA(Leu) mischarged with isoleucine. In comparison, the enzyme's post-transfer hydrolytic activity against tRNA(Leu) mischarged with methionine is weak. Rather, methionyl-adenylate is cleared robustly via an enzyme-mediated pre-transfer editing activity. We hypothesize that, similar to E. coli LeuRS, ycLeuRS has coexisting functional pre- and post-transfer editing activities. In the case of ycLeuRS, a shift between the two editing pathways is triggered by the identity of the noncognate amino acid.     

Probing the nature of the Co(III) ion in corrins: the structural and electronic properties of dicyano- and aquacyanocobyrinic acid heptamethyl ester and a stable yellow dicyano- and aquacyanocobyrinic acid heptamethyl ester

A stable yellow derivative of cobyrinic acid heptamethyl ester, (5R,6R)-Coα,Coβ-dicyano-5,6-dihydro-5-hydroxy-heptamethylcob(III)yrinate-c,6-lactone (DCSYCbs), was prepared from dicyanocobyrinic acid heptamethyl ester (DCCbs). The C5 carbon is oxidized and the c side chain cyclized to form a lactone at C6; the 13 atom, 14 π-e(-) delocalized system of corrins is interrupted, giving a triazamethine system with four conjugated double bonds between N22 and N24 and an isolated double bond between N21 and C4. Stable yellow aquacyanocobyrinic acid heptamethyl ester (ACSYCbs) was prepared by driving off HCN with N(2) in a methanol/acetic acid solution. The electronic spectra of DCCbs and DCSYCbs appear similar except that the bands in DCSYCbs are shifted to shorter wavelengths and the γ-band is much less intense. The experimental spectra were adequately modeled using TD-DFT at the PBE1PBE/6-311G(d,p) level of theory. DCSYCbs crystallizes in the space group P2(1)2(1)2(1) (R(1) = 6.08%) with Z = 4, including one methanol solvent molecule and one water molecule per cobester. The addition of a hydroxyl group at C5 causes loss of the double bond between C5 and C6 and elongation of the C5-C6 bond. From a combination of two-dimensional (1)H TOCSY and ROESY NMR spectra and (1)H/(13)C HSQC and HMBC data, the complete (1)H and (13)C NMR assignments of DCSYCbs were possible, except for two of the ester methyl groups and the (13)C resonances of the two axial cyanide ligands. The latter were assigned using relative chemical shifts calculated by GIAO-DFT methods. The (59)Co resonance of DCCbs was observed at 4074 ppm while that of DCSYCbs is shifted downfield to 4298 ppm. Comparison with available (59)Co data of analogous systems suggests that the more π-conjugated corrin of DCCbs interacts more strongly with the metal than the less extensively conjugated macrocycle of DCSYCbs. As the strength of the interaction between Co(III) and an equatorial macrocycle increases, ν(CN) of axially coordinated CN(-) shifts to lower frequency; in DCSYCbs and DCCbs ν(CN) occurs at 2138 and 2123 cm(-1), respectively. Hence the corrin ligand in DCCbs interacts more strongly with the metal than the stable yellow corrin ligand, with its diminished conjugation. The UV-vis spectral data and DFT-calculated MOs are consistent with greater overlap between the corrin and the metal orbitals in DCCbs relative to DCSYCbs, which gives the metal in the former a softer, more covalent character.     

Dyscusins A-C, three new steroids from the leaves of Dysoxylum cumingianum

Three new steroids dyscusins A-C (1-3), including a stigmastane-type sterol and two pregnanes, together with two known steroids were isolated from the leaves of Dysoxylum cumingianum (Meliaceae). Their structures were elucidated on the basis of extensive spectroscopic analyses. In a cytotoxicity assay, compound 1 showed ten-fold enhanced cytotoxicity against multi-drug resistant cancer cells (KB-C2) in the presence of 2.5 μM colchicine as compared with the absence of colchicine. This notable finding indicated that 1 possessed a multi-drug resistant reversal effect.     

Electrochemical behavior of anthraquinone in aqueous solution in presence of a non-ionic surfactant

Cyclic voltammetric behavior of anthraquinone in aqueous medium has been studied in presence of a non-ionic surfactant, Triton X-100 (TX-100) using sodium salt of anthraquinone-2-sulphonic acid (AQS) as the electro-active species. When cathodic potential is applied, the anthraquinone (AQ) group of AQS is reduced to its dianion. In the reverse scan, the oxidation of AQ²⁻ gives AQ. The electrochemical behavior shows a profound influence from the dissolved state of TX-100 in aqueous media. Spectrophotometric results indicate interaction between AQ and TX-100. A CEC (chemical–electrochemical–chemical) mechanism with the electrochemical reaction coupled with preceding interaction of AQS with TX-100 and following protonation reaction of reduced AQ has been proposed.     

Vitamin B12 as an allosteric cofactor; dual fluorescence, hysteresis, oscillations and the selection of corrin over porphyrin

Studies of the emission spectra of four Co(III) cobinamides (diaquo-, aquohydroxo-, dihydroxo- and dicyano-) show (1) that the excited states corresponding to the alphabeta and epsilon absorption bands behave like the S(1) and S(2) levels in the non-alternant hydrocarbon azulene (with emission from S(2)> S(1) in violation of Kasha's rule) and (2) that the excited states include a TICT (twisted intramolecular charge transfer) mechanism, as in the simpler cyanines, but where the TICT state gives rise to dual fluorescence instead of cis-trans isomerisation. Combined with the previously reported dual fluorescence from the S(1) level in synthetic metal corrinoids and in the naturally-occurring metal-free corrin, this provides evidence that the existence of an additional (metastable) ground state with a significantly different vibronic splitting and nuclear configuration is an intrinsic property of the basic corrin ligand (irrespective of the nature of the side-chains and the metal ion or even the absence of a metal) which distinguishes it from porphyrin. The occurrence of hysteresis (and its associated oscillations) in redox reactions of the cobinamides involving both the Co(III/II) and Co(II/I) couples indicates that the corrin ligand also has an intrinsic ability to exist in different conformations or "allosteric" forms with differing redox potential, which further distinguishes it from the porphyrin ligand. Possible links between the existence of an additional metastable ground state and of allosteric changes and the likely reasons for the selection of corrin over a porphyrin for the vitamin B(12)-dependent enzymes are discussed.