2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence

We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.     

A comparison of quantitative and qualitative superoxide dismutase assays for application to low temperature microalgae

Antioxidant enzymes such as superoxide dismutase (SOD) play a key role in the removal of reactive oxygen species produced during visible and ultraviolet irradiance stress in microalgae and plants. However, little is known about the enzymatic antioxidative stress responses in ecologically important Antarctic marine microalgae. SOD in particular is difficult to analyze, possibly due to problems in obtaining sufficient quantities necessary for reliable and reproducible enzymatic assays. The aim of the present work was to create a sensitive, easy-to-use and reliable method for SOD determination in Antarctic microalgal material by comparing and optimizing existing protein extraction procedures and SOD assays in the marine Antarctic diatom Chaetoceros brevis. Optimization was achieved in cell disruption (sonication) and protein extraction procedures, extraction buffers, SOD assay methods (xanthine/xanthine oxidase and NBT/riboflavin photometric quantitative methods and native gel electrophoresis qualitative method) and the assay temperature. Protein extraction was optimal at low sonication amplitudes after a few pulses, irrespective of the type of buffer used. Extraction efficiency varied highly between the tested buffers; most protein was extracted in the presence of 1% of Triton X-100. SOD activity was best quantified using the NBT/riboflavin method in combination with a buffer containing potassium phosphate and Triton X-100. Moreover, the NBT/riboflavin method was demonstrated to be the most reliable and sensitive method at low temperatures (5 degrees C).     

pH-driven conformational switch of "i-motif" DNA for the reversible assembly of gold nanoparticles

Herein we demonstrate that gold nanoparticles conjugated to "i-motif" DNA behave like a pH dependent switch that undergoes reversible aggregations which can be easily visualized by the naked eye.     

Wavelength-dependent Coulomb explosion in carbon disulphide (CS2) clusters: generation of energetic multiply charged carbon and sulphur ions

A gigawatt laser-induced Coulomb explosion has been observed in carbon disulphide (CS(2)) clusters generating energetic, multiply charged [C](m+) (m = 1-4) and [S](n+) (n = 1-6) atomic ions of carbon and sulphur. The Coulomb explosion shows wavelength dependence. Comparison of these results with our earlier work shows that the polarizability and dipole moment might help in energy absorption from the laser field but they are not mandatory conditions for this low-intensity Coulomb explosion. The results show that in a field of 10(9) W/cm(2), absorption of 266 and 355 nm laser radiation by CS(2) clusters leads to multiphoton dissociation/ionization whereas at 532 nm the whole cluster explodes generating multiply charged atomic ions.     

Contact instability of thin elastic films on patterned substrates

The free surface of a soft elastic film becomes unstable and forms an isotropic labyrinth pattern when a rigid flat plate is brought into adhesive contact with the film. These patterns have a characteristic wavelength, lambda approximately 3H, where H is the film thickness. We show that these random structures can be ordered, modulated, and aligned by depositing the elastic film (cross-linked polydimethylsiloxane) on a patterned substrate and by bringing the free surface of the film in increasing adhesive contact with a flat stamp. Interestingly, the influence of the substrate "bleeds" through the film to its free surface. It becomes possible to generate complex two-dimensional ordered structures such as an array of femtoliter beakers even by using a simple one-dimensional stripe patterned substrate when the instability wavelength, lambda approximately 3H, nearly matches the substrate pattern periodicity. The free surface morphology is modulated in situ by merely varying the stamp-surface separation distance. The free surface structures originating from the elastic contact instability can also be made permanent by the UV-ozone induced oxidation and stiffening.     

Microwave-assisted extraction of active pharmaceutical ingredient from solid dosage forms

The microwave assisted extraction (MAE) technique has been evaluated for the extraction of active pharmaceutical ingredients (API) from various solid dosage forms. Using immediate release tablets of Compound A as a model, optimization of the extraction method with regards to extraction solvent composition, extraction time and temperature was briefly discussed. Complete recovery of Compound A was achieved when samples were extracted using acetonitrile as the extraction solvent under microwave heating at a constant cell temperature of 50 degrees C for 5 min. The optimized MAE method was applied for content uniformity (single tablet extraction) and potency (multiple tablets extraction) assays of release and stability samples of two products of Compound A (5 and 25mg dose strength) stored at various conditions. To further demonstrate the applicability of MAE, the instrumental extraction conditions (50 degrees C for 5 min) were adopted for the extraction of montelukast sodium (Singulair) from various solid dosage forms using methanol-water (75:25, v/v) as the extraction solvent. The MAE procedure demonstrated an extraction efficiency of 97.4-101.9% label claim with the greatest RSD at 1.4%. The results compare favorably with 97.6-102.3% label claim with the greatest RSD at 2.9% obtained with validated mechanical extraction procedures. The system is affordable, user-friendly and simple to operate and troubleshoot. Rapid extraction process (7 min/run) along with high throughput capacity (up to 23 samples simultaneously) would lead to reduced cycle time and thus increased productivity.     

Short haired wormlike micelles in mixed nonionic fluorocarbon surfactants

We have studied the rheological behavior of viscoelastic wormlike micellar solution in a mixed system of nonionic fluorinated surfactants, perfluoroalkyl sulfonamide ethoxylate, C(8)F(17)SO(2)N(C(3)H(7))(CH(2)CH(2)O)(n)H abbreviated as C(8)F(17)EO(n) (n=10 and 20). Above critical micelle concentration, the surfactant, C(8)F(17)EO(20) forms small spherical micelles in water and the viscosity of the solution remains constant regardless of the shear rate, i.e., the solutions exhibit Newtonian behavior. However, upon successive addition of the C(8)F(17)EO(10) the viscosity of the solution increases and at certain C(8)F(17)EO(10) concentration, shear-thinning behavior is observed indicating the formation wormlike micelles. Contrary to what is expected, there is a viscosity increase with the addition of the hydrophilic C(8)F(17)EO(20) to C(8)F(17)EO(10) aqueous solutions at certain temperature and concentration, which could be attributed to an increase in rigidity of the surfactant layer and to the shifting of micellar branching to higher temperatures. The oscillatory-shear rheological behavior of the viscoelastic solution can be described by Maxwell model at low frequency. Small-angle X-ray scattering (SAXS) measurements confirmed the formation of small spherical micellar aggregates in the dilute aqueous C(8)F(17)EO(20) solution. The SAXS data shows the one-dimensional growth on the micellar size with increase in the C(8)F(17)EO(10) concentration. Thus, the present SAXS data supports the rheological data.