The present study investigated the use of local and affordable clinoptilolite for the removal of persistent dyes from water. To improve its adsorption capacity, Na-clinoptilolite was modified chemically with two N-terminated siloxanes (molar mass: 2600 and 11000 g/mol) and used to adsorb the dye phenol red. The results of Fourier-transform infrared spectroscopy (FTIR) showed that N-terminated siloxanes were grafted successfully onto clinoptilolite. Examination by X-ray diffraction and scanning electron microscopy supported the suggestion of modifications observed by FTIR. The modified clinoptilolite showed improved adsorption properties for phenol red: up to 0.32 mg of phenol red were removed per g of clinoptilolite modified with N-terminated siloxanes from water, while HCl-treated clinoptilolite removed only 0.15 mg after 4 h. Langmuir and Freundlich models were used to obtain isotherm parameters. Results (with R2 > 0.84) from pseudo-first and pseudo-second order equations suggested that adsorption could have involved chemisorption and physisorption, probably because of the mineral-organic nature of the materials prepared.

Changes in morphology and local chemical composition due to various methods of modification of surfaces of Cu-Zr, Cu-Hf, and Cu-Ti amorphous alloys (caused by aging in air/dry corrosion or hydrogen charging) were investigated. These modification/activation procedures transform the original amorphous ribbons of low surface area into efficient and stable catalysts, due to the segregation of a distinct amount of Cu and the development of a large specific surface area of Cu on a ZrOx or HfOx support. It was found that aging in air resulted in the formation of a bilayer of rough copper (containing small Cu particles indispensable for catalysis) on top of a rather smooth oxide underlayer (ZrOx, HfOx). Careful examination of the cross sections of the modified Cu-based ribbons revealed that, even after prolonged aging in air, only the first few microns of the surface layer was modified. Cu-Ti alloy was stable in air and did not undergo the expected modification. Hydrogenation followed by air exposure resulted in a disintegration of the ribbons into small pieces. Each piece was covered with many small Cu clusters 0.1–0.5 μm in diameter formed on an oxide underlayer. High-energy resolution Auger spectroscopy allowed identification of the underlayers (ZrO2, HfO2, or TiOx), identification of small Cu clusters, determination of the degree of surface oxidation of them, and mapping of the surface to identify the Cu-covered and “naked” heavy metal.

During the translocation step of the elongation cycle, two tRNAs together with the mRNA move synchronously and rapidly on the ribosome. The movement is catalyzed by the binding of elongation factor G (EF-G) and driven by GTP hydrolysis. Here we study structural changes of the ribosome related to EF-G binding and translocation by monitoring the accessibility of ribosomal RNA (rRNA) for chemical modification by dimethyl sulfate or cleavage by hydroxyl radicals generated by Fe(II)-EDTA. In the state of the ribosome that is formed upon binding of EF-G but before the movement of the tRNAs takes place, residues 1054, 1196, and 1201 in helix 34 in 16S rRNA are strongly protected. The protections depend on EF-G binding, but do not require GTP hydrolysis, and are lost upon translocation. Mutants of EF-G, which are active in ribosome binding and GTP hydrolysis but impaired in translocation, do not bring about the protections. According to cryo-electron microscopy (Stark et al., Cell, 2000, 100:301–309), there is no contact of EF-G with the protected residues of helix 34 in the pretranslocation state, suggesting that the observed protections are due to an induced conformational change. Thus, the present results indicate that EF-G binding to the pretranslocation ribosome induces a structural change of the head of the 30S subunit that is essential for subsequent tRNA-mRNA movement in translocation.

All dsDNA viruses multiply their genome and assemble a procapsid, a protein shell devoid of DNA. The genome is subsequently inserted into the procapsid. The bacterial virus phi29 DNA translocating motor contains a hexameric RNA complex composed of six pRNAs. Recently, we found that pRNA dimers are building blocks of pRNA hexamers. Here, we report the structural probing of pRNA monomers and dimers by chemical modification under native conditions and in the presence or absence of Mg2+. The chemical-modification pattern of the monomer is compared to that of the dimer. The data strongly support the previous secondary-structure prediction of the pRNA concerning the single-stranded areas, including three loops and seven bulges. However, discrepancies between the modification patterns of two predicted helical regions suggest the presence of more complicated, higher-order structure in these areas. It was found that dimers were formed via hand-in-hand and head-to-head contact, as the interacting sequence of the right and left loops and all bases in the head loop were protected from chemical modification. Cryoatomic force microscopy revealed that the monomer displayed a check-mark shape and the dimer exhibited an elongated shape. The dimer was twice as long as the monomer. Direct observation of the shape and measurement of size and thickness of the images strongly support the conclusion from chemical modification concerning the head-to-head contact in dimer formation. Our results also suggest that the role for Mg2+ in pRNA folding is to generate a proper configuration for the right and head loops, which play key roles in this symmetrical head-to-head organization. This explains why Mg2+ plays a critical role in pRNA dimer formation, procapsid binding, and phi29 DNA packaging.

The presence of catalytic metal ions in RNA active sites has often been inferred from metal-ion rescue of modified substrates and sometimes from inhibitory effects of alternative metal ions. Herein we report that, in the Tetrahymena group I ribozyme reaction, the deleterious effect of a thio substitution at the pro-SP position of the reactive phosphoryl group is rescued by Mn2+. However, analysis of the reaction of this thio substrate and of substrates with other modifications strongly suggest that this rescue does not stem from a direct Mn2+ interaction with the SP sulfur. Instead, the apparent rescue arises from a Mn2+ ion interacting with the residue immediately 3′ of the cleavage site, A(+1), that stabilizes the tertiary interactions between the oligonucleotide substrate (S) and the active site. This metal site is referred to as site D herein. We also present evidence that a previously observed Ca2+ ion that inhibits the chemical step binds to metal site D. These and other observations suggest that, whereas the interactions of Mn2+ at site D are favorable for the chemical reaction, the Ca2+ at site D exerts its inhibitory effect by disrupting the alignment of the substrates within the active site. These results emphasize the vigilance necessary in the design and interpretation of metal-ion rescue and inhibition experiments. Conversely, in-depth mechanistic analysis of the effects of site-specific substrate modifications can allow the effects of specific metal ion–RNA interactions to be revealed and the properties of individual metal-ion sites to be probed, even within the sea of metal ions bound to RNA.

Binding of Plasmodium falciparum-infected erythrocytes (PE) to endothelial cells is mediated by the erythrocyte-membrane protein, band 3-related adhesin. To determine its role, the binding of infected cells treated with various chemical modifiers was investigated. Binding was inhibited by a lysine modifier (4,4′-diisothiocyanostilbene-2,2′-di-sulfonate (DIDS)) known to specifically bind to band 3, another lysine modifier (trinitrobenzene sulfonic acid), a tyrosine modifier (sodium iodide in conjunction with lactoperoxidase, hydrogen peroxide) and oxidants (diamide, sodium periodate and ADP-chelated ferric ion), but binding was unaffected by the histidine modifier (diethylpyrocarbonate) and the arginine modifier (phenyl glyoxyl monohydrate). To artificially expose the band 3-related adhesin, uninfected erythrocytes were treated with acridine orange or loaded with calcium. These cells bound to C32 amelanotic melanoma cells, were immunostained with a monoclonal antibody that specifically binds to the band 3-related adhesin on PE, and the binding was inhibited by this monoclonal antibody. The binding of acridine orange-treated and calcium-loaded uninfected erythrocytes, could also be blocked by DIDS. In the case of acridine orange-treated erythrocytes, the patterns of the effects of the chemical modification on binding were consistent with that of PE except for tyrosine modification. These results demonstrate that the band 3-related adhesin, even in the absence of parasite-encoded proteins, contributes to PE adhesion.