Acidity of secondary hydroxyls in ATP and adenosine analogues and the question of a 2',3'-hydrogen bond in ribonucleosides

As sugar-modified nucleosides, nucleotides, and oligonucleotides are much used in pharmacology and enzymatic studies, knowledge on the relative pKa values of the secondary hydroxyls can be of great help in design and interpretations. To obtain this, we have determined the acidity constants for ATP, dATP, 2'-F-dATP, 2'-NH2-ATP, and 2'-O-methyl ATP in aqueous solution. The influence of the relative acidities seem to be mainly from inductive effects since a good correlation between pKa values and group electronegativity is found. There is no clear energetic contribution from a much suggested H-bond between the 2'-OH and 3'-oxyanion in adenosine. To clarify if this kind of H-bond would make a more-prominent energetic contribution in less-polar solvents, we also determined the acidity of secondary hydroxyls in adenosine, 2'-O-methyladenosine, and 3'-O-methyladenosine in water, methanol, and DMSO. The relative differences in pKa values were, however, quite similar in all solvents, suggesting that no major energetic contribution is made by an intramolecular H-bond in adenosine.     

Protein nanostructures formed via direct-write dip-pen nanolithography

We report a tip modification strategy coupled with dip-pen nanolithography for depositing proteins on a surface. This methodology offers patterning capabilities on the scale of 45 nm to many micrometers length. The biorecognition properties of nanofeatures composed of immunoglobulin-gamma (IgG) were confirmed by reacting the array with gold nanoparticles coated with anti-IgG. Furthermore, a two component nanoarray was fabricated in direct-write fashion by DPN, and the biorecognition properties of this structure were investigated by AFM without biodiagnostic labels.     

Primary cultures of chick osteocytes retain functional gap junctions between osteocytes and between osteocytes and osteoblasts.

The inaccessibility of osteocytes due to their embedment in the calcified bone matrix in vivo has precluded direct demonstration that osteocytes use gap junctions as a means of intercellular communication. In this article, we report successfully isolating primary cultures of osteocytes from chick calvaria, and, using anti-connexin 43 immunocytochemistry, demonstrate gap junction distribution to be comparable to that found in vivo. Next, we demonstrate the functionality of the gap junctions by (1) dye coupling studies that showed the spread of microinjected Lucifer Yellow from osteoblast to osteocyte and between adjacent osteocytes and (2) analysis of fluorescence replacement after photobleaching (FRAP), in which photobleaching of cells loaded with a membrane-permeable dye resulted in rapid recovery of fluorescence into the photobleached osteocyte, within 5 min postbleaching. This FRAP effect did not occur when cells were treated with a gap junction blocker (18alpha-glycyrrhetinic acid), but replacement of fluorescence into the photobleached cell resumed when it was removed. These studies demonstrate that gap junctions are responsible for intercellular communication between adjacent osteocytes and between osteoblasts and osteocytes. This role is consistent with the ability of osteocytes to respond to and transmit signals over long distances while embedded in a calcified matrix.     

Experimental and theoretical studies of the conformational structures of the mixed clusters of 1-cyanonaphthalene with water

A concerted experimental (mass-selective, double-resonance laser spectroscopic technique) and theoretical (correlated quantum chemistry calculation) study of hydrogen-bonded clusters of 1-cyanonaphthalene (CNN) with water has been carried out to probe geometrical structures of the conformational isomers. The structures of the two low-energy conformers of CNN-H2O and CNN-(H2O)2, calculated at the MP2/cc-pVDZ level of theory, are consistent with the mass-selective infrared-ultraviolet double-resonance spectra and the partially resolved rotational band contours of the S1 <-- S0 origin bands. The facile loss of a neutral water molecule from the cluster ion of CNN-(H2O)2, relative to that of CNN-H2O, is in accord with the proposed structures of the clusters.     

Optical charge-transfer in iron(III)hexacyanoferrate(II): electro-intercalated cations induce lattice-energy-dependent ground-state energies

The maximum of the color-conferring charge-transfer (CT) band in Prussian Blue (PB) varies with the electrochemically introduced cation M(z+) incorporated (as "supernumerary") for charge neutrality, and the dependence on particular properties of the M(z+) has been sought. With alkali-metal ions, the CT-maximum shifts are in the same sequence as the PB mass changes on M+ insertion; the effect on the CT ground state of the intra-lattice interaction of an M+ with the ferrocyanide CN- moiety (competing with cation hydration), is then implicated in shifts of the maxima, as the ferrocyanide is the donor center in the optical CT. More definitely, for M2+ and Ag+, solubility-products of the insoluble M(z+) ferrocyanides (that provide direct indicators of the intra-lattice M(z+)-[Fe(II)(CN)(6)](4- interactions) show a strong correlation with the spectral shifts. The determining interaction of M(z+) with ferrocyanide within PB is enhanced in some cases by the accessibility of M(z+) oxidation states +/- 1 different from the common values. PB lattice energies and the ground states of the optical CTs thus appear closely interlinked. The electrochemical uptake of appreciable amounts of the M(z+) within the lattices was confirmed by XPS.     

Surface modification of poly(dimethylsiloxane) microchannels

This review looks at the efforts that are being made to modify the surface of poly(dimethylsiloxane) (PDMS) microchannels, in order to enhance applicability in the field of microfluidics. Many surface modifications of PDMS have been performed for electrophoretic separations, but new modifications are being done for emerging applications such as heterogeneous immunoassays and cell-based bioassays. These new modification techniques are powerful because they impart biospecificity to the microchannel surfaces and reduce protein adsorption. Most of these applications require the use of aqueous or polar solvents, which makes surface modification a very important topic.     

Identification of 2D-gel proteins: a comparison of MALDI/TOF peptide mass mapping to mu LC-ESI tandem mass spectrometry

A comparative analysis of protein identification for a total of 162 protein spots separated by two-dimensional gel electrophoresis from two fully sequenced archaea, Methanococcus jannaschii and Pyrococcus furiosus, using MALDI-TOF peptide mass mapping (PMM) and mu LC-MS/MS is presented. 100% of the gel spots analyzed were successfully matched to the predicted proteins in the two corresponding open reading frame databases by mu LC-MS/MS while 97% of them were identified by MALDI-TOF PMM. The high success rate from the PMM resulted from sample desalting/concentrating with ZipTip(C18) and optimization of several PMM search parameters including a 25 ppm average mass tolerance and the application of two different protein molecular weight search windows. By using this strategy, low-molecular weight (<23 kDa) proteins could be identified unambiguously with less than 5 peptide matches. Nine percent of spots were identified as containing multiple proteins. By using mu LC-MS/MS, 50% of the spots analyzed were identified as containing multiple proteins. mu LC-MS/MS demonstrated better protein sequence coverage than MALDI-TOF PMM over the entire mass range of proteins identified. MALDI-TOF and PMM produced unique peptide molecular weight matches that were not identified by mu LC-MS/MS. By incorporating amino acid sequence modifications into database searches, combined sequence coverage obtained from these two complimentary ionization methods exceeded 50% for approximately 70% of the 162 spots analyzed. This improved sequence coverage in combination with enzymatic digestions of different specificity is proposed as a method for analysis of post-translational modification from 2D-gel separated proteins.     

Anionic ligand effect on the nature of epoxidizing intermediates in iron porphyrin complex-catalyzed epoxidation reactions

We have studied an anionic ligand effect in iron porphyrin complex-catalyzed competitive epoxidations of cis- and trans-stilbenes by various terminal oxidants and found that the ratios of cis- to trans-stilbene oxide products formed in competitive epoxidations were markedly dependent on the ligating nature of the anionic ligands. The ratios of cis- to trans-stilbene oxides obtained in the reactions of Fe(TPP)X (TPP = meso-tetraphenylporphinato dianion and X(-) = anionic ligand) and iodosylbenzene (PhIO) were 14 and 0.9 when the X(-) of Fe(TPP)X was Cl(-) and CF(3)SO(3)(-), respectively. An anionic ligand effect was also observed in the reactions of an electron-deficient iron(III) porphyrin complex containing a number of different anionic ligands, Fe(TPFPP)X [TPFPP = meso-tetrakis(pentafluorophenyl)porphinato dianion and X(-) = anionic ligand], and various terminal oxidants such as PhIO, m-chloroperoxybenzoic acid (m-CPBA), tetrabutylammonium oxone (TBAO), and H(2)O(2). While high ratios of cis- to trans-stilbene oxides were obtained in the reactions of iron porphyrin catalysts containing ligating anionic ligands such as Cl(-) and OAc(-), the ratios of cis- to trans-stilbene oxide were low in the reactions of iron porphyrin complexes containing nonligating or weakly ligating anionic ligands such as SbF(6)(-), CF(3)SO(3)(-), and ClO(4)(-). When the anionic ligand was NO(3)(-), the product ratios were found to depend on terminal oxidants and olefin concentrations. We suggest that the dependence of the product ratios on the anionic ligands of iron(III) porphyrin catalysts is due to the involvement of different reactive species in olefin epoxidation reactions. That is, high-valent iron(IV) oxo porphyrin cation radicals are generated as a reactive species in the reactions of iron porphyrin catalysts containing nonligating or weakly ligating anionic ligands such as SbF(6)(-), CF(3)SO(3)(-), and ClO(4)(-), whereas oxidant-iron(III) porphyrin complexes are the reactive intermediates in the reactions of iron porphyrin catalysts containing ligating anionic ligands such as Cl(-) and OAc(-).     

Cellulose nanocrystals from bleached rice straw pulp: acidic deep eutectic solvent versus sulphuric acid hydrolyses

The present work aims to investigate the feasibility of oxalic acid-choline chloride deep eutectic solvent (OA-ChCl DES), which serves as a promising green solvent that utilized in the acidic deep eutectic solvent (DES) hydrolysis. Oxalic acid-choline chloride DES cellulose nanocrystal (OA-ChCl DES CNC) was isolated from the bleached DES treated pulp (BP) through the acidic DES hydrolysis using 1:1 molar ratio of OA-ChCl DES. The functional groups, crystallinity index, morphological structure, particle size, zeta potential, thermal stability and surface chemistry of the OA-ChCl DES CNC were compared with the sulphuric acid cellulose nanocrystal (SA-CNC) that prepared via sulphuric acid hydrolysis. The findings revealed the presence of negatively charged carboxyl groups on OA-ChCl DES CNC surface after the acidic DES hydrolysis. The physicochemical analyses verified that the OA-ChCl DES CNC was in nano-sized range with polydispersity index (PdI) of 0.56, indicating slightly monodispersed nanoparticles. A stable OA-ChCl DES CNC colloidal suspension with zeta potential value of ?52.1?±?5.2 mV was obtained. The OA-ChCl DES CNC outweighed the SA-CNC in term of thermal stability (288 °C) despite having a slightly lower crystallinity index (76.7%). In fact, the OA-ChCl DES CNC with a yield of 55.1% was achieved through the acidic DES hydrolysis, suggesting that the OA-ChCl DES was capable of promoting efficient cleavage of strong hydrogen bonds in BP.

Graphic abstract

     

Source identification and long-term monitoring of airborne particulate matter (PM<Subscript>2.5</Subscript>/PM<Subscript>10</Subscript>) in an urban region of Korea

Summary For the identification of air pollution sources, about 500 airborne particulate matter (PM_2.5and PM₁₀) samples were collected by using a Gent air sampler and a polycarbonate filter in an urban region in the middle of Korea from 2000 to 2003. The concentrations of 25 elements in the samples were measured by using instrumental neutron activation analysis (INAA). Receptor modeling was performed on the air monitoring data by using the positive matrix factorization (PMF2) method. According to this analysis, the existence of 6 to 10PMF factors, such as metal-alloy, oil combustion, diesel exhaust, coal combustion, gasoline exhaust, incinerator, Cu-smelter, biomass burning, sea-salt, and soil dust were identified.