小分子在致密聚合物膜中扩散新模型

依据改进的Scatchard-Hildebrand模型、Flory-Huggins理论、线性黏弹性理论,建立一个新的传质模型．模型可以描述温度低于聚合物材料玻璃化温度时,气体小分子在聚合物膜中Fick及non-Fick扩散行为．应用此模型计算293．15K、298．15K及303．15K下,乙醇气体在PPES（杂萘联苯聚醚砜）,PPESK（杂萘联苯聚醚砜酮）膜中吸收／解吸曲线,并与实验结果相比较,最大相对偏差11．54％,平均偏差4．53％．     

Importance of fundamental sp, sp2, and sp3 hydrocarbon radicals in the growth of polycyclic aromatic hydrocarbons

The most basic chemistry of products formation in hydrocarbons pyrolysis has been explored via a comparative experimental study on the roles of fundamental sp, sp(2), and sp(3) hydrocarbon radicals/intermediates such as ethyne/ethynyl (C(2)H(2)/C(2)H), ethene/ethenyl (C(2)H(4)/C(2)H(3)), and methane/methyl (CH(4)/CH(3)) in products formations. By using an in situ time-of-flight mass spectrometry technique, gas-phase products of pyrolysis of acetylene (ethyne, C(2)H(2)), ethylene (ethene, C(2)H(4)), and acetone (propanone, CH(3)COCH(3)) were detected and found to include small aliphatic products to large polycyclic aromatic hydrocarbons (PAHs) of mass 324 amu. Observed products mass spectra showed a remarkable sequence of mass peaks at regular mass number intervals of 24, 26, or 14 indicating the role of the particular corresponding radicals, ethynyl (C(2)H), ethenyl (C(2)H(3)), or methyl (CH(3)), in products formation. The analysis of results revealed the following: (a) product formation in hydrocarbon pyrolysis is dominated by hydrogen abstraction and a vinyl (ethenyl, C(2)H(3)) radical addition (HAVA) mechanism, (b) contrary to the existing concept of termination of products mass growth at cyclopenta fused species like acenaphthylene, novel pathways forming large PAHs were found succeeding beyond such cyclopenta fused species by the further addition of C(2)H(x) or CH(3) radicals, (c) production of cyclopenta ring-fused PAHs (CP-PAHs) such as fluoranthene/corannulene appeared as a preferred route over benzenoid species like pyrene/coronene, (d) because of the high reactivity of the CH(3) radical, it readily converts unbranched products into products with aliphatic chains (branched product), and (e) some interesting novel products such as dicarbon monoxide (C(2)O), tricarbon monoxide (C(3)O), and cyclic ketones were detected especially in acetone pyrolysis. These results finally suggest that existing kinetic models of product formation should be modified to include the reported novel species and their formation pathways. It is expected that outcomes of this study will be useful to understand the products formation from reactors to interstellar atmospheres as well as the growth mechanism of carbon nanomaterials.     

Oxidation artifacts in the electrospray mass spectrometry of Abeta Peptide

Gradual corrosion of stainless steel electrospray emitters under conditions of normal use generates surface irregularities that can promote electrical discharge. The increased emission current affects the electrochemical reactions associated with the spray process. When sampling the peptide Abeta(1-40), this is manifest by oxidation of methionine at position 35 to methionine sulfoxide. The resultant mass shift and reduced sensitivity can adversely affect H/D exchange experiments. These effects can be avoided by adding a redox buffer or (preferably) by repolishing the emitter, especially to a rounded geometry.     

Raman and infrared spectroscopic investigations on aqueous alkali metal phosphate solutions and density functional theory calculations of phosphate-water clusters

Phosphate (PO(4)(3-)) solutions in water and heavy water have been studied by Raman and infrared spectroscopy over a broad concentration range (0.0091-5.280 mol/L) including a hydrate melt at 23 degrees C. In the low wavenumber range, spectra in R-format have been constructed and the R normalization procedure has been briefly discussed. The vibrational modes of the tetrahedral PO(4)(3-)(aq) (T(d) symmetry) have been assigned and compared to the calculated values derived from the density functional theory (DFT) method for the unhydrated PO(4)(3-)(T(d)) and phosphate-water clusters: PO(4)(3-).H(2)O (C(2v)), PO(4)(3-).2H(2)O (D(2d)), PO(4)(3-).4H(2)O (D(2d)), PO(4)(3-).6H(2)O (T(d)), and PO(4)(3-).12H(2)O (T), a cluster with a complete first hydration sphere of water molecules. A cluster with a second hydration sphere of 12 water molecules and 6 in the first sphere, PO(4)(3-).18H(2)O (T), has also been calculated. Agreement between measured and calculated vibrational modes is best in the case of the PO(4)(3-).12H(2)O cluster and the PO(4)(3-).18H(2)O cluster but far less so in the case of the unhydrated PO(4)(3-) or phosphate-water cluster with a lower number of water molecules than 12. The asymmetric, broad band shape of v(1)(a(1)) PO(4)(3-) in aqueous solutions has been measured as a function of concentration and the asymmetric and broad band shape was explained. However, the same mode in heavy water has only half the full width at half-height compared to the mode in normal water. The PO(4)(3-) is strongly hydrated in aqueous solutions. This has been verified by Raman spectroscopy comparing v(2)(H(2)O), the deformation mode of water, and the stretching modes, the v(1)OH and v(3)OH of water, in K(3)PO(4) solutions as a function of concentration and comparison with the same modes in pure water. A mode at approximately 240 cm(-1) (isotropic R spectrum) has been detected and assigned to the restricted translational mode of the strong hydrogen bonds formed between phosphate and water, P-O...HOH. In very concentrated K(3)PO(4) solutions (C(0) > or = 3.70 mol/L) and in the hydrate melt, formation of contact ion pairs (CIPs) could be detected. The phosphate in the CIPs shows a symmetry lowering of the T(d) symmetry to C(3v). In the less concentrated solutions, PO(4)(3-)(aq) solvent separated ion pairs and doubly solvent separated ion pairs exist, while in very dilute solutions fully hydrated ions are present (C(0) < or = 0.005 mol/L). Quantitative Raman measurements have been carried out to follow the hydrolysis of PO(4)(3-)(aq) over a very broad concentration range. From the hydrolysis data, the pK(3) value for H(3)PO(4) has been determined to be 12.45 at 23 degrees C.     

Adsorption on molecularly imprinted polymers of structural analogues of a template. Single-component adsorption isotherm data

The equilibrium adsorption isotherms on two otherwise identical polymers, one imprinted with Fmoc-L-tryptophan (Fmoc-L-Trp) (MIP), the other nonimprinted (NIP), of compounds that are structural analogues of the template were acquired by frontal analysis (FA) in an acetonitrile/acetic acid (99/1 v/v) mobile phase, over a wide concentration range (from 0.005 to 50 mM). These analogues were Fmoc-L-tyrosine, Fmoc-L-serine, Fmoc-L-phenyalanine, Fmoc-glycine (Fmoc-Gly), Fmoc-L-tryptophan pentafluorophenyl ester (Fmoc-L-Trp(OPfp)), and their antipodes. These substrates have different numbers of functional groups able to interact with the 4-vinylpyridine groups of the polymer. For a given number of the functional groups, these substrates have different hydrophobicities of their side groups (as indicated by their partition coefficients (log P(ow)) in the octanol-water system (e.g., from 4.74 for Fmoc-Trp to 2.53 for Fmoc-Gly)). Statistical results from the fitting of the FA data to Langmuirian isotherm models, the calculation of the affinity energy distribution, and the comparison of calculated and experimental band profiles show that all these sets of FA data are best accounted for by a tri-Langmuir isotherm model, except for the data of Fmoc-L-Trp(OPfp) that are best modeled by a simple Langmuir isotherm. So, all compounds but Fmoc-L-Trp(OPfp) find three different types of adsorption sites on both the MIP and the NIP. The properties of these different types of sites were studied systematically. The results show that the affinity of the structural analogues for the NIP is controlled mostly by the number of the functional groups on the substrates and somewhat by the hydrophobicity of their side groups. These two factors control also the MIP affinity toward the enantiomers of the structural analogues that have a stereochemistry different from that of the template. In contrast, the affinity of the highest affinity sites of the MIP toward the enantiomers of these structural analogues that have the same stereochemistry as the template is highest for the imprinted molecule (Fmoc-L-Trp). The separation of the template from the substrates with the same stereochemistry is influenced by the number of the functional groups on the substrates that can interact with the highest affinity sites on the MIP. The separation of the enantiomers of the analogues of the substrates was also achieved on the MIP, and these enantiomeric separations are influenced by the hydrophobicity of the substrates.     

Combining mass spectrometry and pull-down techniques for the study of receptor heteromerization. Direct epitope-epitope electrostatic interactions between adenosine A2A and dopamine D2 receptors

Previous results from FRET and BRET experiments and computational analysis (docking simulations) have suggested that a portion of the third intracellular loop (I3) of the human dopamine D2 receptor (D2R) and the C-tail from the human adenosine A2A receptor (A2AR) are involved in A2AR-D2R heteromerization. The results of the present studies, using pull-down and mass spectrometry experiments, suggest that A2AR-D2R heteromerization depends on an electrostatic interaction between an Arg-rich epitope from the I3 of the D2R (217RRRRKR222) and two adjacent Asp residues (DD401-402) or a phosphorylated Ser (S374) residue in the C-tail of the A2AR. A GST-fusion protein containing the C-terminal domain of the A2AR (GST-A2ACT) was able to pull down the whole D2R solubilized from D2R-tranfected HEK-293 cells. Second, a peptide corresponding to the Arg-rich I3 region of the D2R (215VLRRRRKRVN224) and bound to Sepharose was able to pull down both GST-A2ACT and the whole A2AR solubilized from A2AR-tranfected HEK-293 cells. Finally, mass spectometry and pull-down data showed that the Arg-rich D2R epitope binds to two different epitopes from the C-terminal part of the A2AR, containing the two adjacent Asp residues or the phosphorylated Ser residue (388HELKGVCPEPPGLDDPLAQDGAVGS412 and 370SAQEpSQGNT378). The present results are the first example of epitope-epitope electrostatic interaction underlying receptor heteromerization, a new, expanding area of protein-protein interactions.     

Estimation of absorption and backscattering coefficients from in situ radiometric measurements: theory and validation in case II waters

A model that relates the coefficients of absorption (a) and backscattering (b(b)) to diffuse attenuation (K(d)), radiance reflectance (R(L)), and the mean cosine for downward irradiance (mu(d)) is presented. Radiance transfer simulations are used to verify the physical validity of the model for a wide range of water column conditions. Analysis of thee radiance transfer simulations suggest that absorption and backscattering can be estimated with average errors of 1% and 3%, respectively, if the value of mu(d) is known with depth. If the input data set is restricted to variables that can be derived from measurements of upward radiance (L(u)) and downward irradiance (E(d)), it is necessary to use approximate values of mu(d). Examination of three different approximation schemes for mu(d) shows that the average error for estimating a and b(b) increases to approximately 13%. We tested the model by using measurements of L(u) and E(d) collected from case II waters off the west coast of Scotland. The resulting estimates of a and b(b) were compared with independent in situ measurements of these parameters. Average errors for the data set were of the order of 10% for both absorption and backscattering.     

Unambiguous assignment of intramolecular chemical cross-links in modified mammalian membrane proteins by Fourier transform-tandem mass spectrometry

Fourier transform tandem mass spectrometry (FT-MS/MS) can be used to unambiguously assign intramolecular chemical cross-links to specific amino acid residues even when two or more possible cross-linking sites are adjacent in the cross-linked protein. Bovine rhodopsin (Rho) in its dark-adapted state was intramolecularly cross-linked with lysine-cysteine (K-C) or lysine-lysine (K-K) cross-linkers to obtain interatomic distance information. Large, multiply charged, cross-linked peptide ions containing adjacent lysines, corresponding to Rho(50-86) (K(66) or K(67)) cross-linked to Rho(310-317) (C(316)) or Rho(318-348) (K(325) or K(339)), were fragmented by collision-induced dissociation (CID), infrared multiphoton dissociation (IRMPD), and electron capture dissociation (ECD). Complementary sequence-specific information was obtained by combining cross-link assignments; however, only ECD revealed full palmitoylation of adjacent cysteines (C(322) and C(323)) and cross-linking of K(67) (and not K(66)) to C(316), K(325), and K(339). ECD spectra contained crucial c- and z-ions resulting from cleavage of the bond between K(66) and K(67). To our knowledge, this work also presents the first demonstration that ECD can be used to characterize S-linked fatty acid acylation on cysteines. The comprehensive fragmentation of large peptides by CID, IRMPD, and particularly ECD, in conjunction with the high resolution and mass accuracy of FT-MS/MS, is shown to be a valuable means of characterizing mammalian membrane proteins with both chemical and posttranslational modifications.     

Examination of competitive lanthanide sorption onto smectites and its significance in the management of radioactive waste

The competitive effect of La and Lu (analogues of radionuclides appearing in radioactive waste) in the sorption in four smectites was examined. Sorption and desorption distribution coefficients (K(d); K(d,des)), and desorption rates (R(des)) were determined from batch tests in two media: deionized water and, to consider the influence of cement leachates, 0.02 mol L(-1) Ca. The competitive effect was lower when high-affinity sites were available, as in the water medium at the lowest range of initial lanthanide concentration, with high K(d) for La and for Lu (5-63×10(4) L kg(-1)). Lower K(d) was measured at higher initial concentrations and in the Ca medium, where Lu showed a stronger competitive effect. This was confirmed by fitting the sorption data to a two-solute Langmuir isotherm. The desorption data indicated that sorption was virtually irreversible for the scenarios with high sorption, with an excellent correlation between K(d) and K(d,des) (R(2) around 0.9 for the two lanthanides). Assuming that radioactive waste is a mixture of radionuclides, and that Ca ions will be provided by the cement leachates, this would reduce the retention capacity of clay engineered barriers.     

Intercalation of collagen and soybean peptides into Zn-Al layered double hydroxide

In order to develop a new type biocompatible organic/inorganic nanohybrid material, an intercalation of collagen peptides (CP) and soybean peptide (SP) into Zn-Al layered double hydroxide (LDH) by the coprecipitation reaction has been investigated. The peptide/LDH has been characterized by chemical analysis, powder X-ray diffraction (XRD), Raman spectroscopy, thermal gravimetric analysis (TG) and transmission electron microscopy (TEM). According to the XRD patterns and Raman spectra, the solid products were found to contain peptide and to show broad diffraction peaks with LDH structures. The CP/LDH and SP/LDH possess the expanding LDH structure, d(00l) = 2-3 nm, confirming that both peptides were intercalated into the LDH interlayer space with low organized stacking arrangement.     

Reference wavelengths for strong lines of atomic hydrogen and deuterium

Wavelengths of the individual fine-structure components of the n = 1-2 (Ly(alpha)), n = 1-3 (Ly(beta)), n = 1-4 (Ly(gamma)), n = 1-5 (Ly(delta)), n = 1-6 (Ly(epsilon)), n = 1-7 (Ly(zeta)), n = 2-3 (H(alpha)), n = 2-4 (H(beta)), n = 2-5 (H(gamma)), n = 2-6 (H(delta)), and n = 2-7 (H(epsilon)) transitions of H and D are determined from theoretical values for the binding energies. Theoretical line strengths are used to obtain recommended values for the peaks of unresolved blends of these components as likely to be observed with discharge light sources and spectrometers with low to moderate resolution.     

pH- and temperature-sensitive polymeric microspheres for drug delivery: the dissolution of copolymers modulates drug release

Most pH-/temperature-responsive polymers for controlled release of drugs are used as cross-linked hydrogels. However, the solubility properties of the linear polymers below and above the lower critical solution temperature (LCST) are not exploited. Here, the preparation and characterization of poly (N-isopropylacrylamide-co-methacrylic acid-co-methyl methacrylate) (poly (NIPAAm-co-MA-co-MM)) and poly (N-isopropylacrylamide-co-acrylamide) (poly (NIPAAm-co-AAm)), known as “smart” polymers (SP), is reported. Both poly (NIPAAm-co-MA-co-MM) and poly (NIPAAm-co-AAm) display pH- and temperature-responsive properties. Poly (NIPAAm-co-MA-co-MM) was designed to be insoluble in the gastric fluid (pH = 1.2), but soluble in the intestinal fluid (pH = 6.8 and 7.4), at the body temperature (37°C). Poly (NIPAAm-co-AAm) was designed to have a lower critical solution temperature (LCST) corresponding to 37°C at pH = 7.4, therefore it is not soluble above the LCST. The solubility characteristics of these copolymers were exploited to modulate the rate of release of drugs by changing pH and/or temperature. These copolymers were solubilized with hydrophobic cellulose acetate butyrate (CAB) and vitamin B₁₂ (taken as a water soluble drug model system) in an acetone/methanol mixture and dispersed in mineral oil. By a progressive evaporation of the solvent, the liquid droplets were transformed into loaded CAB/SP microspheres. Differential scanning calorimetric studies and scanning electron microscopy analysis demonstrated that the polymeric components of the microspheres precipitated separately during solvent evaporation forming small microdomains. Moreover, vitamin B₁₂ was found to be molecularly dispersed in both microdomains with no specific affinity for any polymeric component of microspheres. The release of vitamin B₁₂ was investigated as a function of temperature, pH, and the CAB/SP ratio.     

Characterization of nonenzymatic glycation on a monoclonal antibody

We present here an improved analytical method for the analysis of glycation events in proteins. Nonenzymatic glycation of an IgG2 monoclonal antibody was studied using affinity chromatography, mass spectrometry, and chemical derivatization. Analysis of both forced-degraded and bulk-drug substance (BDS) samples showed the presence of glycated protein. A new peptide mapping procedure, incorporating derivatization using sodium borohydride, allowed the development of a sensitive method for detecting and identifying the sites of modification. When combined with tandem mass spectrometry, peptides glycated by glucose showed dramatically improved MS/MS spectra as compared to underivatized controls. Using these methods we were able to map a number of glycation sites in both forced-degraded and BDS samples that were distributed across both light and heavy chain subdomains. The combination of affinity chromatography, high-resolution mass spectrometry, and a simple derivatization procedure should allow the facile analysis of glycation for other antibody and protein samples.     

Covalent Cross-Linking within Supramolecular Peptide Structures

β-Sheet peptide nanostructures (e.g., amyloid fibrils) are recognized as important entities in biological systems and as functional materials in their own right. Their unique physical properties and architectural complexity, however, present a challenge for structure determination at atomic resolution. Covalent cross-linking and mass spectrometry are appealing methods for this endeavor because, potentially, a large amount of information can be extracted from a small sample in a single experiment. Previously, we described preliminary studies on the use of a photoreactive diazirine-containing amino acid to cross-link peptide monomers in nanostructures, together with the integrated separation and analysis of the products using ion mobility spectrometry coupled to conventional mass spectrometry. Here, a pH-switchable system (Aβ(16-22), a sequence from the amyloid-β peptide) was used to examine cross-linking chemistry in morphologically distinct supramolecular structures containing, or entirely composed of, diazirine-functionalized peptides. We examine the relationship between cross-linker chemistry, covalent cross-links (identified using chemical derivatization and tandem mass spectrometry), and noncovalent structure, and report differences in the site of cross-linking that can only be explained by supramolecular templating. The results demonstrate the applicability of the approach for obtaining structural restraints in ordered supramolecular assemblies, provided that a considered evaluation of the cross-linked products is undertaken.     

Sequence-dependent enrichment of a model phosphopeptide: a combined MALDI-TOF and NMR study

The goal of this study was to detect and quantify by MALDI-TOF MS the phosphorylation of a peptide containing the recognition motif of the Protein Kinase C (PKC). Such model peptide can be used as a phosphorylation probe to follow intracellular kinase/phosphatase activities. This study allowed us to establish relationships between sequence specificities and affinity for TiO(2) or IMAC media. The peptide has the sequence biotin-GGGGCFRTPSFLKK-NH(2) in which the serine residue can be phosphorylated. Enrichment of the corresponding phosphopeptide, by the dedicated IMAC and TiO(2) affinity chromatography methods, proved inefficient. By combining MALDI-TOF and NMR data, we first showed that the lack of affinity of the phosphopeptide for TiO(2) was partly related to the basic property of its peptide sequence. Furthermore, the peptide shows local structuration around the P(9)- S(10) segment, with formation of a salt bridge between the guanidinium group of the R(7) side chain and the phosphate moiety. In conjunction with an inadequate position of the {biotin-G(4)} N-terminal tag, this local structure could shield the phosphate group, preventing interaction with TiO(2). To improve TiO(2) affinity, the peptide sequence was modified accordingly. The new sequences retained the biological properties while their enrichment by IMAC or TiO(2) became possible.     

Real-time surface plasmon resonance imaging measurements for the multiplexed determination of protein adsorption/desorption kinetics and surface enzymatic reactions on peptide microarrays

The kinetics of protein adsorption/desorption onto peptide microarrays was studied using real-time surface plasmon resonance (SPR) imaging. S protein binding interactions were examined using an array composed of five different peptides: N terminal and C terminal immobilized wild-type S peptide (S1 and S2), an alternate binding sequence derived by phage display (LB2), an NVOC-protected S peptide, and a FLAG peptide control sequence (F). Kinetic measurements of the S protein-S1 peptide interaction were analyzed to determine a desorption rate constant (k(d)) of 1.1 (+/-0.08) x 10(-2) s(-1), an adsorption rate constant (k(a)) of 1.9 (+/-0.05) x 10(5) M(-1) s(-1), and an equilibrium adsorption constant (K(Ads)) of 1.7 (+/-0.08) x 10(7) M(-1). SPR imaging equilibrium measurements of S protein to S1 peptide were performed to independently confirm the kinetically determined value of K(Ads). Rate constants for the S2 and LB2 peptides on the array were measured as follows: 1.6 (+/-0.04) x 10(5) M(-1) s(-1) (k(a)) and 1.1 (+/-0.07) x 10(-2) s(-1) (k(d)) for S2, 1.2 (+/-0.05) x 10(5) M(-1) s(-1) (k(a)) and 1.1 (+/-0.03) x 10(-2) s(-1) (k(d)) for LB2. In addition to S protein adsorption/desorption, real-time SPR imaging of peptide arrays was applied to study the surface enzymatic activities of the protease factor Xa. Enzymatic cleavage of the substrate peptide (P1) was shown to follow first-order kinetics and proceed at a rate 10 times faster than that of the mutant peptide (P2), with cleavage velocities of 5.6 (+/-0.3) x 10(-4) s(-1) for P1 and 5.7 (+/-0.3) x 10(-5) s(-1) for P2.     

Color removal from textile dyebath effluents in a zeolite fixed bed reactor: determination of optimum process conditions using Taguchi method

Taguchi method was applied as an experimental design to determine optimum conditions for color removal from textile dyebath house effluents in a zeolite fixed bed reactor. After the parameters were determined to treat real textile wastewater, adsorption experiments were carried out. The breakthrough curves for adsorption studies were constructed under different conditions by plotting the normalized effluent color intensity (C/C(0)) versus time (min) or bed volumes (BV). The chosen experimental parameters and their ranges are: HTAB concentration (C(htab)), 1-7.5 gL(-1); HTAB feeding flowrate (Q(htab)), 0.015-0.075 L min(-1); textile wastewater flowrate (Q(dye)), 0.025-0.050 L min(-1) and zeolite bed height (H(bed)), 25-50 cm, respectively. Mixed orthogonal array L(16) (4(2)x2(2)) for experimental plan and the larger the better response category were selected to determine the optimum conditions. The optimum conditions were found to be as follows: HTAB concentration (C(htab))=1g L(-1), HTAB feeding flowrate (Q(htab))=0.015 L min(-1), textile wastewater flowrate (Q(dye))=0.025 L min(-1) and bed height (H(bed))=50 cm. Under these conditions, the treated wastewater volume reached a maximum while the bed volumes (BV) were about 217. While HTAB concentration, gL(-1) (A); zeolite bed height, cm (D) and wastewater flowrate, L min(-1) (C) were found to be significant parameters, respectively, whereas, HTAB flowrate, L min(-1) (B) was found to be an insignificant parameter.     

Analytic remote-sensing optical algorithms requiring simple and practical field parameter inputs

Spectral in-water measurements of downward irradiance (E(d)), upward irradiance (E(u)), and nadir radiance (L(u)) are sufficient to calculate the scalar irradiances E(0), E(0d), and E(0u), the average cosines mu, mu(d), and mu(u), the light absorption coefficient a, the backscattering coefficient b(b), and the so-called f factor that relates to R, a, and b(b). The solar elevation of 42 degrees is a special case in which mu(d) is independent of all variables except solar elevation. The algorithms are valid for solar elevations between 12 degrees and 81 degrees for horizontally stratified clear and turbid deep waters.     

Probing biomolecular interactions with dual polarization interferometry: real-time and label-free coralyne detection by use of homoadenine DNA oligonucleotide

We incorporated the specific recognition of adenine-rich singled-stranded DNA (ssDNA) into dual polarization interferometry (DPI) measurements for direct, selective, and sensitive detection of the small molecule coralyne, and we simultaneously employed the real-time and label-free technique for detailed investigation of the interaction between coralyne and adenine-rich ssDNA. Data from UV-visible spectroscopy, circular dichroism (CD) spectroscopy, and DNA melting firmly confirmed that 48-mer homoadenine ssDNA oligonucleotide (A(48)) had highly specific recognition for coralyne, whereas 48-mer homothymine ssDNA oligonucleotide (T(48)) as the control had no such recognition. The immobilization of ssDNA (A(48) or T(48)) on a silicon oxynitride chip could be achieved through a preadsorbed poly(ethylenimine) (PEI) layer. Mass, thickness, and refractive index (RI) changes resolved by DPI during the whole process of ssDNA immobilization suggested that most ssDNA molecules were likely to lie on the PEI surface mainly in the form of a flat monolayer and insert themselves partly into the PEI layer. Qualitative and quantitative analysis of mass, thickness, and RI changes in A(48)/PEI layer upon addition of different concentrations of coralyne revealed that A(48) most likely underwent a conformational change from single-stranded to double-stranded structure. By evaluation of the binding curves from changes in mass, the association rate constant (k(a)), dissociation rate constant (k(d)), and association constant (K(A)) between coralyne and A(48) were determined to be 4.95 × 10(3) M(-1) s(-1), 0.031 s(-1), and 1.6 × 10(5) M(-1), respectively. Good linear correlations between coralyne concentrations ranging from 0.5 to 12 μM and three parameters (mass, thickness, and RI) resolved by the response to coralyne binding were obtained. The detection limits were 0.22 μM for mass calibration, 0.14 μM for thickness calibration, and 0.32 μM for RI calibration. The high selectivity of the biosensor to coralyne at the A(48)/PEI interface was successfully confirmed by using the other two interfaces (T(48)/PEI and PEI) and three typical intercalators (ethidium bromide, daunomycin, and methylene blue). It is expected that the biosensing platform may be extended to simultaneously detect and characterize the interactions of a variety of target molecules with functional DNA molecules with high sensitivity.     

Divinyl sulfone as a postdigestion modifier for enhancing the a(1) Ion in MS/MS and postsource decay: potential applications in proteomics

Divinyl sulfone reacts at pH 8-9 with the alpha-amino groups of N-terminal residues, proline, the epsilon-amino groups of lysine, and the histidine side chains of peptides. This reaction leads to great enhancement of the abundance of the normally weak or missing "a(1)" fragment ion in MS/MS analysis defining the N-terminal residue of a peptide in a digest. This provides "one-step Edman-like" information that, together with a fairly accurately determined mass, often enables one to correctly identify a protein or family of proteins. The applicability of this procedure in proteomics was demonstrated with several peptides and tryptic digests of protein mixtures by LC-MS/MS experiments using a QTOF and MALDI-PSD analyses. Advantages of this approach are its simple chemistry, retention of charge multiplicity, and possibly, shortening of database search time. Used with other MS/MS data, it provides higher confidence in the scores and identification of a protein found in peptide mass fingerprinting. Moreover, this approach has an advantage in "de novo" sequencing due to its ability to decipher the first amino acid of a peptide whose information is normally unavailable in MS/MS spectra.