Adlayers of dimannoside thiols on gold: surface chemical analysis

Carbohydrate films on gold based on dimannoside thiols (DMT) were prepared, and a complementary surface chemical analysis was performed in detail by X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), near-edge X-ray absorption fine structure (NEXAFS), FT-IR, and contact angle measurements in order to verify formation of ω-carbohydrate-functionalized alkylthiol films. XPS (C 1s, O 1s, and S 2p) reveals information on carbohydrate specific alkoxy (C-O) and acetal moieties (O-C-O) as well as thiolate species attached to gold. Angle-resolved synchrotron XPS was used for chemical speciation at ultimate surface sensitivity. Angle-resolved XPS analysis suggests the presence of an excess top layer composed of unbound sulfur components combined with alkyl moieties. Further support for DMT attachment on Au is given by ToF-SIMS and FT-IR analysis. Carbon and oxygen K-edge NEXAFS spectra were interpreted by applying the building block model supported by comparison to data of 1-undecanethiol, poly(vinyl alcohol), and polyoxymethylene. No linear dichroism effect was observed in the angle-resolved C K-edge NEXAFS.     

Base-dependent competitive adsorption of single-stranded DNA on gold

We characterize the room-temperature adsorption of single-stranded DNA homo-oligonucleotides from solution onto polycrystalline Au films, including competitive adsorption between all possible pairs of unmodified oligomers. Fourier transform infrared (FTIR) and X-ray photoelectron (XPS) spectroscopy analysis of the resulting films shows that oligonucleotides adsorb with a strongly base-dependent affinity, adenine (A) > cytosine (C) >/= guanine (G) > thymine (T). In competitive adsorption experiments on Au, oligo(dA) strongly dominates over the other oligonucleotides. The relative adsorption affinity of oligo(dA) is so great that it competes effectively against adsorption of thiolated oligomers and even causes hybridized oligo(dA).oligo(dT) duplexes to denature in the presence of Au.     

Characteristics of migration patterns of DNA oligomers in gels and the relationship to the question of intrinsic DNA bending

We have developed a methodology that is capable of quantitatively describing the electrophoretic mobility patterns of oligomeric B-DNA through polyacrylamide gels (PAG) in the presence of varying concentration of the organic solvent 2-methyl-2,4-pentanediol (MPD), used routinely to induce DNA crystallization. The model includes the ion atmosphere and its polarization, electrostatic excluded volume, hydrodynamic interactions, and fluctuation effects that characterize the overall size of the migrating polyion. Using this model, and by critically examining the mobility patterns of linear random-sequence B-DNA molecules in PAG as a function of MPD, we address the question of the discrepancy between current models used to explain the molecular origins of A-tract-induced DNA bending. Direct analysis of the mobility of B-DNA oligomers on PAG, and comparison to the mobility of A-tract-containing oligomers, shows a significant apparent effect of MPD on the mobility of generic B-DNA sequences, which is larger than the effect on A-tract-containing oligomers. The effect is chain-length dependent, especially at lower MPD concentration. Thus, the apparent reduction in gel mobility, as a function of MPD, is not unique to A-tract regions or A-tract-containing molecules. However, our analysis suggests that MPD molecules are probably excluded from the surface of both B-DNA and A-tract molecules. This is supported by circular dichroism studies on A-tract and B-DNA molecules in solutions containing various MPD concentrations.     

Characterization of poly(sodium styrene sulfonate) thin films grafted from functionalized titanium surfaces

Biointegration of titanium implants in the body is controlled by their surface properties. Improving surface properties by coating with a bioactive polymer is a promising approach to improve the biological performance of titanium implants. To optimize the grafting processes, it is important to fully understand the composition and structure of the modified surfaces. The main focus of this study is to provide a detailed, multitechnique characterization of a bioactive poly(sodium styrene sulfonate) (pNaSS) thin film grafted from titanium surfaces via a two-step procedure. Thin titanium films (～50 nm thick with an average surface roughness of 0.9 ± 0.2 nm) prepared by evaporation onto silicon wafers were used as smooth model substrates. X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) showed that the titanium film was covered with a TiO(2) layer that was at least 10 nm thick and contained hydroxyl groups present at the outermost surface. These hydroxyl groups were first modified with a 3-methacryloxypropyltrimethoxysilane (MPS) cross-linker. XPS and ToF-SIMS showed that a monolayer of the MPS molecules was successfully attached onto the titanium surfaces. The pNaSS film was grafted from the MPS-modified titanium through atom transfer radical polymerization. Again, XPS and ToF-SIMS were used to verify that the pNaSS molecules were successfully grafted onto the modified surfaces. Atomic force microscopy analysis showed that the film was smooth and uniformly covered the surface. Fourier transform infrared spectroscopy indicated that an ordered array of grafted NaSS molecules were present on the titanium surfaces. Sum frequency generation vibration spectroscopy and near edge X-ray absorption fine structure spectroscopy illustrated that the NaSS molecules were grafted onto the titanium surface with a substantial degree of orientational order in the styrene rings.     

Multi-technique surface characterization of bio-based films from sisal cellulose and its esters: a FE-SEM, μ-XPS and ToF-SIMS approach

Bio-based films were prepared from LiCl/DMAc solutions containing sisal cellulose esters (acetates, butyrates and hexanoates) with different degrees of substitution (DS 0.7–1.8) and solutions prepared with the cellulose esters and 20 wt% sisal cellulose. A novel approach for characterizing the surface morphology utilized field emission scanning electron microscopy (FE-SEM), X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS) and contact angle analysis. XPS and ToF-SIMS were a powerful combination while investigating both the ester group distribution on the surface and effects of cellulose content on the film. The surface coverage by ester aliphatic chains was estimated using XPS measurements. Fibrous structures were observed in the FE-SEM images of the cellulose and bio-based films, most likely because the sisal cellulose chains aggregated during dissolution in LiCl/DMAc. Therefore, the cellulose aggregates remained after the formation of the films and removal of the solvent. The XPS results indicated that the cellulose loading on the longer chain cellulose esters films (DS 1.8) increased the surface coverage by ester aliphatic chains (8.2 % for butyrate and 45 % for hexanoate). However, for the shortest ester chains, the surface coverage decreased (acetate, 42 %). The ToF-SIMS analyses of cellulose acetate and cellulose hexanoate films (DS 1.8) revealed that the cellulose ester groups were evenly distributed across the surface of the films.     

Application of XPS and ToF-SIMS for surface chemical analysis of DNA microarrays and their substrates

The chemical composition of the functional surfaces of substrates used for microarrays is one of the important parameters that determine the quality of a microarray experiment. In addition to the commonly used contact angle measurements to determine the wettability of functionalized supports, X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) are more specific methods to elucidate details about the chemical surface constitution. XPS yields information about the atomic composition of the surface, whereas from ToF-SIMS, information on the molecular species on the surface can be concluded. Applied on printed DNA microarrays, both techniques provide impressive chemical images down to the micrometer scale and can be utilized for label-free spot detection and characterization. Detailed information about the chemical constitution of single spots of microarrays can be obtained by high-resolution XPS imaging. Figure Eye-catching image for the graphical online abstract     

Determining the electrophoretic mobility and translational diffusion coefficients of DNA molecules in free solution

The free solution mobility of DNA molecules of different molecular weights, the sequence dependence of the mobility, and the diffusion coefficients of small single- and double-stranded DNA (ss- and dsDNA) molecules can be measured accurately by capillary zone electrophoresis, using coated capillaries to minimize the electroosmotic flow (EOF) of the solvent. Very small differences in mobility between various analytes can be quantified if a mobility marker is used to correct for small differences in EOF between successive experiments. Using mobility markers, the molecular weight at which the free solution mobility of dsDNA becomes independent of molecular weight is found to be approximately 170 bp in 40 mM Tris-acetate-EDTA buffer. A DNA fragment containing 170 bp has a contour length of approximately 58 nm, close to the persistence length of DNA under these buffer conditions. Hence, the approach of the free solution mobility of DNA to a plateau value may be associated with the transition from a rod-like to a coil-like conformation in solution. Markers have also been used to determine that the free solution mobilities of ss- and dsDNA oligomers are sequence-dependent. Double-stranded 20-bp oligomers containing runs of three or more adenine residues in a row (A-tracts) migrate somewhat more slowly than 20-mers without A-tracts, suggesting that somewhat larger numbers of counterions are condensed in the ion atmospheres of A-tract DNAs, decreasing their net effective charge. Single-stranded 20-mers with symmetric sequences migrate approximately 1% faster than their double-stranded counterparts, and faster than single-stranded 20-mers containing A(5)- or T(5)-tracts. Interestingly, the average mobility of two complementary single-stranded 20-mers is equal to the mobility of the double-stranded oligomer formed upon annealing. Finally, the stopped migration method has been used to measure the diffusion coefficients of single- and double-stranded oligomers. The diffusion coefficients of ssDNA oligomers containing 20 nucleotides are approximately 50% larger than those of double-stranded DNA oligomers of the same size, reflecting the greater flexibility of ssDNA molecules. The methods used to carry out these experiments are also described in detail.     

Dynamics of Excess‐Electron Transfer through Alternating Adenine:Thymine Sequences in DNA

This paper presents the results of an investigation into the sequence‐dependent excess‐electron transfer (EET) dynamics in DNA, which plays an important role in DNA damage/repair. There are many published studies on EET in consecutive adenine:thymine (A:T) sequences ( Tn ), but those in alternating A:T sequences ( ATn ) remain limited. Here, two series of functionalized DNA oligomers, Tn and ATn , were synthesized with a strongly electron‐donating photosensitizer, a trimer of ethylenedioxythiophene ( 3 E ), and an electron acceptor, diphenylacetylene ( DPA ). Laser flash photolysis experiments showed that the EET rate constant of AT3 is two times lower than that of T3 due to the lack of π‐stacking of Ts in AT3 . Thus, it was indicated that excess‐electron hopping is affected by the interaction between LUMOs of nucleotides.     

Electron-transfer oxidation properties of DNA bases and DNA oligomers

Kinetics for the thermal and photoinduced electron-transfer oxidation of a series of DNA bases with various oxidants having the known one-electron reduction potentials (E(red)) in an aqueous solution at 298 K were examined, and the resulting electron-transfer rate constants (k(et)) were evaluated in light of the free energy relationship of electron transfer to determine the one-electron oxidation potentials (E(ox)) of DNA bases and the intrinsic barrier of the electron transfer. Although the E(ox) value of GMP at pH 7 is the lowest (1.07 V vs SCE) among the four DNA bases, the highest E(ox) value (CMP) is only 0.19 V higher than that of GMP. The selective oxidation of GMP in the thermal electron-transfer oxidation of GMP results from a significant decrease in the pH dependent oxidation potential due to the deprotonation of GMP*+. The one-electron reduced species of the photosensitizer produced by photoinduced electron transfer are observed as the transient absorption spectra when the free energy change of electron transfer is negative. The rate constants of electron-transfer oxidation of the guanine moieties in DNA oligomers with Fe(bpy)3(3+) and Ru(bpy)3(3+) were also determined using DNA oligomers containing different guanine (G) sequences from 1 to 10 G. The rate constants of electron-transfer oxidation of the guanine moieties in single- and double-stranded DNA oligomers with Fe(bpy)3(2+) and Ru(bpy)3(3+) are dependent on the number of sequential guanine molecules as well as on pH.     

DNA oligomers having a diazapyrenium dication (DAP2+); synthesis and DNA cleavage activities.

Aiming at the creation of functionalized antisense DNA oligomers possessing site-selective DNA cleaving activity, viologen and a related compound, diazapyrenium dication (DAP2+), were selected and introduced into oligodeoxyribonucleotides as a functionalized molecule. The conjugation of these functionalized molecules with DNA proceeded smoothly by using standard H-phosphonate chemistry. A part of the DAP(2+)-tethered DNA oligomers was synthesized by a combination of solid support method and liquid phase technique. Viologen-tethered DNA oligomers showed no significant activity toward DNA cleavage in spite of their characteristic ESR spectra. On the other hand, it was observed that the DAP(2+)-tethered DNA oligomers formed more stable duplexes with their complementary strands than the corresponding wild type, and these molecules effectively cleaved the complementary strands at the specific site of 2-3 bases away from the modified phosphoramidate linkage. The effect of position and length of the linker arm on the selectivity in the cleavage reaction was also investigated, and it was found that introduction at the 3'- or 5'-end phosphate site is more favorable, probably due to duplex stabilization.     

Self-assembled organic monolayers terminated in perfluoroalkyl pentafluoro-lambda(6)-sulfanyl (-SF5) chemistry on gold

Recently synthesized (Winter, R.; Nixon, P. G.; Gard, G. L.; Radford, D. H.; Holcomb, N. R.; Grainger, D. W. J. Fluorine Chem. 2001, 107, 23-30) SF5-terminated perfluoroalkyl thiols (SF5(CF2)nCH2CH2SH, where n = 2, 4, and 6) and a symmetric SF5-terminated dialkyl disulfide ([SF5-CH=CH-(CH2)8-S-]2) were assembled as thin films chemisorbed onto gold surfaces. The adsorbed monolayer films of these SF5-containing molecules on polycrystalline gold were compared using ellipsometry, contact angle, X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), and infrared spectroscopy (FTIR) surface analytical methods. The resulting SF5-dialkyl disulfide monolayer film shows moderate angle dependence in depth-dependent XPS analysis, suggesting a preferentially oriented film. The SF5-terminated perfluoroalkyl thiols exhibit angular-dependent XPS compositional variance depending on perfluoroalkyl chain length, consistent with improved film assembly (increasingly hydrophobic, fewer defects, and more vertical chain orientation increasing film thickness) with increasing chain length. Tof-SIMS measurements indicate that both full parent ions for these film-forming molecules and the unique SF5 terminal group are readily detectable from the thin films without substantial contamination from other adsorbates.     

Quantitative characterization of DNA films by X-ray photoelectron spectroscopy

We describe the use of self-assembled films of thiolated (dT)25 single-stranded DNA (ssDNA) on gold as a model system for quantitative characterization of DNA films by X-ray photoelectron spectroscopy (XPS). We evaluate the applicability of a uniform and homogeneous overlayer-substrate model for data analysis, examine model parameters used to describe DNA films (e.g., density and electron attenuation length), and validate the results. The model is used to obtain quantitative composition and coverage information as a function of immobilization time. We find that when the electron attenuation effects are properly included in the XPS data analysis, excellent agreement is obtained with Fourier transform infrared (FTIR) measurements for relative values of the DNA coverage, and the calculated absolute coverage is consistent with a previous radiolabeling study. Based on the effectiveness of the analysis procedure for model (dT)25 ssDNA films, it should be generally valid for direct quantitative comparison of DNA films prepared under widely varying conditions.     

Ambient-ageing processes in amine self-assembled monolayers on microarray slides as studied by ToF-SIMS with principal component analysis, XPS, and NEXAFS spectroscopy

We investigated the ageing of amine-terminated self-assembled monolayers (amine-SAMs) on different silica substrates due to exposure to different ambient gases, pressures, and/or temperatures using time-of-flight secondary ion mass spectrometry (ToF-SIMS) with principal component analysis and complementary methods of surface analysis as X-ray photoelectron spectroscopy (XPS) and near edge X-ray absorption fine structure (NEXAFS). The goal of this study is to examine the durability of primary amine groups of amine-SAMs stored in a user laboratory prior to being used as supports for biomolecule immobilization and other applications. We prepared amine-SAMs on the native oxides of silicon wafers and glass slides using 3-aminopropyl triethoxysilane, by using optimized conditions such as anhydrous organic solvent and reaction time scale of hours to avoid multilayer growth. Selected commercial amine-SAM slides have been investigated, too. When the amine-SAMs are exposed to air, oxygen incorporation occurs, followed by formation of amide groups. The formation of oxygen species due to ageing was proved by ToF-SIMS, XPS, and NEXAFS findings such as CNO(-) secondary ion emission at m/z 42, observation of the N 1s HNC=O component peak at 400.2-400.3 eV in XPS, and, last but not least, by formation of a π*(HNC=O) resonance at 401 eV in the N K-edge X-ray absorption spectrum. It is concluded that the used multi-method approach comprising complementary ToF-SIMS, XPS, and NEXAFS analyses is well suited for a thorough study of chemical aspects of ageing phenomena of amine-SAM surfaces.     

ON THE DNA BENDING BY PSORALEN INTERSTRAND CROSSLINKING. A GEL ELECTROPHORETIC STUDY

Abstract— A synthetic, partially double stranded decadeoxyribonucleotide with cohesive ends, containing one potential psoralen photo-crosslinking site centrally positioned (5'-d(CGGGCTACCC) + 3'-d(CCGATGGGGC)), has been ligated to double stranded DNA oligomers, which were subsequently photoreacted with 4,5',8-trimethylpsoralen. It was found that psoralen DNA interstrand crosslinking does not significantly alter the electrophoretic mobility of these DNA molecules in polyacrylamide gels. Based on this, we conclude that any bends in the DNA helix that may be induced by psoralen DNA interstrand crosslinking must be significantly less than the 45^° proposed by Tomic et at. (1987) (Science, 238, 1722) and/or of a different nature than the DNA sequence dependent bends due to d(A)_n tracts.     

Preparation and heck reaction of multidentate carbosilane films derived from focally functionalized and allyl-terminated dendrons on hydrogen-terminated silicon(111) surfaces

Multidentate carbosilane films were prepared by thermally induced hydrosilylation of allyl-terminated carbosilane dendrons of generations 0, 1, and 2 (G0-G2) on hydrogen-terminated silicon(111) surfaces. The dendron molecules contain three (G0), nine (G1), and twenty-seven (G2) allyl groups at the periphery, and a bromophenyl functional group at the focal point. The dendron films were characterized by contact-angle goniometry, ellipsometry, Fourier transform infrared spectroscopy in the attenuated total reflection mode, and X-ray photoelectron spectroscopy (XPS). Upon hydroboration of the remaining allyl groups in the films, the percentage of the introduced boron atoms in the films were measured by XPS. The results indicate the presence of roughly 20%, 27%, and 46% of unreacted allyl groups in the G0, G1, and G2 films, respectively. The mechanistic aspects of the chemisorption of these dendron molecules on H-Si(111) surfaces are discussed. XPS studies indicate that seven G0 molecules cover approximately the same area on the substrate as three G1 molecules and one G2 molecule. After treatment of the G0, G1, and G2 films with 4-fluorostyrene under the Heck reaction conditions, the XPS studies indicate that about 84%, 71%, and 55% of the Br atoms were consumed, yielding the replacement of ca. 58-70% of the reacted Br atoms by the fluorostyryl groups. The remaining bromophenyl groups were inactive toward the Heck reaction, probably due to their disfavorable position/orientation in the films.     

Spectroscopic quantification of covalently immobilized oligonucleotides

Quantitative determination of surface coverage, film thickness and molecular orientation of DNA oligomers covalently attached to aminosilane self‐assembled monolayers has been obtained using complementary infrared and photoelectron studies. Spectral variations between surface immobilized oligomers of the different nucleic acids are reported for the first time. Carbodiimide condensation was used for covalent attachment of phosphorylated oligonucleotides to silanized aluminum substrates. Fourier transform infrared (FTIR) spectroscopy and x‐ray photoelectron spectroscopy (XPS) were used to characterize the surfaces after each modification step. Infrared reflection–absorption spectroscopy of covalently bound DNA provides orientational information. Surface density and layer thickness are extracted from XPS data. The surface density of immobilized DNA, 2–3 (×10¹³) molecules cm^?2, was found to depend on base composition. Comparison of antisymmetric to symmetric phosphate stretching band intensities in reflection–absorption spectra of immobilized DNA and transmission FTIR spectra of DNA in KBr pellet indicates that the sugar–phosphate backbone is predominantly oriented with the sugar–phosphate backbone lying parallel to the surface, in agreement with the 10–20 Å DNA film thickness derived from XPS intensities. Copyright © 2004 John Wiley & Sons, Ltd.     

DNA removal on different chromatography supports used for EPO purification by spike studies

Chromatographic techniques are used in the purification step of human recombinant erythropoietin production process to obtain a reliable product with high purity. Anion-exchange chromatography supports have proved high efficient in removing contaminants such as DNA. For that reason, the DNA removal was determined by spike studies, on three anion-exchange chromatographic supports: gel, membrane, and monolithic column, which is used in intermediate purification stage. This study showed that membrane and monolith columns have very good results in the removal of contaminants at this step. Log removal values (LRV) greater than 3.5 were obtained from DNA spike clearance studies. Monolithic column was determined as the best technological proposal, with more than 4 LRV, 7.72?mg DNA per milliliter of adsorbent and 85% protein recovery in nonspike run. The results of this study may be used as a guide in the selection of commercially available chromatography supports for intermediate purification steps in recombinant protein production.     

Raman and surface enhanced Raman microscopy of microstructured polyethylenimine/DNA multilayers

We analyze microstructured multilayer films of poly(ethyleneimine) (PEI) and DNA by employing Raman and surface enhanced Raman spectroscopy (SERS). The microstructuring of the samples allows a simultaneous measurement of signal and reference in a single analytic process. Silver nanoparticles are implemented in the microstructured multilayers for SERS measurements. The recorded SERS spectra of PEI/DNA are dominated by the Raman bands of the DNA bases which show a larger mean enhancement than bands belonging to DNA backbone vibrations. Our results show that the combination of SERS and microstructured multilayer films provides an adapted way to characterize the polyelectrolytes as well as to measure the enhancement factor and the distance dependence for the SERS active silver nanoparticles. Furthermore, microstructured polyelectrolyte films containing SERS active nanoparticles are used for sensing molecules.     

Effect of divalent metal ions on DNA studied by capillary electrophoresis

Divalent metal ions, such as Zn(2+), Co(2+), and Ni(2+), are capable of incorporating into DNA under certain conditions to form complexes termed M-DNA. To better understand the effects of these cations on DNA we used capillary electrophoresis (CE). The presence of these metal ions in a typical genotyping buffer led to broad peaks with low fluorescence intensities. In addition, some of the metal-complexed DNA molecules had different electrophoretic mobilities than their normal DNA counterparts. It is likely that the mobility shifts observed in the electropherograms of these affected fragments are due to the divalent cations causing structural changes in the single-stranded DNA. However, as can be seen from the resulting peak shapes, the structure, charge, and/or mass changes due to metal binding are not conserved among all of the DNA fragments. The extent of both peak-broadening and mobility shifts were found to be dependent on the metal cation and its concentration, the length of time that the DNA sample existed in formamide prior to injection into the capillary, and also the fragment size and sequence. These results suggest that the presence of metal ions might be responsible for the poor CE performance that occurs when genotyping certain kinds of DNA samples.     

ToF-SIMS depth profiling of oral drug delivery films for 3D visualization of active pharmaceutical particles

The size, shape, and spatial distribution of active pharmaceutical ingredient (API) are important physical characteristics of drug delivery systems that can affect the performance, stability, appearance, and even bulk properties of the end product. This study explores the feasibility of using time-of-flight secondary ion mass spectrometry (ToF-SIMS) for the 3D characterization of API particles in two commercially available oral dissolvable drug delivery films. It was found that ToF-SIMS imaging with argon gas cluster ion beam (GCIB) sputtering allowed production of 3D chemical maps that could be utilized to obtain size distributions of buprenorphine particles whose effective diameters ranged from approximately 6 μm to 41 μm, with shapes that were generally spherical with a few nonspherical structures. The particles were heterogeneously distributed both laterally and as a function of depth in the film. In addition, ToF-SIMS was able to differentiate between different oral drug delivery films based on differences in the spatial distribution of buprenorphine; in one case, the particles were distributed throughout the depth of the film, whereas the particles in the other case were localized close to the surface. Preliminary studies suggest that ToF-SIMS with argon GCIB sputtering may also allow us to provide a very rough estimate of the concentration of the APIs (factors of 2 to 4), namely buprenorphine and naloxone, at pharmacologically relevant concentrations inside organic drug delivery systems with a thickness of hundreds of micrometers.