Exploring the frontiers of synthetic eumelanin polymers by high-resolution matrix-assisted laser/desorption ionization mass spectrometry

New trends in material science and nanotechnologies have spurred growing interest in eumelanins black insoluble biopolymers derived by tyrosinase-catalysed oxidation of tyrosine via 5,6-dihydroxyindole (DHI) and its 2-carboxylic acid (DHICA). Efficient antioxidant and photoprotective actions, associated with peculiar optoelectronic properties, are recognised as prominent functions of eumelanin macromolecules within the human and mammalian pigmentary system, making them unique candidates for the realisation of innovative bio-inspired functional soft materials, with structure-based physical-chemical properties. An unprecedented breakthrough into the mechanism of synthetic eumelanin buildup has derived from a detailed investigation of the oxidative polymerization of DHI and its N-methyl derivative (NMDHI) by linear and reflectron matrix-assisted laser/desorption ionization mass spectrometry. Regular collections of oligomers of increasing masses, spanning the entire m/z ranges up to 5000?Da (>30-mer) and 8000?Da (> 50-mer) for the two building blocks, respectively, were disclosed. It is the first time that the in vitro polymerisation of dihydroxyindoles to form synthetic eumelanins is explored up to its high mass limits, giving at the same time information on the polymerisation mode, whether it follows a stepwise pattern (being this the conclusion in our case) or a staking sequencing of small-sized entities. It also highlighted the influence of the N-methyl substituent on the polymerization process; this opens the way to the production of N-functionalized, synthetic eumelanin-inspired soft materials, for possible future technological applications.     

Crystallization and Melting Behavior of Monodisperse Oligomers of ϵ-Caprolactone

Monodisperse ?-caprolactone (CL) oligomers with different end groups (t-butyldimethylsilyl, benzyl, hydroxyl, and carboxylic acid) and different numbers of repeating units (4–64) have been studied by differential scanning calorimetry and small-angle X-ray scattering (SAXS) in order to gather information regarding the melting temperature, long period, and melting enthalpy. Oligomers crystallized at their maximum temperatures (different for the different oligomers) to full crystallinity yielded extended-chain crystals for oligomers with 4, 8, and 16 repeating units with the important exception of the oligomers with four and eight repeating units and hydroxyl and benzyl end groups that showed double-layer crystals. Oligomers with 32 and 64 repeating units exhibited remarkably stable once-folded (32-mer) and thrice-folded (64-mer) crystals. Only the oligomer with 16 repeating units showed two crystallization temperature regimes resulting in once-folded crystals (low temperatures) and extended-chain crystals (high temperatures). The end groups had a profound effect on the structures. Hydrogen-bonding groups promoted the formation of crystal bilayers and led to a very high melting enthalpy (150 J g^?1) exceeding the melting enthalpy of 100% crystalline poly (?-caprolactone). The bulky end groups, in particular t-butyldimethylsilyl, reduced the crystallinity and favored chain tilting and probably preventing the unfolding of crystal stems in the oligomers with 32 and 64 repeating units. Melting temperatures of mature crystals obeyed a linear relationship with inverse CL stem length. The intercept (equilibrium melting temperature) was in the range of 350 to 357 K.     

Probing DNA Hybridization in Homogeneous Solution and at Interfaces via Measurement of the Intrinsic Fluorescence Decay Time of a Single Label

The hybridization of DNA oligomers including molecular beacons can be detected by measurement of either the decay time or the intensity of a single fluorescent label attached to the end of the respective oligonucleotide. The method works both in solution and solid phase and can distinguish between fully complementary and mismatch sequences as demonstrated for a 15-mer oligonucleotide and a 25-mer molecular beacon. The fluorescence lifetime method is advantageous in (a) requiring a single label (and therefore a single labeling step) only; and (b), being based on measurement of a self-referenced magnitude that is hardly affected by parameters such as fluctuations in light intensity that make measurement of intensity more prone to interferences.     

A new compact disc format of high density array synthesis applied to peptide nucleic acids and in situ MALDI analysis

A fully automated synthesizer was constructed and designed to perform high speed miniaturized syntheses of compound libraries using the SPOT technique. Utilizing magnetically controlled drop-on-demand ink jet nozzles, an r/phi array format of 2500 spots can be simultaneously dispensed from up to 24 separate reagent valves onto a rotating disc as the solid phase in less than three minutes. In addition, a complete wash station is on board allowing for fully programmable combinatorial syntheses without manual attention. A new carbon black/polypropylene composite solid phase disc was developed and tested for its functionalisation/loading, spot detection, durability and MALDI-TOF target capabilities. The carbon black/polypropylene composite was then successfully employed jointly as the solid phase in the syntheses of short peptide and PNA oligomers and as the target probe holder for MALDI-TOF measurement without transfer of the material. Several protocols for PNA syntheses were also investigated and an optimised PNA methodology for the carbon black/polypropylene composite is reported.     

GenoMass software: a tool based on electrospray ionization tandem mass spectrometry for characterization and sequencing of oligonucleotide adducts

The analysis of DNA adducts is of importance in understanding DNA damage, and in the last few years mass spectrometry (MS) has emerged as the most comprehensive and versatile tool for routine characterization of modified oligonucleotides. The structural analysis of modified oligonucleotides, although routinely analyzed using mass spectrometry, is followed by a large amount of data, and a significant challenge is to locate the exact position of the adduct by computational spectral interpretation, which still is a bottleneck. In this report, we present an additional feature of the in-house developed GenoMass software, which determines the exact location of an adduct in modified oligonucleotides by connecting tandem mass spectrometry (MS/MS) to a combinatorial isomer library generated in silico for nucleic acids. The performance of this MS/MS approach using GenoMass software was evaluated by MS/MS data interpretation for an unadducted and its corresponding N-acetylaminofluorene (AAF) adducted 17-mer (5'OH-CCT ACC CCT TCC TTG TA-3'OH) oligonucleotide. Further computational screening of this AAF adducted 17-mer oligonucleotide (5'OH-CCT ACC CCT TCC TTG TA-3'OH) from a complex oligonucleotide mixture was performed using GenoMass. Finally, GenoMass was also used to identify the positional isomers of the AAF adducted 15-mer oligonucleotide (5'OH-ATGAACCGGAGGCCC-3'OH). GenoMass is a simple, fast, data interpretation software that uses an in silico constructed library to relate the MS/MS sequencing approach to identify the exact location of adduct on oligonucleotides.     

用荧光探针签别CYP2C9*3基因

用一种基激复合物荧光探针系统来签别碱基错配的CYP2C9*3基因,该系统选择两个分开的与靶点碱基相对应的12碱基荧光标记的寡核苷酸作为探针,分别对24碱基、47碱基、质粒(3165bp)的靶点CYP2C9基因和CYP2C9*3基因进行杂交配对,结果该基激复合物荧光探针系统能有效签别各种长度的CYP2C9基因和CYP2C9*3基因,背景干扰很低,灵敏度高,可尝试用于其他基因型的遗传多态性的签别。     

Silicon nanowires for sequence-specific DNA sensing: device fabrication and simulation

Highly sensitive, sequence-specific and label-free DNA sensors were demonstrated by monitoring the electronic conductance of silicon nanowires (SiNWs) with chemically bonded single-stranded (ss) DNA or peptide nucleic acid (PNA) probe molecules. For a 12-mer oligonucleotide, tens of pM of target ss-DNA in solution was recognized when the complementary DNA oligonucleotide probe was attached to the SiNW surfaces. In contrast, ss-DNA samples of ×1000 concentration with a single-base mismatch produce only a weak signal due to nonspecific binding. In order to gain a physical understanding of the change in conductance of the SiNWs with the attachment of the DNA targets and the probes, process and device simulations of the two-dimensional cross sections of the SiNWs were performed. The simulations explained the width dependence of the SiNW conductance and provided understanding to improve the sensor performance. PACS 85.35.-p; 87.83.+a; 07.07.Df     

A New Fluorescence Resonance Energy Transfer Pair and Its Application to Oligonucleotide Labeling and Fluorescence Resonance Energy Transfer Hybridization Studies

We describe two new fluorescence resonance energy transfer (FRET) compatible labels, their covalent linkage to oligonucleotides, and their use as donor and acceptor, respectively, in FRET hybridization studies. The dyes belong to the cyanine dyes, and water solubility is imparted by a phosphonate which represents a new solubilizing group in DNA labels. They were linked to amino-modified synthetic oligonucleotides via oxysuccinimide (OSI) esters. The studies performed include binding assays, determinations of molecular distances, homogeneous competitive assays, and limits of detection, which are in the order of 5 pmol/L for a 15-mer.     

Experimental (FT-IR) and theoretical (DFT) studies on the adsorption behavior of p-nitroaniline (PNA) on gold nanoparticales

This paper reports the studies on the adsorption behavior of p-nitroaniline (PNA) on gold nanoparticales by experiment (FT-IR) and theory (DFT). On dried filter paper coated with gold nanoparticles and in gold aqueous colloids, surface-enhanced Raman scattering (SERS) spectra of p-nitroaniline (PNA) are studied by FT-IR excitation. The Raman frequencies of these two models for the p-nitroaniline (PNA) molecules on different substrate using DFT-B3PW91 with lanl2dz are calculated. Here it is demonstrated the calculated Raman frequencies are in good agreement with experimental values. Experimental (FT-IR) and theoretical (DFT) studies indicate that the adsorption behaviors of PNA molecules are different on these two substrates: in gold aqueous colloids, PNA molecules are adsorbed through the nitro group; while on the gold-coated filter paper, they are titled and there is a certain angle between the benzene rings and the surfaces of gold nanoparticles.     

Preparation of surfactant-stabilized gold nanoparticle–peptide nucleic acid conjugates

A simple, two-step method of producing stable and functional peptide nucleic acid (PNA)-conjugated gold nanoparticles using a surfactant stabilization step is presented. PNA are DNA analogs with superior chemical stability and target discrimination, but their use in metallic nanoparticle systems has been limited by the difficulty of producing stable colloids of nanoparticle–PNA conjugates. In this work, the nonionic surfactant Tween 20 (polyoxyethylene (20) sorbitan monolaurate) was used to sterically shield gold surfaces prior to the addition of thiolated PNA, producing conjugates which remain dispersed in solution and retain the ability to hybridize to complementary nucleic acid sequences. The conjugates were characterized using transmission electron microscopy, dynamic light scattering, and UV–visible absorbance spectroscopy. PNA attachment to gold nanoparticles was confirmed with an enzyme-linked immunoassay, while the ability of nanoparticle-bound PNA to hybridize to its complement was demonstrated using labeled DNA.     

The force law for the dynamic two-body problem in the second post-Newtonian approximation of general relativity

We calculate the force between two well-separated bodies in a fully dynamic system of two extended bodies up to and including the second post-Newtonian approximation (PNA). We use the iteration procedure as formulated by Anderson and Decanio in a version whose divergences have been pushed to the third PNA. We show the following, (i) The force law assumes the Newtonian form if a second approximation in 1/(separation of the bodies) is made; (ii) the mass terms appearing in the force law are the (Tolman) masses of the individual bodies expanded up the second PNA; the interal masses equal the (passive and active) gravitational masses of the bodies in order considered; they are all constants of the motion; (iii) the self-fields of the bodies vanish in the second PNA; hence there is no Nordvedt effect in the second PNA; (iv) the compactness of the bodies, i.e., (gravitational radius)/(body size), does not appear in the force law; only the relation between mass and the matter variables is changed in the PNA as compared with the corresponding Newtonian result.     

Effect of solvent on the characteristics of nanostructured composites of poly (1-naphthylamine) with poly (vinyl alcohol)

Efficient utilization of inherently conducting polymers in nano technological applications faces the challenge to assemble them into highly ordered structures which may yield novel properties. The present study reports for the first time the synthesis and characterization of nanostructured poly (1-naphthylamine) (PNA) dispersed polyvinyl alcohol (PVA) composites. The composites were prepared by loading PNA from 2 wt% to 10 wt% in PVA in aqueous as well as nonaqueous media. The composites were characterized by UV–visible spectroscopy, TEM, stress–strain studies, electrical conductivity measurements and moisture absorption studies under controlled humidity. A discrete but uniform distribution of nanoparticles was obtained in PNA/PVA composites synthesized in water having particle size between 5 and 30 nm. A self assembled network of nanostructured PNA particles was obtained in case of PNA/PVA composites synthesized in N-methylpyrolidone (NMP) with particle sizes between 10 and 65 nm. The variation in the nanostructured morphology of PNA particles in PVA matrix in the two cases resulted from the pronounced interaction of PVA with NMP through hydrogen bonding. This leads to the formation of a homogeneous matrix that facilitates the formation of a self assembled network of PNA nano particles. In case of PNA/PVA composites synthesized in water, lower affinity of PVA towards water was responsible for a discrete, agglomerate free distribution of PNA particles. We have found that the PNA/PVA nano composite synthesized in water exhibited good mechanical properties and electrical conductivity (8.1 × 10⁻¹ S/cm) as well as lowest moisture absorption (4 wt%) which holds potential for use in semiconductor and biomedical devices.     

Improved high-k stacks with chemical oxide interfacial layer by DPN/PNA treatment

A decoupled plasma nitridation (DPN) with post nitridation annealing (PNA) treatment method was introduced to improve the performances of MOS devices with high-k (HK)-last/gate-last integration scheme and chemical oxide interface layer (IL). By introducing N to form HfSiON, it was found that DPN + PNA treatments could provide smaller equivalent oxide thickness (EOT) for both nMOS and pMOS devices. It was also found that we could achieve the best overall device performance for the HK-last/gate-last integration scheme with a chemical oxide IL by introducing nitrogen gas with low percentage content during DPN followed by high temperature PNA.     

Soft X-ray photoemission study of nitrogen diffusion in TiN/HfO:N gate stacks

The impact of HfO:N post nitridation anneal (PNA) and gate fabrication on the physico-chemical properties of the TiN/HfO:N/SiO₂/Si stack are investigated using Soft X-ray Photoelectron Spectroscopy (S-XPS) and Vacuum UltraViolet Spectroscopic Ellipsometry (VUV-SE). Defects created in the high-k during plasma nitridation are passivated by PNA under O₂. Both oxygen and nitrogen diffusion is observed towards the bottom SiO₂/Si interface together with a regrowth of the SiO₂. These defects play a major role regarding nitrogen diffusion during gate fabrication. Without PNA, no diffusion is observed because O and N atoms are trapped inside the high-k. With PNA and simultaneous defects passivation, nitrogen from both metal gate and high-k diffuses towards the bottom SiO₂/Si interface.     

Liquid-crystal phase equilibria of Lennard-Jones chains

Liquid-crystal phase equilibria of Lennard-Jones chain fluids and the solubility of a Lennard-Jones gas in the coexisting phases are calculated from Monte Carlo simulations. Direct phase equilibria calculations are performed using an expanded formulation of the Gibbs ensemble. Monomer densities, order parameters, and equilibrium pressures are reported for the coexisting isotropic and nematic phases of: (1) linear Lennard-Jones chains, (2) a partially-flexible Lennard-Jones chain, and (3) a binary mixture of linear Lennard-Jones chains. The effect of chain length is determined by calculating the isotropic-nematic coexistence of linear Lennard-Jones chain fluids made of 8, 10, and 12 segments (8-, 10-, 12-mer). The effect of molecular flexibility on the isotropic-nematic equilibrium is studied for a Lennard-Jones 10-mer chain fluid with one freely-jointed segment at the end of the chain. An isotropic-nematic phase split and fractionation are reported for a binary mixture of linear 7-mer and 12-mer chains. Simulation results are compared with theoretical results as obtained from a recently developed analytical equation of state based on perturbation theory. Excellent agreement between theory and simulations is observed. The solubility of a monomer Lennard-Jones gas in the coexisting isotropic and nematic phases is estimated using the Widom test-particle insertion method. A linear relationship between solubility difference and density difference at isotropic-nematic coexistence is observed. It is shown that gas solubility is independent of the nematic ordering of the fluid, at constant temperature and density conditions.     

Relativistic celestial mechanics of binary stars

We present the results of a systematic study of the dynamics of realistic binary systems in the post-Newtonian approximation (PNA) of general relativity. We propose definitions valid in the PNA for the self-angular-momenta of the binary's members, as well as for the angular momentum of their relative orbital motion, and we examine under which conditions they can be considered as constant in the PNA. This enables us to define to the same approximation the plane relative orbital motion. Then we find the form of the differential equations of motion from an integration of which we prove that in the PNA the relative motion is a processing ellipse composed of a basic orbit and a correction, both of which are of post-Newtonian character. Moreover, using the polar equation of the above ellipse we define the elements of the post-Newtonian, relative, basic orbit, we generalize to the PNA the three well-known laws of classical celestial mechanics of Kepler, and we derive the precessional motion of the relative orbit's pericenter. Finally, we compare our method with other methods existing in the literature, and we expose its theoretical and conceptual differences with them.     

High-resolution scanning tunneling microscopy and dI/dV map studies of peptidenucleic acid and fluorescein isothiocyanate

We used scanning tunneling microscopy (STM) to spatially map the local density of states of individual PNA molecules labeled with fluorescein isothiocyanate (FITC) on a Cu(1 1 1) surface. From the observed bias voltage dependences of the topographic height and the dI/dV map of FITC and individual PNA molecules, we confirmed that FITC and PNA have different electrical properties. We clearly differentiated the FITC and PNA molecules by mapping the density of states feature. This study shows that STM with the dI/dV map method is useful in FITC mapping.     

运用表面增强拉曼散射(SERS)和密度泛函数理论(DFT)模拟计算研究对硝基苯胺在金纳米颗粒表面吸附行为

在沉积金纳米颗粒的干燥滤纸上进行对硝基苯胺的表面增强拉曼散射(SERS)光谱研究,并与对硝基苯胺在金胶水溶液中的表面增强拉曼散射(SERS)光谱相比,分子拉曼光谱发生了很大变化。同时利用DFT理论计算对硝基苯胺在金胶颗粒上的吸附行为的拉曼光谱。DFT理论模拟计算和FI-Raman实验分析都表明这种变化源于对硝基苯胺的不同吸附方式。SERS和DFT结合研究分子的吸附是一种有效的技术。     

Automated detection of alarm sounds

Two approaches to the automated detection of alarm sounds are compared, one based on a change in overall sound level (RMS), the other a change in periodicity, as given by the power of the normalized autocorrelation function (PNA). Receiver operating characteristics in each case were obtained for different exemplars of four classes of alarm sounds (bells/chimes, buzzers/beepers, horns/whistles, and sirens) embedded in four noise backgrounds (cafeteria, park, traffic, and music). The results suggest that PNA combined with RMS may be used to improve current alarm-sound alerting technologies for the hard-of-hearing.     

Immobilization and AFM of single 4 x 6-mer tarantula hemocyanin molecules

The high molecular mass respiratory protein of the tarantula Eurypelma californicum, a 4 × 6-mer hemocyanin, was investigated by atomic force microscopy (AFM). Various substrates and methods were evaluated for immobilization of individual hemocyanin molecules on a solid surface. Samples were imaged after physisorption on mica and self-assembled monolayers, and after chemisorption on Au(111) and N-hydroxy-succinimide (NHS) functionalized surfaces. AFM measurements were carried out preferable in solution and contact mode, but also in Tapping mode and on air-dried samples. Adsorption of the protein on mica followed by drying and carrying out the measurements in Tapping mode gave the best results. In the AFM images the four hexamers of the native 4 × 6-mer hemocyanin have been defined. The results were compared with independent available structural data and represent a validation case for this technique applied for the first time on such giant and complex molecules. As observable in images taken by transmission electron microscopy and also proposed from SAXS data, 4 × 6-mers could be found where the half-molecules are tilted against each other. This study is a step in resolving conformational heterogeneities, involved in oxygen binding of hemocyanins, at the single-molecule level by AFM.