Atomic force microscope investigation of large-circle DNA molecules

A circular bacterial artificial chromosome of 148.9 kbp on human chromosome 3 has been extended and fixed on bare mica substrates using a developed fluid capillary flow method in evaporating liquid drops. Extended circular DNA molecules were imaged with an atomic force microscope (AFM) under ambient conditions. The measured total lengths of the whole DNA molecules were in agreement with sequencing analysis data with an error range of +/-3.6%. This work is important groundwork for probing single nucleotide polymorphisms in the human genome, mapping genomic DNA, manipulating biomolecular nanotechnology, and studying the interaction of DNA-protein complexes investigated by AFM.

Immobilization of the nanoparticle monolayer onto self-assembled monolayers by combined sterically enhanced hydrophobic and electrophoretic forces

The immobilization of surface-derivatized gold nanoparticles onto methyl-terminated self-assembled monolayers (SAMs) on gold surface was achieved by the cooperation of hydrophobic and electrophoretic forces. Electrochemical and scanning probe microscopy techniques were utilized to explore the influence of the SAM's structure and properties of the nanoparticle/SAM/gold system. SAMs prepared from 1-decanethiol (DT) and 2-mercapto-3-n-octylthiophene (MOT) were used as hydrophobic substrates. The DT SAM is a closely packed and organized monolayer, which can effectively block the underlying gold and inhibit a variety of solution species including organic and inorganic molecules from penetrating, whereas the MOT monolayer is poorly packed or disorganized (because of a large difference in dimension between the thiophene head and the alkylchain tail) and permeable to many organic probes in aqueous solution but not to inorganic probes. Thus, the MOT monolayer provides a more energetically favorable hydrophobic surface for the penetration and adsorption of organic species than the DT monolayer.

Study on charge transfer reactions at multilayers of polyoxometalates clusters and poly(allylamine hydrochloride) (Grotthuss-018)

Multilayers of anionic phosphotungstic acid (PTA) clusters and positively charged protonated poly(allylamine hydrochloride) (PAH) were assembled by layer-by-layer self-assembled method on Au electrode modified by 3-mercaptopropionic acid (3-MPA). The effect of the charge of the surface of the multilayer assembly on the kinetics of the charge transfer reaction was studied by using the redox probes [Fe(CN)(6)](3-)/(4-) [Ru(NH3)(6)](2+/3+). The cyclic voltammetry experiments showed that the peak currents and peak-to-peak potential differences changed after assembling different layers on the electrode surface indicating that the charge of the surface has a significant effect on the kinetics of the studied charge transfer reactions. These reactions were studied in more detail by electrochemical impedance spectroscopy. When [Fe(CN)(6)](3-/-) was used as the redox label, multilayers that terminated with negatively charged PTA showed a high charge transfer resistance but multilayers that terminated with positively charged PAH showed lower charge transfer resistance. With [Ru(NH3)(6)](2+/3+) as the redox label, the charge transfer resistance at multilayers that terminated with positively charged PAH was much higher than at the multilayer terminated by the negatively charged PTA.

Preparation and luminescence properties of hybrid materials containing europium(III) complexes covalently bonded to a silica matrix

A new kind of luminescent organic-inorganic hybrid material (denoted Hybrid I) consisting of europium 1,10-phenanthroline complexes covalently attached to a silica-based network was prepared by a sol-gel process. 1,10-Phenanthroline grafted to 3-(triethoxysilyl)propyl isocyanate was used as one of the precursors for the preparation of an organic-inorganic hybrid materials. For comparison purposes, the hybrid material (denoted Hybrid II) in which phenanthroline was not grafted onto the silica backbone of the frameworks was also prepared. Elemental analysis; NMR, FT-IR, UV/vis absorption, and luminescence spectroscopies, and luminescence decay analysis were used to characterize the obtained hybrid materials. It is shown that the homogeneity of Hybrid I is superior to that of Hybrid II, and a higher concentration europium can be incorporated into Hybrid I than Hybrid II. Excitation at the ligand absorption wavelength (283 nm) resulted in the strong emission of the Eu3+ D-5(0)-F-7(J) (J = 0-4) transition lines as a result of the efficient energy transfer from the ligands to the EU3+ in Hybrid I. The number of water molecules coordinated to the europium ion was estimated, and the structure of the as-synthesized Hybrid I was predicted on the basis of the experimental results.

Grafting of diaminoalkane on glassy carbon surface and its functionalization

Diaminoalkanes (NH2(CH2)(n)NH2, n = 7,10,12) were grafted onto a glassy carbon electrode (GCE) surface by amino cation radical formed during electrooxidation of amino group. The presence of diamine grafted layer at the GCE is demonstrated by X-ray photoelectron spectroscopy. The effect of the grafted layer at the GCE surface on the redox responses of Ru(NH3)(6)(3+) and Fe(CN)(6)(3-) redox probes has been investigated. Electrochemical impedance experiments indicate that the kinetics of electron transfer are slowed down when the scan rate taken to modify the GCE is low, and that diaminoalkane with longer alkyl-chain used has higher blocking characteristics. The amine-functionalized GCE is versatile not only to further covalently immobilize ferrocene acetic acid via carbodiimide coupling, but also as a charge-rich substrate to successfully adsorb heteropolyanion P2W18 in acidic solution by electrostatic interaction. (C) 2000 Elsevier Science S.A. All rights reserved.

Covalent modification of a glassy carbon surface by 4-aminobenzoic acid and its application in fabrication of a polyoxometalates-consisting monolayer and multilayer films

4-Aminobenzoic acid (4-ABA) was covalently grafted on a glassy carbon electrode (GCE) by amine cation radical formation in the electrooxidation process of the amino-containing compound. X-ray photoelectron spectroscopy measurement proves the presence of 4-carboxylphenylamine monolayer on the GCE. The redox responses of various electroactive probes were investigated on the 4-ABA-modified GCE. Electron transfer to Fe(CN)(6)(3-) in solutions of various pHs was studied by both cyclic voltammetry and electrochemical impedance analysis on the modified electrode. Changes in the solution pH value result in the variation of the terminal group charge state, based on which surface pK(a) values are estimated. The 4-ABA-modified GCE was used as a suitable charged substrate to fabricate polyoxometalates-consisting (POM-consisting) monolayer and multilayer films through layer-by-layer assembly based on electrostatic attraction. Cyclic voltammetry shows the uniform growth of these three-dimensional multilayer films. Taking K10H3[Pr-(SiMo7W4O39)(2)]. H2O (abbreviated as Pr(SiMo7W4)(2)), for example, the preparation and electrochemical behavior of its monolayer and multilayer film had been investigated in detail. This modification strategy is proven to be a general one suitable for anchoring many kinds of POMs on the 4-ABA-modified GCE.

Excimer formation in uniaxially stretched polymer films

The steady-state fluorescence properties of naphthalene-labeled polymers dispersed in poly(methyl methacrylate) (PMMA) cast films were studied under tensile loadings at 80 degreesC. The labeled polymers were composed of methyl methacrylate (MMA) and 1-naphthylmethyl methacrylate (NMMA). Three of the copolymers were used in this work, and the contents of NMMA were 0.59 mol % (CP1), 22.0 mol % (CP2), and 56.7 mol % (CP3), respectively. The fluorescence spectra of the films containing CP1 and CP2were unchanged during elongation. For the film containing CP3, the excited monomer emission of naphthyl groups at around 337 nm decreased with increasing applied tensile strain. The strain enhanced the emission ascribed to the excimer of the naphthyl groups in the region of 390-420 nm. The ratio of fluorescence intensities at 400 nm and 337 mn, I-400/I-337, increased with the applied strain, which indicates that CP3 is a sensitive probe for detecting the structural changes of polymer matrices. The obtained results mean that the excimer-forming sites in the PMMA films during elongation depend both on the applied strain and the concentration of naphthyl groups in the dispersed polymer probes. (C) 2001 John Wiley & Sons, Inc.

Formation of a self-assembled monolayer of 2-mercapto-3-n-octylthiophene on gold

Monolayer assembly of 2-mercapto-3-n-octylthiophene (MOT) having a relatively large headgroup onto gold surface from its dilute ethanolic solutions has been investigated by electrochemistry. An electrochemical capacitance measurement on the permeability of the monolayer to aqueous ions, as compared with its alkanethiol counterpart [CH3(CH2)(9)SH (DT)] with a similar molecular length, shows that the self-assembled monolayers (SAMs) of MOT can be penetrated by aqueous ions to some extent. Furthermore, organic molecular probes, such as dopamine, can sufficiently diffuse into the monolayer because a diffusion-limited current peak is observed when the dopamine oxidation reaction takes place, showing that the monolayer is loosely packed or dominated by defects. But the results of electron transfer to aqueous redox probes (including voltammetry in Fe(CN)(6)(3-/4-) solutions and electrochemical ac impedance spectrum) confirm that the monolayer can passivate the gold electrode surface effectively for its very low ratio of pinhole defects. Moreover, a heterogeneous patching process involving addition of the surfactants into the SAMs provides a mixed or hybrid membrane that has superior passivating properties. These studies show that the MOT monolayer on the electrode can provide an excellent barrier for hydrated ionic probe penetration but cannot resist the organic species penetration effectively. The unusual properties of the SAMs are attributed to the entity of the relatively large thiophene moiety between the carbon chain and the thiol group.

Preparation and luminescence properties of lanthanide complexes and their silica-based composites

Binary complexes of europium and terbium with N-propyl-4-carboxyphthalimide (NP) were prepared and characterized. The luminescence behaviors of the lanthanide complexes as well as their doped silica-based composites were investigated by fluorescence spectra. The results indicated that the lanthanide complexes showed fewer emission lines and slightly lower intensities in silica matrix than that of corresponding pure complexes. The lifetimes of the lanthanide complexes became longer when they were incorporated in silica matrix. (C) 2001 Elsevier Science B.V. All rights reserved.

Effect of hydrogen bonds on optical nonlinearities of inorganic crystals

This work probes the role of hydrogen bonds (such as O-H ... O and N-H ... O) in some inorganic nonlinear optical (NLO) crystals, such as HIO3, NH4H2PO4 (ADP), K[B5O6(OH)(4)] . 2H(2)O (KB5) and K2La(NO3)(5) . 2H(2)O (KLN), from the chemical bond standpoint. Second order NLO behaviors of these four typical inorganic crystals have been quantitatively studied, results show hydrogen bonds play a very important role in NLO contributions to the total nonlinearity. Conclusions derived here concerning the effect of hydrogen bonds on optical nonlinearities of inorganic crystals have important implications with regard to the utilization of hydrogen bonds in the structural design of inorganic NLO crystals. (C) 1999 Elsevier Science B.V. All rights reserved.

Electrochemical investigation of DNA adsorbed on conducting polymer modified electrode

Detection of DNA is a very important task for molecular biology and biomedical field. We have investigated electrochemical behavior of double-stranded DNA and single-stranded DNA adsorbed on conducting polymer modified electrode in presence of cobalt complex. The possibility of using such electrode as gene detector is discussed.

Studies on three-dimensional quantitative structure-activity relationships between the structures of N-nitroso compounds and their carcinogenic activities

Comparative molecular fiels analysis (CoMFA) has been applied to the studies of the correlation of the N-nitroso compounds and their carcinogenic activities, The comparison of CoMFA results with different lattice spacing and different atom probes was investigated, CoMFA resulted in a quantitative description of the major steric and electrostatic field effects and gave significant new insights to factors governing potency.

EFFECTS OF METAL-IONS ON THE CONFORMATION OF POLAR HEADGROUP OF SPHINGOMYELIN BILAYER

With the wide application of rare earth in agriculture, medicament, especially the application of Gd-DTPA as nuclear magnetic resonance image reagent in clinical practice([1]), the studies on the toxicology in biological body, as well as the study on the use as informative probes instead of divalent calcium ion in biological and biochemical research have attracted intensive concern([2]). Phospholipids bilayers have served as a model of biomembrane in the last two decades. The effects of metal ions on the conformation of polar headgroup of dipalmitoylphosphatidylcholine (DPPC) bilayers have been reported([3]). Sphingomyelin is major component of several biological tissues such as brain and nerve cells and has identical polar headgroup to DPPC. The interaction of metal ions with sphingomyelin bilayer remains nonrevealed. This note presents the results of the study on this aspect.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

Differences in the rDNA-bearing chromosome divide the Asian-Pacific and Atlantic species of Crassostrea (Bivalvia, Mollusca)

Karyotype and chromosomal location of the major ribosomal RNA genes (rDNA) were studied using fluorescence in situ hybridization (FISH) in five species of Crassostrea: three Asian-Pacific species (C. gigas, C. plicatula, and C. ariakensis) and two Atlantic species (C. virginica and C. rhizophorae). FISH probes were made by PCR amplification of the intergenic transcribed spacer between the 18S and 5.8S rRNA genes, and labeled with digoxigenin-11-dUTP. All five species had a haploid number of 10 chromosomes. The Atlantic species had 1-2 submetacentric chromosomes, while the three Pacific species had none. FISH with metaphase chromosomes detected a single telomeric locus for rDNA in all five species without any variation. In all three Pacific species, rDNA was located on the long arm of Chromosome 10 (10q)-the smallest chromosome. In the two Atlantic species, rDNA was located on the short arm of Chromosome 2 (2p)-the second longest chromosome. A review of other studies reveals the same distribution of NOR sites (putative rDNA loci) in three other species: on 10q in C. sikamea and C. angulata from the Pacific Ocean and on 2p in C. gasar from the western Atlantic. All data support the conclusion that differences in size and shape of the rDNA-bearing chromosome represent a major divide between Asian-Pacific and Atlantic species of Crassostrea. This finding suggests that chromosomal divergence can occur under seemingly conserved karyotypes and may play a role in reproductive isolation and speciation.