Soil microbial community analysis using terminal restriction fragment length polymorphisms

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a polymerase chain reaction (PCR)-fingerprinting method that is commonly used for comparative microbial community analysis. The method can be used to analyze communities of bacteria, archaea, fungi, other phylogenetic groups or subgroups, as well as functional genes. The method is rapid, highly reproducible, and often yields a higher number of operational taxonomic units than other, commonly used PCR-fingerprinting methods. Sizing of terminal restriction fragments (T-RFs) can now be done using capillary sequencing technology allowing samples contained in 96- or 384-well plates to be sized in an overnight run. Many multivariate statistical approaches have been used to interpret and compare T-RFLP fingerprints derived from different communities. Detrended correspondence analysis and the additive main effects with multiplicative interaction model are particularly useful for revealing trends in T-RFLP data. Due to biases inherent in the method, linking the size of T-RFs derived from complex communities to existing sequence databases to infer their taxonomic position is not very robust. This approach has been used successfully, however, to identify and follow the dynamics of members within very simple or model communities. The T-RFLP approach has been used successfully to analyze the composition of microbial communities in soil, water, marine, and lacustrine sediments, biofilms, feces, in and on plant tissues, and in the digestive tracts of insects and mammals. The T-RFLP method is a user-friendly molecular approach to microbial community analysis that is adding significant information to studies of microbial populations in many environments.

Layer-by-layer assembly of functional silica and Au nanoparticles for fabricating electrogenerated chemiluminescence sensor

We described the use of silica nanoparticles as building blocks for the immobilization of electrogenerated chemiluminescence (ECL) reagent Ru(bpy)3" and the fabrication of layer-by-layer assembly film by alternating the deposition of the Ru(bpy)3 2'-doped silica nanoparticles and Au nanoparticles.

Construction of hollow DNA/PLL microcapsule as a dual carrier for controlled delivery of DNA and drug

DNA/poly-L-lysine (PLL) capsules were constructed through a layer-by-layer (LbL) self-assembly of DNA and PLL on CaCO3 microparticles, and then used as dual carriers for DNA and drug after dissolution of carbonate cores. The permeability of DNA/PLL microcapsules was investigated with fluorescence probes with different molecular weights by confocal microscopy. The result revealed that the fluorescence probes were able to penetrate the capsule walls even its molecular weight up to 150 kDa. The resultant capsules were used to load drug model molecules-fluorescein isothiocyanate (FITC)-dextran (4 kDa) via spontaneous deposition mechanism.

Metallic Cation Induced One-Dimensional Assembly of Poly(acrylic acid)-1-Dodecanethiol-Stabilized Gold Nanoparticles

In this work, we report a simple approach for controllable synthesis of one-dimensional (ID) gold nanoparticle (AuNP) assemblies in solution. In the presence of divalent metallic ions, poly(acrylic acid)-1-dodecanethiol-stabilized AuNPs (PAA-DDT@AuNPs) are found to form I D assemblies in aqueous solution by an ion-templated chelation process; this causes an easily measurable change in the absorption spectrum of the particles. The assemblies are very stable and remain suspended in solution for more than one month without significant aggregation.

Self-assembly of single-stranded RNA on carbon nanotube: Polyadenylic acid to form a duplex structure

All messenger-RNA (mRNA) molecules in eukaryotic cells have a polyadenylic acid [poly (rA)] tail at the 3'-end and human poly (rA) polymerase (PAP) has been considered as a tumor-specific target. A ligand that is capable of recognizing and binding to the poly(M) tail of mRNA might interfere with the full processing of mRNA by PAP and can be a potential therapeutic agent. We report here for the first time that single-walled carbon nanotubes (SWNTs) can cause single-stranded poly (M) to self-structure and form a duplex structure, which is studied by UV melting, atomic force microscopy, circular dichroism spectroscopy, and NMR spectrometry.

A one-dimensional network from the self-assembly of gold nanoparticles by a necklace-like polyelectrolyte template mediated by metallic ion coordination

A new approach to one-dimensional organization of gold nanoparticles (2-4 nm) is described, using poly(4-vinylpyridine) (P4VP) molecular chain as a template with the mediation of free Cu2+ ion coordination. The assembly was conducted on freshly prepared mica surfaces and in aqueous solution, respectively. The surface assembly was characterized by tapping mode atomic force microscopy (AFM), observing the physisorbed molecules in their chain-like conformation with an average height of 0.4 nm.

Hollow DNA/PLL microcapsules with tunable degradation property as efficient dual drug delivery vehicles by alpha-chymotrypsin degradation

Hollow deoxyribonucleic acid (DNA)/poly-L-lysine (PLL) capsules were successfully fabricated through a layer-by-layer (LbL) self-assembly of DNA and PLL on porous CaCO3 microparticles, followed by removal of templates with ethylenediamine tetraacetic acid disodium salt (EDTA). The enzymatic degradation of the capsules in the presence of alpha-chymotrypsin was explored. The higher the enzyme concentration, the higher is the degradation rate of hollow capsules. in addition, glutaric dialdehyde (GA) cross-linking was found to be another way to manipulate degradation rate of hollow capsules.

Type I collagen-mediated synthesis and assembly of UV-photoreduced gold nanoparticles and their application in surface-enhanced Raman scattering

We reported a simple method to synthesize gold nanoparticles (NPs) by photoreducing HAuCl4 in acetic acid solution in the presence of type I collagen. It was found that the collagen takes an important role in the formation of gold NPs. The introduction of collagen made the shape of the synthesized gold nanocrystals change from triangular and hexangular gold nanoplates to size-uniform NPs. On the other hand, thanks to the special characters of collagen molecules, such as its linear nanostructure, are positively charged when the pH < 7, and the excellent self-assembly ability, photoreduced gold NPs were assembled onto the collagen chains and formed gold NPs films and networks. A typical probe molecule, 4-aminothiophenol, was used to test the surface-enhanced Raman scattering activity of these gold NPs films and networks and the results indicated good Raman activity on these substrates.

Nucleobase-metal hybrid materials: Preparation of submicrometer-scale, spherical colloidal particles of adenine-gold(III) via a supramolecular hierarchical self-assembly approach

We report a simple and effective supramolecular route for facile synthesis of submicrometer-scale, hierarchically self-assembled spherical colloidal particles of adenine - gold(III) hybrid materials at room temperature. Simple mixture of the precursor aqueous solutions of adenine and HAuCl4 at room temperature could result in spontaneous formation of the hybrid colloidal particles. Optimization of the experimental conditions could yield uniform-sized, self-assembled products at 1:4 molar ration of adenine to HAuCl4. Transmission electron microscopy results reveal the formation of hierarchical self-assembled structure of the as-prepared colloidal particles. Concentration dependence, ratio dependence, time dependence, and kinetic measurements have been investigated. Moreover, spectroscopic evidence [i.e., Fourier transform infrared (FTIR) and UV-vis spectra and wide-angle X-ray scattering data] of the interaction motives causing the formation of the colloidal particles is also presented.

Silver nanoparticles coated with adenine: preparation, self-assembly and application in surface-enhanced Raman scattering

We describe herein the preparation of silver nanoparticles (AgNPs) using nucleobase adenine as protecting agent through the in situ chemical reduction of AgNO3 with NaBH4 in an aqueous medium at room temperature. As-prepared AgNPs were characterized by UV-visible spectra, transmission electron microscopy and x-ray photoelectron spectroscopy. All these data confirmed the formation of AgNPs. On the basis of electrostatic interactions between as-prepared AgNPs and anionic polyelectrolyte poly(sodium 4-styrenesulfonate) (PSS), we successfully fabricated (PSS/AgNP)n (n = 0-9) multilayers on a 3-mercaptopropyltrimethoxysilane/AgNP functionalized indium tin oxide (ITO) substrate via the layer-by-layer self-assembly technique and characterized as-formed multilayers with UV-visible spectra. Furthermore, these ITO substrates coated with multilayers of different thickness were investigated as surface-enhanced Raman scattering (SERS)-active substrates using p-aminothiophenol as a probe molecule, implying that these multilayers substrates may be promising for a new type of SERS-active substrate.

Electrochemical impedance detection of DNA hybridization based on dendrimer modified electrode

Bioactive ultrathin films with the incorporation of amino-terminated G4 PAMAM dendrimers have been prepared via layer-by-layer self-assembly methods on a gold electrode and used for the DNA hybridization analysis. Surface plasmon resonance (SPR), X-ray photoelectron spectroscopy (XPS), and electrochemical impedance spectroscopy (EIS) are used to characterize the successful construction of the multicomponent film on the gold substrate. The dendrimer-modified surfaces improve the immobilization capacity of the probe DNA greatly, compared to the AET (2aminoethanethiol) SAM sensor surfaces without dendrimer molecules. DNA hybridization analysis is monitored by EIS. The dendrimer-based electrochemical impedance DNA biosensor shows high sensitivity and selectivity for DNA hybridization assay. The multicomponent films also display a high stability during repeated regeneration and hybridization cycles.

Preparation of DNA - Silver nanohybrids in multilayer nanoreactors by in situ electrochemical reduction, characterization, and application

Novel nanocomposite films containing DNA-silver nanohybrids have been successfully fabricated by combined use of the layer-by-layer self-assembly technique and an in situ electrochemical reduction method with the DNA-Ag+ complex as one of the building blocks. UV-vis absorption spectroscopy was employed to monitor the buildup of the multilayer films, which suggested a progressive deposition with almost an equal amount of the DNA-Ag+ complex in each cycle. The following electrochemical reduction of silver resulted in the formation of metal nanoparticles in the film, which was evidenced by the evolution of the intense plasmon absorption band originating from silver. Scanning electron microscopy indicated that the particles formed in the multilayer films possessed good monodispersity and stability, thanks to the surrounding polymers. X-ray photoelectron spectroscopy further confirmed the presence of the main components (such as DNA and metallic silver) of the nanocomposite films. In addition, we show that the size of the metal nanoparticles and the optical property of the film could be readily tuned by manipulating the assembly conditions.

Surface plasmon resonance and electrochemistry characterization of layer-by-layer self-assembled DNA and Zr4+ thin films, and their interaction with cytochrome c

Through electrostatic layer-by-layer (LbL) assembly, negatively charged calf thymus double stranded DNA (CTds-DNA), and positively charged Zr4+ ions were alternately deposited on gold substrate modified with chemisorbed cysteamine. Thus-prepared three-dimensional DNA networks were characterized by surface plasmon resonance (SPR) spectroscopy, X-ray photoelectron spectroscopy (XPS) and infrared reflection-absorption spectroscopy (IR-RAS). SPR spectroscopy indicates that the effective thickness of DNA monolayer in the (DNA/Zr4+), bilayer was 1.5 +/- 0.1 nm, which corresponds to the surface coverage of 79% of its full packed monolayer. At the same time, a linear increase of film thickness with increasing number of layers was also confirmed by SPR characterizations. The data of XPS and IR-RAS show that Zr4+ ions interact with both the phosphate groups and nitrogenous bases of DNA and load into the framework of DNA. Furthermore, the interactions between this composite film and heme protein cytochrome c (Cyt c) were investigated by SPR spectroscopy and electrochemistry.

Surface plasmon resonance and electrochemistry characterization of layer-by-layer self-assembled DNA and Zr4+ thin films, and their interaction with cytochrome c

Through electrostatic layer-by-layer (LbL) assembly, negatively charged calf thymus double stranded DNA (CTds-DNA), and positively charged Zr4+ ions were alternately deposited on gold substrate modified with chemisorbed cysteamine. Thus-prepared three-dimensional DNA networks were characterized by surface plasmon resonance (SPR) spectroscopy, X-ray photoelectron spectroscopy (XPS) and infrared reflection-absorption spectroscopy (IR-RAS). SPR spectroscopy indicates that the effective thickness of DNA monolayer in the (DNA/Zr4+), bilayer was 1.5 +/- 0.1 nm, which corresponds to the surface coverage of 79% of its full packed monolayer. At the same time, a linear increase of film thickness with increasing number of layers was also confirmed by SPR characterizations. The data of XPS and IR-RAS show that Zr4+ ions interact with both the phosphate groups and nitrogenous bases of DNA and load into the framework of DNA. Furthermore, the interactions between this composite film and heme protein cytochrome c (Cyt c) were investigated by SPR spectroscopy and electrochemistry. Compared with the adsorption of Cyt c on DNA monolayer, this composite multilayer film can obviously enhance the amount of immobilized Cyt c confirmed by SPR reflectivity-incident angle (R-theta) curves.

Synthesis, characterization, and self-assembly of protein lysozyme monolayer-stabilized gold nanoparticles

Lysozyme monolayer-protected gold nanoparticles (Au NPs) which are hydrophilic and biocompatible and show excellent colloidal stability at low temperature, ca. 4 degrees C, were synthesized in aqueous medium by chemical reduction of HAuCl4 with NaBH4 in the presence of a familiar small enzyme, lysozyme. UV-vis spectra, transmission electron microscopy (TEM), atomic force microscopy, and X-ray photoelectron spectroscopy characterization of the as prepared nanoparticles revealed the formation of well-dispersed An NPs of ca. 2 nm diameter. Moreover, the color change of the An NP solution as well as UV-vis spectroscopy and TEM measurements have also demonstrated the occurrence of Ostwald ripening of the nanoparticles at low temperature. Further characterization with Fourier transform infrared spectroscopy (FTIR) and dynamic light scattering indicated the formation of a monolayer of lysozyme molecules on the particle surface. FTIR data also indicated the intactness of the protein molecules coated on An NPs. All the characterization results showed that the monodisperse An NPs are well-coated directly with lysozyme. Driven by the dipole-dipole attraction, the protein-stabilized Au NPs self-assembled into network structures and nanowires upon aging under ambient temperature.