Major groove substituents and polymerase recognition of a class of predominantly hydrophobic unnatural base pairs

Expansion of the genetic alphabet with an unnatural base pair is a long‐standing goal of synthetic biology. We have developed a class of unnatural base pairs, formed between d 5SICS and analogues of d MMO2 that are efficiently and selectively replicated by the Klenow fragment (Kf) DNA polymerase. In an effort to further characterize and optimize replication, we report the synthesis of five new d MMO2 analogues bearing different substituents designed to be oriented into the developing major groove and an analysis of their insertion opposite d 5SICS by Kf and Thermus aquaticus DNA polymerase I (Taq). We also expand the analysis of the previously optimized pair, d NaM –d 5SICS , to include replication by Taq. Finally, the efficiency and fidelity of PCR amplification of the base pairs by Taq or Deep Vent polymerases was examined. The resulting structure–activity relationship data suggest that the major determinants of efficient replication are the minimization of desolvation effects and the introduction of favorable hydrophobic packing, and that Taq is more sensitive than Kf to structural changes. In addition, we identify an analogue (d NMO1 ) that is a better partner for d 5SICS than any of the previously identified d MMO2 analogues with the exception of d NaM . We also found that d NaM –d 5SICS is replicated by both Kf and Taq with rates approaching those of a natural base pair.     

Surface-initiated growth of poly d(A-T) by Taq DNA polymerase

In this paper, we report surface-initiated d(A-T) polymerization by Taq DNA polymerase as a method for constructing DNA-tethered surfaces using an enzyme. The enzymatic polymerization was conducted successfully via two steps: tethering of oligo d(A-T)s onto the surface presenting carboxylic acids by amide coupling and surface-initiated polymerization using Taq DNA polymerase. In this enzymatic polymerization process, the design and construction of carboxylic acid-presenting surfaces were found to be an important factor: DNA growth did not occur on the gold surface coated only with the self-assembled monolayer (SAM) of 16-mercaptohexadecanoic acid (MHDA), but effectively proceeded on the surfaces presenting mixed SAMs of MHDA and 1-pentadecanethiol. The coupling of oligo d(A-T)s and the subsequent DNA polymerization reaction were characterized by polarized infrared external reflectance spectroscopy, ellipsometry, X-ray photoelectron spectroscopy, and atomic force microscopy.     

胶体金在DNA分子识别中的应用——胶体金对罗丹明B与单双链DNA识别作用的影响

通过研究罗丹明B与单双链DNA作用过程中，胶体金加入前后的紫外可见吸收光谱的变化，发现在胶体金加入的前后，罗丹明B均以沟槽方式与单双链DNA相作用；胶体金的加入可以较大程度地增大化合物与DNA之间的相互作用．     

Resonance light scattering spectroscopy study of interaction between gold colloid and thiamazole and its analytical application

In this paper, we used resonance light scattering (RLS) spectroscopy to study the interaction between thiol-containing pharmaceutical-thiamazole and gold colloid. At pH 5.2, the resonance light scattering spectrum of gold nanoparticles has a maximum peak at 555 nm and the RLS intensity is enhanced by trace amount of thiamazole due to the interaction between thiamazole and gold colloid. The binding of colloidal gold to thiamazole results in ligand-induced aggregation of colloidal gold, which was characterized by RLS spectrum, ultraviolet-visible (UV-Vis) spectrum, and transmission electron microscopy (TEM). Based upon the study, we proposed a highly sensitive, gold colloid-based assay using RLS spectrum to detect pharmaceuticals for the first time. The mechanism of binding interaction between Au colloid and thiamazole was also discussed.     

Interaction between metallic gold and support and its influence on catalysis

The interaction between gold particles and support in Au/TiO₂ and Au/Al₂O₃ catalysts prepared by immobilizing colloidal gold on the support was evidenced by X-ray photoelectron spectroscopy. The reducibility of the support is more responsible than the interaction between the nanogold particles and support for the activity of catalysts.     

Investigation on the interaction between colloidal gold and human complement factor 4 at different pH by spectral methods

The interaction between colloidal gold and human complement factor 4 (human C4) at different pH was investigated by spectral methods, including absorption and resonance light-scattering spectrometry. According to the changes of color and absorption spectra of colloidal gold solution in presence of human C4, the interaction between colloidal gold and human C4 was quantitatively investigated using a semi-empirical "flocculation parameter". At the same time, the changes of resonance light-scattering spectra and transmission electron microscopy (TEM) images indicate that the aggregation of colloidal gold happens by electrostatic interaction in presence of human C4 in the pH range 5-6. However, the colloidal gold solution remains stable at pH >6 and pH <5 due to the repulsive electrostatic interaction between colloidal gold and human C4. The flocculation parameter is directly proportional to the concentration of human C4 in the range from 9.7 to 233.0 microgl(-1). In addition, the interactions between the colloidal gold and bovine serum albumin (BSA) as well as human serum albumin (HSA) were also investigated using the same methods. It was found that there was no aggregation of colloidal gold in presence of BSA and HSA in the pH range 5-6. However, when the pH of solution is 4, the aggregation of colloidal gold happens. Because BSA and HSA have different structure, the intensity of aggregation of colloidal gold in presence of BSA is greater than that in presence of HSA at pH 4.     

Spectroscopic identification of S-Au interaction in cysteine capped gold nanoparticles

This study deals with the synthesis of cysteine capped gold nanoparticles with an average size of 12 nm by borohydride reduction and spectroscopic identification of SAu interaction. We have studied the interaction of thiol with gold nanoparticles in aqueous medium by employing UV-vis, Raman, NMR, and FT-IR spectroscopy. The shifting of gold plasmon resonance in the UV-vis spectra shows the stabilization of gold nanoparticles by cysteine. The disappearance of S-H stretching in both the IR and Raman spectra and the shifting of the NMR signals of the protons in close proximity to the metal center supported the existence of the S-Au interaction in cysteine capped gold nanoparticles. The TEM images shows cysteine capped gold nanoparticles as distinct and spherical entities as compared to free colloidal gold nanoparticles.     

Immunosensors Based on Layer‐by‐Layer Self‐Assembled Au Colloidal Electrode for the Electrochemical Detection of Antigen

Colloidal Au particles have been deposited on the gold electrode through layer‐by‐layer self‐assembly using cysteamine as cross‐linkers. Self‐assembly of colloidal Au on the gold electrode resulted in an easier attachment of antibody, larger electrode surface and ideal electrode behavior. The redox reactions of [Fe(CN)₆]^4?/[Fe(CN)₆]^3? on the gold surface were blocked due to antibody immobilization, which were investigated by cyclic voltammetry and impedance spectroscopy. The interaction of antigen with grafted antibody recognition layers was carried out by soaking the modified electrode into a phosphate buffer at pH 7.0 with various concentrations of antigen at 37 °C for 30 min. Further, an amplification strategy to use biotin conjugated antibody was introduced for improving the sensitivity of impedance measurements. Thus, the sensor based on this immobilization method exhibits a large linear dynamic range, from 5–400 μg/L for detection of Human IgG. The detection limit is about 0.5 μg/L.     

DNA dissociation and degradation at gold nanoparticle surfaces

The instability of DNA-functionalized gold nanoparticles (Au-DNA conjugates) upon exposure to high temperatures is characterized using fluorescence spectroscopy, gel electrophoresis and ion-exchange chromatography. Above 70 °C, aqueous Au-DNA conjugates decompose within hours due to both desorption of thiol-terminated DNA from the gold nanoparticle surface and chemical degradation of DNA in the presence of colloidal gold. Although the chemical mechanism for DNA degradation was not identified in this study, the gold surface participates directly in the cleavage reaction. These results have important implications for the use of Au-DNA conjugates in biotechnological and clinical applications that require high temperatures, such as polymerase chain reaction (PCR).     

Control of gold nanoparticle aggregates by manipulation of interparticle interaction

The size of gold nanoparticle aggregates was controlled by manipulating the interparticle interaction. To manipulate the interparticle interaction of gold nanoparticles prepared by citrate reduction, we applied the substitutive adsorption of benzyl mercaptan on the particle surface in the absence of the cross-linking effect. Various experimental techniques such as UV-vis absorption spectroscopy, surface-enhanced Raman scattering, quasi-elastic light scattering, and zeta-potential measurement were used to characterize the nanoparticle aggregates. Our results suggest that the replacement of the trivalent citrate ions adsorbed on the nanoparticle surface with monovalent benzyl mercaptan ions should destabilize the particles, causing aggregation and hence the increase in the size of nanoparticle aggregates. These experimental results were successfully rationalized by the classical DLVO (Derjaguin-Landau-Vervey-Overbeek) theory that describes the interparticle interaction and colloidal stability in solution. Our findings suggest that the control of surface potential is crucial in the design of stable gold nanoparticle aggregates.     

Spectrophotometric Determination of Human Immunoglobulin G Based on Enlargement of Gold Nanoparticles

Based on the sandwich immunoreaction and enlargement of colloidal gold, a simple spectrophotometric determination of human immunoglobulin G (IgG) was developed. The sandwich immunoreaction among the goat‐anti‐human IgG, the human IgG and goat‐anti‐human IgG labeled with colloidal gold was completed on the surface of 96 well clear polystyrene high bind stripwell(tm) microplate. The immobilized colloidal gold was enlarged by the reaction of 0.01% HAuCl₄ with 0.4 mmol·L^?1 NH₂OH·HCl. A common UV‐Vis spectrophotometer was employed to measure the absorption of the colloidal gold enlarged. The absorption signal of colloidal gold is proportional to the logarithm of human IgG concentration ranging from 5.0×10^?9 to 2.0×10^?5 g·mL^?1, which is comparable with those obtained by other immunoassays. In the proposed method, the immobilized colloidal gold can be easily enlarged and a new absorption band is present at about 620 nm, which makes the signal be recorded with a common medical analyzer. This spectrophotometric determination can be made in a common laboratory without the well‐trained technician and the special equipment.     

Selective Janus Particle Assembly at Tipping Points of Thermally‐Switched Wetting

Thermal wetting can simply, selectively and reversibly join patchy particles into clusters (2D and 3D) and also colloidal crystals over the narrow temperature range of 1–2 °C. This is demonstrated with Janus particles (gold half‐coated silica spheres) immersed in a binary mixture of water/2,6‐lutidine, such that the relative strength of gold–gold bonding through hydrophobic interaction and silica–silica bonding through the wetting‐induced attraction is reversibly switched according to temperature.     

Preparation of Amino-functionalized Multiwall Carbon Nanotube/Gold Nanoparticle Composites

Multiwall carbon nanotubes (MWNT) were modified orderly with carboxyl groups and amino groups. The MWNT/gold nanoparticle composites were formed when the amino‐functionalized MWNT was interacted with gold colloids. The functionalized MWNT was characterized using Fourier transform infrared spectroscopy and X‐ray photoelectron spectroscopy. The amino‐functionalized MWNT allows further attaching gold nanoparticles through electrostatic interaction between the negatively charged gold nanoparticles and amino groups on the surface of the MWNT. The composite of gold nanoprticles and amino‐functionalized MWNT was characterized by transmission electron microscopy. This method decorating carbon nanotubes can be used to identify the location of functional groups, i.e. defect sites on carbon nanotubes.     

Gold nanoparticle multilayer films based on surfactant films as a template: preparation, characterization, and application

Highly ordered gold nanoparticle multilayer films were achieved conveniently using didodecyldimethylammonium bromide (DDAB) films as a template. The template was produced by casting DDAB chloroform solution onto the surface of a (3-aminopropyl)trimethoxysilane-modified indium tin oxide substrate and then evaporating the organic solvent. Gold nanoparticle multilayer films were prepared by soaking the template in 2.6 nm colloidal gold solution for 120 min. The well-ordered superlattice structure of the DDAB template and the gold nanoparticle multilayer films was identified by x-ray diffraction. The characterizations of the gold nanoparticle multilayer films by UV-vis spectroscopy, atomic force microscopy, and cyclic voltammerty were described in detail. The application of the as-prepared gold nanoparticle multilayer films in surface-enhanced Raman spectroscopy (SERS) was investigated by using Rhodamine 6G as a probe molecule. It was found that the colloidal gold nanoparticle multilayer films exhibit remarkable enhancement ability and can be used as SERS substrates.     

Development of colloidal gold-based flow-through and lateral-flow immunoassays for the rapid detection of the insecticide carbaryl

One-step membrane-based competitive colloidal gold-based immunoassays in flow-through and lateral-flow formats for the rapid detection of carbaryl were developed. Nitro-cellulose membrane strip was separately coated with goat anti-rabbit IgG (control line) and carbaryl hapten-OVA conjugate (test line). Anti-carbaryl antibody labeled with colloidal gold particles was firstly incubated with carbaryl. A positive reaction as a result of the remaining antibody-gold conjugate combining with antigen coated on the membrane was obvious by visual detection, with detection limits for flow-through and lateral flow of 50 and l00 μg/L, respectively. The assay time for both tests was less than 5 min, suitable for rapid testing on-site.     

Continuous‐flow Polymerase Chain Reaction Microfluidics by Using Spiral Capillary Channel Embedded on Copper

Abstract

This paper presents a novel method for performing polymerase chain reaction (PCR) amplification by using spiral channel fabricated on copper where a transparent polytetrafluoroethylene (PTFE) capillary tube was embedded. The channel with 25 PCR cycles was gradually developed in a spiral manner from inner to outer. The durations of PCR mixture at the denaturation, annealing and extension zones were gradually lengthened at a given flow rate, which may benefit continuous‐flow PCR amplification as the synthesis ability of the Taq polymerase enzyme usually weakens with PCR time. Successful continuous‐flow amplification of DNA fragments has been demonstrated. The PCR products of 249, 500 and 982 bp fragments could be obviously observed when the flow rates of PCR mixture were 7.5, 7.5 and 3.0 mm s^?1, respectively, and the required amplification times were about 25, 25, and 62 min, respectively. Besides, the successful segmented‐flow PCR of three samples (249, 500 and 982 bp) has also been reported, which demonstrates the present continuous‐flow PCR microfluidics can be developed for high‐throughput genetic analysis.     

Biotin-doped porous polypyrrole films for electrically controlled nanoparticle release

A novel method for the preparation of biotin-doped porous conductive surfaces has been suggested for a variety of applications, especially for an electrically controlled release system. Well-ordered and three-dimensional porous conductive structures have been obtained by the electrochemical deposition of the aqueous biotin-pyrrole monomer mixture into particle arrays, followed by subsequent removal of the colloidal particles. Advantageously, direct incorporation of biotin molecules enhances the versatility by modifying surfaces through site-directed conjugate formation, thus facilitating further reactions. In addition, the porosity of the surfaces provides a significant impact on enhanced immobilization and efficient release of streptavidin-tagged gold nanoparticles. Biotinylated porous polypyrrole (Ppy) films were characterized by several techniques: (1) scanning electron microscopy (SEM) to evaluate surface topography, (2) X-ray photoelectron spectroscopy (XPS) to assess the potential-dependent chemical composition of the films, (3) four-point probe evaluation to measure the conductivity, cyclic voltammetry to observe surface eletroactivity, and contact angle measurement to evaluate the surface wettability, and (4) fluorescence microscopy to image and quantify the adsorption and release of gold nanoparticles. Overall, our results demonstrate that these biotinylated porous Ppy films, combined with electrical stimulation, permit a programmable release of gold nanoparticles by altering the chemical strength of the Ppy-biotin interaction.     

Pretreatment-free immunochromatographic assay for the detection of streptomycin and its application to the control of milk and dairy products

A rapid pretreatment-free immunochromatographic assay was developed for the control of the streptomycin (STR) content in milk and dairy products. The assay is based on the competition between an immobilized STR–protein conjugate and STR in a sample to be tested for the binding to monoclonal anti-STR antibodies conjugated to colloidal gold during the flow of the sample along a membrane strip with immobilized reactants. It is possible to improve the cut-off level of positive and negative samples distinguished by a change in the molar STR to protein ratio in the immobilized conjugate. The cut-off level (500 ng mL⁻¹) thus achieved corresponds to the stated MRL of STR in milk and dairy products. For STR concentrations in the range of 16–250 ng mL⁻¹ its content can be quantitatively measured based on the degree of binding of a colloidal gold label in the test strip zone with the immobilized STR–protein conjugate. The duration of the assay is 10 min. The selected sizes of membrane pores and colloidal gold particles allow the assay to be carried out at room temperature without additional reactants and pretreatment. The applicability of the assay for milk, whole milk, sour clotted milk, and kefir with different fat content (from 0.5% to 6%) was confirmed. The results of quantitative immunochromatographic assay show good correlation with traditional ELISA (r was equal to 0.935 and 0.940 for the series tested).     

Optimization of on-chip elongation for fabricating double-stranded DNA microarrays

The sequence-specific recognitions between DNA and proteins are playing important roles in many biological functions. The double-stranded DNA microarrays (dsDNA microarrays) can be used to study the sequence-specific recognitions between DNAs and proteins in highly parallel way. In this paper, two different elongation processes in forming dsDNA from the immobilized oligonucleotides have been compared in order to optimize the fabrication of dsDNA microarrays: (1) elongation from the hairpins formed by the self-hybridized oligonucleatides spotted on a glass; (2) elongation from the complementary primers hybridized on the spotted oligonucleatides. The results suggested that the dsDNA probes density produced by the hybridized-primer extension was about four times lower than those by the self-hybridized hairpins. Meanwhile, in order to reduce the cost of dsDNA microarrays, we have replaced the Klenow DNA polymerase with Taq DNA polymerase, and optimized the reaction conditions of on-chip elongation. Our experiements showed that the elongation temperature of 50 °C and the Mg²⁺ concentration of 2.5 mM are the optimized conditions in elongation with Taq DNA polymerase. A dsDNA microarray has been successfully constructed with the above method to detect NF-kB protein.     

Application of Single—labelled Probe—primer in PCR Amplification to the Detection of Hepatitis B Virus DNA

A new method based on the incorporation of a single-lablled probe-primer into polymerase chain reaction(PCR) for the detection of PCR-amplified DNA in a closed system is reported.The probeprimerc consists of a specific probe sequence on the 5‘‘‘‘‘‘‘‘-end and a primer sequence on the 3‘‘‘‘‘‘‘‘-end.A flurophore is located at the 5‘‘‘‘‘‘‘‘end.The primeR-quencher is an oligonucleotide,which is complementary to the probe sequence of probe-primer and labelled with a quencher at the 3‘‘‘‘‘‘‘‘-end.In the duplex formed by probe-primer and primer-quencher.the fluorophore and quencher are kept in close proximity to each other.Therefore the fluorescence is quenched.During PCR amplificatio,the specific probe sequence of probeprimer binds to its complement within the same strand of DNA,and is cleaved by Taq DNA polymerase,resulting in the restoration of fluorescence.This system has the same energy transfer mechanism as molecular beacons,and a good quenching effciency can be ensured.Following optimization of PCR conditions,this method was used to detect hepatitis b virus(HBV) dna in patient sera.This technology eliminates the risk of carry-over contamination,simplifies the amplification assay and opens up new possibilities for the real-time detection of the amplified DNA.