DNA bound to polypyrrole films: high-resolution imaging, DNA binding kinetics and internal migration

A Label-Free Fluorescent Aptasensor for Detection of Staphylococcal Enterotoxin A Based on Aptamer-Functionalized Silver Nanoclusters

Staphylococcal enterotoxin A (SEA) is a worldwide public health problem accounting for the majority of food poisoning which is produced by Staphylococcus aureus, threatening human health and leading to various foodborne diseases. Therefore, it is of great significance to develop a sensitive detection method for SEA to ensure food safety and prevent foodborne diseases in humans. In this study, an adaptive fluorescence biosensor for the detection of staphylococcal enterotoxin A (SEA) was designed and developed by combining DNA silver nanoclusters (DNA-AgNCs) with polypyrrole nanoparticles (PPyNPs). Fluorescent AgNCs, synthesized using aptamers as templates, were used as fluorescence probes, whose fluorescence was quenched by PPyNPs. In the presence of the target SEA, DNA-AgNCs were forced to desorb from the surface of PPyNPs through the binding of SEA with the aptamer-DNA-AgNCs, thereby resulting in fluorescence recovery. Under the optimized conditions, the relative fluorescence intensity (FI) showed a linear relationship with the SEA concentration in the range from 0.5 to 1000 ng/mL (Y = 1.4917X + 0.9100, R² = 0.9948) with a limit of detection (LOD) of 0.3393 ng/mL. The sensor was successfully used to evaluate the content of SEA in milk samples, and the recovery efficiency of SEA was between 87.70% and 94.65%. Thus, the sensor shows great potential for application in food analysis. In short, the proposed platform consisted of an aptamer fluorescent sensor that can be used for the ultrasensitive detection of various toxins by taking advantage of the excellent affinity and specificity of corresponding aptamers.

The inhibitory effects of polypyrrole on the biofilm formation of Streptococcus mutans

Streptococcus mutans primary thrives on the biofilm formation on the tooth surface in sticky biofilms and under certain conditions can lead to carious lesions on the tooth surface. To search for a new preventive material for oral biofilm-associated diseases, including dental caries, we investigated the effects of polypyrrole, which contains an electrochemical polymer and causes protonation and incorporation of anion under low pH condition, on the biofilm formation of S. mutans and other streptococci. In this study, polypyrrole was applied in biofilm formation assays with the S. mutans strains UA159 and its gtfB and gtfC double mutant (gtfBC mutant), S. sanguinis, S. mitis and S. gordonii on human saliva and bovine serum albumin-coated 96-well microtiter plates in tryptic soy broth supplemented with 0.25% sucrose. The effects of polypyrrole on biofilm formation were quantitatively and qualitatively observed. High concentrations of polypyrrole significantly inhibited the biofilm formation of S. mutans UA159 and S. sanguinis. As an inhibition mechanism, polypyrrole attached to the surface of bacterial cells, increased chains and aggregates, and incorporated proteins involving GTF-I and GTF-SI produced by S. mutans. In contrast, the biofilm formation of gtfBC mutant, S. sanguinis, S. mitis and S. gordonii was temporarily induced by the addition of low polypyrrole concentrations on human saliva-coated plate but not on the uncoated and bovine serum albumin-coated plates. Moreover, biofilm formation depended on live cells and, likewise, specific interaction between cells and binding components in saliva. However, these biofilms were easily removed by increased frequency of water washing. In this regard, the physical and electrochemical properties in polypyrrole worked effectively in the removal of streptococci biofilms. Polypyrrole may have the potential to alter the development of biofilms associated with dental diseases.

DNA Computing Systems Activated by Electrochemically-triggered DNA Release from a Polymer-brush-modified Electrode Array

An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA-based Identity, AND and XOR logic gates. Single-stranded DNA molecules were loaded on the mixed poly(N,N-di-methylaminoethyl methacrylate) (PDMAEMA)/poly-(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAE-MA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at -1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals.

High-capacity conductive nanocellulose paper sheets for electrochemically controlled extraction of DNA oligomers

Highly porous polypyrrole (PPy)-nanocellulose paper sheets have been evaluated as inexpensive and disposable electrochemically controlled three-dimensional solid phase extraction materials. The composites, which had a total anion exchange capacity of about 1.1 mol kg⁻¹, were used for extraction and subsequent release of negatively charged fluorophore tagged DNA oligomers via galvanostatic oxidation and reduction of a 30–50 nm conformal PPy layer on the cellulose substrate. The ion exchange capacity, which was, at least, two orders of magnitude higher than those previously reached in electrochemically controlled extraction, originated from the high surface area (i.e. 80 m² g⁻¹) of the porous composites and the thin PPy layer which ensured excellent access to the ion exchange material. This enabled the extractions to be carried out faster and with better control of the PPy charge than with previously employed approaches. Experiments in equimolar mixtures of (dT)₆, (dT)₂₀, and (dT)₄₀ DNA oligomers showed that all oligomers could be extracted, and that the smallest oligomer was preferentially released with an efficiency of up to 40% during the reduction of the PPy layer. These results indicate that the present material is very promising for the development of inexpensive and efficient electrochemically controlled ion-exchange membranes for batch-wise extraction of biomolecules.

Investigation of SPR and electrochemical detection of antigen with polypyrrole functionalized by biotinylated single-chain antibody: a review

An electrochemical label-free immunosensor based on a biotinylated single-chain variable fragment (Sc-Fv) antibody immobilized on copolypyrrole film is described. An efficient immunosensor device formed by immobilization of a biotinylated single-chain antibody on an electropolymerized copolymer film of polypyrrole using biotin/streptavidin system has been demonstrated for the first time. The response of the biosensor toward antigen detection was monitored by surface plasmon resonance (SPR) and electrochemical analysis of the polypyrrole response by differential pulse voltammetry (DPV). The composition of the copolymer formed from a mixture of pyrrole (py) as spacer and a pyrrole bearing a N-hydroxyphthalimidyl ester group on its 3-position (pyNHP), acting as agent linker for biomolecule immobilization, was optimized for an efficient immunosensor device. The ratio of py:pyNHP for copolymer formation was studied with respect to the antibody immobilization and antigen detection. SPR was employed to monitor in real time the electropolymerization process as well as the step-by-step construction of the biosensor. FT-IR demonstrates the chemical copolymer composition and the efficiency of the covalent attachment of biomolecules. The film morphology was analyzed by electron scanning microscopy (SEM). Results show that a well organized layer is obtained after Sc-Fv antibody immobilization thanks to the copolymer composition defined with optimized pyrrole and functionalized pyrrole leading to high and intense redox signal of the polypyrrole layer obtained by the DPV method. Detection of specific antigen was demonstrated by both SPR and DPV, and a low concentration of 1 pg mL(-1) was detected by measuring the variation of the redox signal of polypyrrole.

Isolation of microtubules and microtubule proteins

This unit describes various protocols for the isolation and purification of the main constituents of microtubules, chiefly alpha- and beta-tubulin, and the most significant microtubule associated proteins (MAPs), specifically MAP1A, MAP1B, MAP2, and tau. We include a classical isolation method for soluble tubulin heterodimer as the first basic purification protocol. In addition, we show how to analyze the tubulin and MAPs obtained after a phosphocellulose chromatography purification procedure. This unit also details a powerful and simple method to determine the native state of the purified tubulin based on one-dimensional electrophoresis under nondenaturing conditions (UNIT 6.5). The last protocol describes the application of a new technique that allows visualizing the quality of polymerized microtubules based on atomic force microscopy (AFM).

Photoinduced transparency in polypyrrole films

For the first time we have discovered drastic photoinduced effects in the transparency for the pyrrole films. Photoinduced investigations of transparency were performed for the polypyrroles with different number of the pyrrole rings. We have established a considerable increase of the transparency from 70-75% up to 82-84% for the wavelengths of the probing lasers operating within the 530-1040 nm spectral range. The photoexcitation was performed by nanosecond pulsed polarized Nd-YAG laser generating at 1.34 microm. The phototransparent changes are completely reversible and disappear after switching off the laser treatment. The typical relaxation time for the photoinduced transparency is equal to about 10-20 micros and the changes of the transparency are strictly related with the values of state dipole moments of the polypyrroles. As a possible mechanism for explanation of the observed dependences one can consider existence of the charged trapping levels intra the forbidden energy gaps which effectively interact with the electric strength of the external polarized optical field and state dipole moments of the particular polymers.