Electric Single-Molecule Hybridization Detector for Short DNA Fragments.

By combining DNA nanotechnology and high-bandwidth single-molecule detection in nanopipets, we demonstrate an electric, label-free hybridization sensor for short DNA sequences (<100 nucleotides). Such short fragments are known to occur as circulating cell-free DNA in various bodily fluids, such as blood plasma and saliva, and have been identified as disease markers for cancer and infectious diseases. To this end, we use as a model system an 88-mer target from the RV1910c gene in Mycobacterium tuberculosis, which is associated with antibiotic (isoniazid) resistance in TB. Upon binding to short probes attached to long carrier DNA, we show that resistive-pulse sensing in nanopipets is capable of identifying rather subtle structural differences, such as the hybridization state of the probes, in a statistically robust manner. With significant potential toward multiplexing and high-throughput analysis, our study points toward a new, single-molecule DNA-assay technology that is fast, easy to use, and compatible with point-of-care environments.

Delivering precision antimicrobial therapy through closed-loop control systems.

Sub-optimal exposure to antimicrobial therapy is associated with poor patient outcomes and the development of antimicrobial resistance. Mechanisms for optimizing the concentration of a drug within the individual patient are under development. However, several barriers remain in realizing true individualization of therapy. These include problems with plasma drug sampling, availability of appropriate assays, and current mechanisms for dose adjustment. Biosensor technology offers a means of providing real-time monitoring of antimicrobials in a minimally invasive fashion. We report the potential for using microneedle biosensor technology as part of closed-loop control systems for the optimization of antimicrobial therapy in individual patients.

Glucose sensors: a review of current and emerging technology.

Glucose monitoring technology has been used in the management of diabetes for three decades. Traditional devices use enzymatic methods to measure glucose concentration and provide point sample information. More recently continuous glucose monitoring devices have become available providing more detailed data on glucose excursions. In future applications the continuous glucose sensor may become a critical component of the closed loop insulin delivery system and, as such, must be selective, rapid, predictable and acceptable for continuous patient use. Many potential sensing modalities are being pursued including optical and transdermal techniques. This review aims to summarize existing technology, the methods for assessing glucose sensing devices and provide an overview of emergent sensing modalities.

Radical intermediates in veratryl alcohol oxidation by ligninase. NMR evidence.

Proton nuclear magnetic resonance (NMR) spectra of veratryl alcohol (3,4-dimethoxybenzyl alcohol) were obtained during its oxidation by ligninase. It was observed that a substantial increase in the linewidths of the resonances occurred only in the presence of both the enzyme and hydrogen peroxide. Quenching the reaction by the addition of alkali immediately restored the normal linewidths of the resonances. Furthermore, inversion-recovery experiments showed a decrease in the longitudinal relaxation time of the substrate when the enzyme was actively turning over. Changes in both these NMR parameters are consistent with the generation of radical intermediates during the ligninase-catalysed oxidation of veratryl alcohol.

Alkaline phosphatase-Strep tag fusion protein binding to streptavidin: resonant mirror studies.

The properties of a fusion protein comprising a streptavidin recognition sequence (Strep tag) fused to the C terminus of Escherichia coli alkaline phosphatase are described. The catalytic properties were determined with p-nitrophenyl phosphate and compared to those of the native E. coli alkaline phosphatase. It was found that the Km values were similar in both cases (8 microM for transferase and 2 microM for hydrolase activities) whilst the Vmax values were lower for the fusion protein, possibly due to the presence of misfolded forms. An optical biosensor based on the resonant mirror was used to determine the binding kinetics between the fusion protein and the immobilised streptavidin. The association and dissociation rate constants were determined to be 2.1(+/-0.3) x 10(-2) microM(-1) s(-1) and 11(+/-0.2) x 10(-3) s(-1), respectively, which results in an equilibrium dissociation constant of 0.5 microM. This is larger than previously reported affinities based on titration calorimetry and may be a consequence of the presence of two streptavidin binding sequences on the dimeric alkaline phosphatase simultaneously binding to two subunits of streptavidin.

Generation of a pair of independently binding DNA aptamers in a single round of selection using proximity ligation.

The ability to rapidly generate a pair of aptamers that bind independently to a protein target would greatly extend their use as reagents for two site ('sandwich') assays. We describe here a method to achieve this through proximity ligation. Using lysozyme as a target we demonstrate that under optimal conditions such a pair of aptamers, with nanomolar affinities, can be generated in a single round.

Biotransformation of aromatic compounds. Monitoring fluorinated analogues by NMR.

The results presented here illustrate the power of NMR in the non-invasive analysis of microbial transformations. Whilst the definitive identification of products requires purification and full structural elucidation. NMR can provide rapid insights into the nature of these reactions and their regulation in vivo. In addition, once the products have been identified NMR methods allow rapid assessment of the effects of genetic and physiological manipulation, and on competing metabolic fluxes with mixed substrates and branched pathways.

Mediated electrochemistry of peroxidases--effects of variations in protein and mediator structures.

The kinetics of a range of ferrocene derivatives with horseradish peroxidase (HRP), cytochrome c peroxidase (CCP) and 3 charge reversal mutants of cytochrome c peroxidase were measured using cyclic voltammetry. Substantial differences in rate constant (100 fold) were observed between HRP and CCP for the same mediator with smaller differences (4-5 fold) for different mediators with the same enzyme. The rate constant did not seem to be dependent on redox potential differences. Cluster analysis is proposed as a way of classifying mediator reactivity.

Inhibited enzyme electrodes. Part 1: Theoretical model.

A theoretical model is developed for an electrochemical sensor for toxic substances which works by measuring the inhibition of the enzyme activity. The enzyme is assumed to follow Michaelis-Menten kinetics and the diffusion kinetic equation describing the concentration profile of the enzyme's substrate in the electrolyte layer between the electrode and the membrane covering the electrode is solved. A complete set of analytical solutions is found which corresponds to a number of different rate limiting processes. The set of solutions is described in a case diagram. The use of cytochrome oxidase in particular is discussed.

Inhibited enzyme electrodes. Part 2: The kinetics of the cytochrome oxidase system.

An inhibition enzyme electrode to measure toxic gases can be constructed using the respiratory enzyme cytochrome oxidase. The rate of enzyme turnover is followed by reducing cytochrome c on a gold electrode modified with the mediator bis(4-pyridyl) disulphate. The kinetics and mechanism of the system have been measured. The electrochemical kinetics for the oxidation of cytochrome c have been studied by rotating disc voltammetry and are shown to obey the Koutecky-Levich equation. The standard electrochemical rate constant is found to be 3 x 10(-3) cms-1. At ambient oxygen concentration the orders of the current with respect to the concentration of cytochrome oxidase, cytochrome c and oxygen are found to be 1/2, 1/2 and zero respectively. These orders are consistent with the rate limiting step being the turnover of the enzyme under saturated conditions in a thin reaction layer close to the electrode. At lower oxygen concentrations a good fit between the experimental results and a theoretical model further confirms the assignation of the mechanism. The rate constants describing the oxidation and reduction of the enzyme have been measured. The pH dependence of the current has been studied.

Inhibited enzyme electrodes. Part 3. A sensor for low levels of H2S and HCN.

It is shown that an inhibited enzyme electrode, using cytochrome oxidase, will respond to H2S, HCN and azide ion. For all three inhibitors the kinetics of the inhibiton and recovery processes have been analysed using the theoretical model presented previously (Albery et al., 1990a). Rearrangement of the differential equation describing inhibition and the development of the necessary software has enabled us to obtain values of the concentration of inhibitor in a matter of seconds after exposure of the sensor. The sensor will measure concentrations of H2S down to 1 ppm in the gas phase and concentrations of HCN and azide ion down to 0.4 mumol dm-3 in the solution phase.

DNA optical sensor: a rapid method for the detection of DNA hybridization.

A DNA optical sensor system is proposed based on the combination of sandwich solution hybridization, magnetic bead capture, flow injection and chemiluminescence for rapid detection of DNA hybridization. Bacterial alkaline phosphatase (phoA) gene and Hepatitis B virus (HBV) DNA were used as target DNA. A biotinylated DNA probe was used to capture the target gene onto the streptavidin-coated magnetic beads and a calf intestine alkaline phosphatase (CAP)-labelled DNA probe was used for subsequent enzymatic chemiluminescence detection. The detection cycle was less than 30 min, excluding the DNA hybridization time, which was about 100 min. Both the phoA gene and HBV DNA could be detected at picogramme or femtomole level. No response signal was obtained when target DNA did not exist in the sample. Successive sample detection could be made by removing the magnetic field and a washing step.

Isolation of a membrane protein by chromatofocusing: cytochrome b-561 of the adrenal chromaffin granule.

Chromatofocusing, a form of ion-exchange chromatography in which proteins are separated on the basis of their differing isoelectric points, has been adapted for use with membrane proteins, solubilized by the non-ionic detergent Nonidet P-40. Using a two-step detergent extraction followed by chromatofocusing under high pressure, the highly hydrophobic protein cytochrome b-561 was isolated from chromaffin granule membranes and purified to near homogeneity in a functionally active form, in less than 5 h. Chromatofocusing conditions were optimized empirically since the behaviour of the chromaffin granule membrane proteins conformed less to the theory than that of soluble proteins, and the various factors affecting yield and resolution are discussed. The speed, high resolution and focusing effect could make this method particularly suitable for rapid isolation in a functionally active form of the many membrane proteins that are unstable in dilute solution and when removed from their lipid environment.

Ocular injury and infection in dental practice. A survey and a review of the literature.

Dental surgeons, dental surgery assistants and patients are at risk of eye injury during certain dental procedures. We have reviewed the literature to reemphasise these hazards and have conducted a survey to determine how often injuries occur and what measures are taken to prevent them.

Aptamer-based biosensors for the rapid visual detection of flu viruses.

RNA aptamers showing affinity and specificity for different strains of human influenza virus were assembled onto gold nanoparticles that subsequently formed a gold nanoshell (AuNS) around the viral envelope. These shells could be visualised by transmission electron microscopy (TEM). Changes in size and structure of the AuNS coated virus can be used to detect the viruses. We show that sedimentation with a low cost centrifuge and visual determination can detect 3 × 10(8) viral particles.

A step towards understanding the folding mechanism of horseradish peroxidase. Tryptophan fluorescence and circular dichroism equilibrium studies.

The guanidinium chloride denaturation/renaturation of the holo- and apo-horseradish peroxidase isoenzyme c (HRP) has been studied by fluorescence and circular dichroism spectroscopies. A distinct equilibrium intermediate of the apoprotein could be detected at low concentrations of guanidinium chloride (0.5 M). This intermediate has a secondary structure content like that of the native protein but a poorly defined tertiary structure. Renaturation of the apo-HRP is reversible and 100% activity could be obtained after addition of a twofold excess of free haem. The denaturation of the holo-HRP is more complex and occurs in two distinct steps; unfolding of the protein backbone and loss of the haem. The denatured protein folds back to its native conformation but the incorporation of the haem occurs only after the secondary structure is formed. Ca2+ appears to be important for the stability of the protein as the apo-HRP is more resistant to denaturation in the presence of Ca2+. The free-energy change during unfolding of the apo-HRP was determined in the absence and presence of Ca2+ and found to be 9.2 kJ/mol and 16.7 kJ/mol, respectively. The importance of Ca2+ to the protein stability was also supported by studies on the loss of the haem from the protoporphyrin-IX-apo-HRP complex.

Copper proteins and copper enzymes.

The copper proteins that function in homeostasis, electron transport, dioxygen transport and oxidation are discussed. Particular emphasis is placed on the role of the ligands, their type and disposition which, in conjunction with other residues in the active site, determine the role of the copper ion. It is proposed that copper proteins can be considered in four groups. Those in Group I contain a single copper ion in an approximately tetrahedral environment with nitrogen and sulphur-containing ligands. Group II proteins have a single copper ion in a square-planar-like arrangement. Group III proteins have two copper ions in close proximity. Group IV consists of multi-copper proteins, composed of sites representative of the other three groups.

Partition coefficient of luciferase from photobacteria in PEG/salt two aqueous phase system.

The relationship between the logarithmic partition coefficient (K) of luciferase of photobacteria and PEG MW in the PEG/salt two aqueous phase system was shown to be a linear function. The hydrophilic PEG of lower MW facilitated the partition of luciferase into the top PEG-riching phase and gave a higher K value, while PEG of higher MW, its hydrophobic characteristic, made more enzyme partition into the bottom salt-riching phase and lower K value was obtained. In the PEG/trivalent salt system, such as phosphate and citrate, there was a turning-point on the linear relation between the log K and the PEG MW, but which never appeared if a divalent salt such as sulfate, succinate or tartrate was used in the system. When the system was composed of homogeneous PEG and ammonium sulfate, the K value was increased with the increment of the salt concentration, but after the salt concentration had reached at certain level, the K value was uninfluenced. When two kinds of PEG with different MW were used in this system a minimal K value appeared at certain concentration of ammonium sulfate, and the K value was raised when the salt concentration was either increased or decreased. Neither the proportion of the two kinds of PEG nor their total concentration used in the system showed any effect on the above patterns, although the K value may give some corresponding changes. (ABSTRACT TRUNCATED AT 250 WORDS)