scholarly journals DNAzyme Sensor for the Detection of Metal Ions Using Resistive Pulse Sensing

Author(s):  
Imogen Heaton ◽  
Mark Platt

<b>DNAzymes are DNA based catalysts that can undergo cleavage upon binding of the target analyte. The cleavage reaction is highly specific, and DNAzymes exists for a wide range of metal ions. The change of structure upon binding of a specific metal ion has given rise to many sensing strategies, but few exist with nanopore sensors. Resistive Pulse Sensing, RPS, is a platform that has emerged in recent years capable of identifying changes in DNA structure and sequence. Here we develop the use of DNAzymes with RPS technologies for the detection of Ca2+ ions in solution. Ca2+ plays an important role in biological processes, critical for cell signally, protein folding and catalysis. Extreme concentrations of Ca2+ within drinking water have also been linked to problems with corrosion, scaling and the taste of water. Using DNAzyme functionalised nanocarriers and RPS, it was possible follow the Ca2+ ions binding to the DNAzyme. The binding of Ca2+ caused a conformation change in the DNAzyme which was monitored as a change in translocation speed. By following the changes to the translocation speed, it is hypothesised that RPS can verify the changes in structure. In addition, the assay allowed the quantification of Ca2+ between 1 – 9 μM, and due its catalytic nature, increasing incubation time from 30 to 90 minutes allowed lower detection limits, down to 0.3 μM. We demonstrate that the speed changes are specific to Ca2+ in the presence of other metal ions, and we can quantify Ca2+ in tap and pond water samples.</b><br>

2020 ◽  
Author(s):  
Imogen Heaton ◽  
Mark Platt

<b>DNAzymes are DNA based catalysts that can undergo cleavage upon binding of the target analyte. The cleavage reaction is highly specific, and DNAzymes exists for a wide range of metal ions. The change of structure upon binding of a specific metal ion has given rise to many sensing strategies, but few exist with nanopore sensors. Resistive Pulse Sensing, RPS, is a platform that has emerged in recent years capable of identifying changes in DNA structure and sequence. Here we develop the use of DNAzymes with RPS technologies for the detection of Ca2+ ions in solution. Ca2+ plays an important role in biological processes, critical for cell signally, protein folding and catalysis. Extreme concentrations of Ca2+ within drinking water have also been linked to problems with corrosion, scaling and the taste of water. Using DNAzyme functionalised nanocarriers and RPS, it was possible follow the Ca2+ ions binding to the DNAzyme. The binding of Ca2+ caused a conformation change in the DNAzyme which was monitored as a change in translocation speed. By following the changes to the translocation speed, it is hypothesised that RPS can verify the changes in structure. In addition, the assay allowed the quantification of Ca2+ between 1 – 9 μM, and due its catalytic nature, increasing incubation time from 30 to 90 minutes allowed lower detection limits, down to 0.3 μM. We demonstrate that the speed changes are specific to Ca2+ in the presence of other metal ions, and we can quantify Ca2+ in tap and pond water samples.</b><br>


1984 ◽  
Vol 62 (1) ◽  
pp. 49-54 ◽  
Author(s):  
D. J. Farmer ◽  
B. R. Hollebone

The in vitro inhibition of hydroxymethylbilane synthase (EC 4.3.1.8, uroporphyrinogen I synthetase) obtained from livers of Sprague–Dawley rats has been studied with a wide range of di- and tri-valent metal ions. After purification by cell lysis, heat treatment, and centrifugation, the stable, soluble enzyme yielded sigmoidal inhibition curves with increasing concentrations of each of the 16 test ions. Using the negative logarithm of metal concentration for 50% inhibition (the pM50 value), the metal ions could be classified according to their Klopman hardness values. Very soft ions including Hg2+, intermediate ions including Cr3+, and very hard ions including Al3+ all yielded large pM50 values indicating strong inhibition. In comparison to known metal-ion chemical behaviour, these three ions could indicate three different types of inhibitory binding sites at or near the active site: Hg2+ corresponding to sulfur in cysteine, Cr3+ corresponding to nitrogen in histidine, and Al3+ corresponding to oxygen in carboxyl groups. The presence of the first two sites is also indicated by the pH dependence of activity.


Author(s):  
Miha Purg ◽  
Anna Pabis ◽  
Florian Baier ◽  
Nobuhiko Tokuriki ◽  
Colin Jackson ◽  
...  

Diverse organophosphate hydrolases have convergently evolved the ability to hydrolyse man-made organophosphates. Thus, these enzymes are attractive model systems for studying the factors shaping enzyme functional evolution. Methyl parathion hydrolase (MPH) is an enzyme from the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphate, aryl ester and lactone substrates. In addition, MPH demonstrates metal-ion-dependent selectivity patterns. The origins of this remain unclear, but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. Here, we present detailed mechanistic studies of the paraoxonase and arylesterase activities of MPH complexed with five different transition metal ions, and demonstrate that the hydrolysis reactions proceed via similar pathways and transition states. However, while it is possible to discern a clear structural origin for the selectivity between different substrates , the selectivity between different metal ions appears to lie instead in the distinct electrostatic properties of the metal ions themselves, which causes subtle changes in transition state geometries and metal–metal distances at the transition state rather than significant structural changes in the active site. While subtle, these differences can be significant for shaping the metal-ion-dependent activity patterns observed for this enzyme. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’.


2000 ◽  
Vol 182 (22) ◽  
pp. 6374-6381 ◽  
Author(s):  
Bastiaan P. Krom ◽  
Jessica B. Warner ◽  
Wil N. Konings ◽  
Juke S. Lolkema

ABSTRACT Citrate uptake in Bacillus subtilis is stimulated by a wide range of divalent metal ions. The metal ions were separated into two groups based on the expression pattern of the uptake system. The two groups correlated with the metal ion specificity of two homologousB. subtilis secondary citrate transporters, CitM and CitH, upon expression in Escherichia coli. CitM transported citrate in complex with Mg2+, Ni2+, Mn2+, Co2+, and Zn2+ but not in complex with Ca2+, Ba2+, and Sr2+. CitH transported citrate in complex with Ca2+, Ba2+, and Sr2+ but not in complex with Mg2+, Ni2+, Mn2+, Co2+, and Zn2+. Both transporters did not transport free citrate. Nevertheless, free citrate uptake could be demonstrated in B. subtilis, indicating the expression of at least a third citrate transporter, whose identity is not known. For both the CitM and CitH transporters it was demonstrated that the metal ion promoted citrate uptake and, vice versa, that citrate promoted uptake of the metal ion, indicating that the complex is the transported species. The results indicate that CitM and CitH are secondary transporters that transport complexes of divalent metal ions and citrate but with a complementary metal ion specificity. The potential physiological function of the two transporters is discussed.


2021 ◽  
Author(s):  
◽  
Peter Hauer

<p>The detection and characterisation of micro- and nanoscale particles has become increasingly important in many scientific fields, spanning from colloidal science to biomedical applications. Resistive Pulse Sensing (RPS) and its derivative Tuneable Resistive Pulse Sensing (TRPS), which both use the Coulter principle, have proven to be useful tools to detect and analyse particles in solution over a wide range of sizes. While RPS uses a fixed size pore, TRPS uses a dynamically stretchable pore in a polyurethane membrane, which has the advantages that the pore geometry can be tuned to increase the device's sensitivity and range of detection. The technique has been used to accurately determine the size, concentration and charge of many different analytes.  However, the information obtained using TRPS does not give any insight into the particle's composition. In an attempt to overcome this, an experimental technique was developed in order to obtain simultaneous, time-resolved, high-resolution optical spectra of particles passing through the pore. Due to the ordered and controllable fashion in which the particles are guided through the sensing region, this approach has an advantage over diffusion based optical techniques. The experimental setup for the coordinated electrical and optical measurements involves many underlying physical phenomena, e.g. microuidics, electrokinetic effects, and Gaussian beam optics. A significant proportion of this work was therefore devoted to the development and the optimisation of the experimental setup by adapting a commercial TRPS device and a spectrometer with an attached microscope. Methods to engineer the spot size of a Gaussian beam to account for the different pore diameters, and the development of algorithms to filter, analyse and coordinate the recorded data are essential to the technique.  The results using fluorescently labelled polystyrene particle sets with diameters from 190nm to 2 µm show that matching rates between the electrical and optical measurements of over 90% can repeatedly be achieved. Mixtures of particle species with similar diameters but with different fluorescent labels were used to demonstrate the technique's capability to characterise the analyte on a particle-by-particle basis and extend the information that can be obtained by TRPS alone. It was also shown that the data acquired with the electrical and optical measurements complement each other and can be used to better understand the TRPS technique itself. The influence of experimental parameters, such as the particle velocity, the beam size and the optical detection volume, on the intensity of the optical signals and the matching rates was studied intensively. These studies showed that the technique requires a careful experimental design to achieve the best results. Overall, the developed technique enhances the particle-by-particle specificity of conventional RPS measurements, and could be useful for a range of particle characterization and bio-analysis applications.  Alongside the experiments, semi-analytic modelling and simulations using the Finite Element Method (FEM) were used to understand the particle motion through the pores, to interpret the experimental data, and predict the optical signals. The models were also used to assist the design and the optimization of the experiments. The FEM models were implemented with increasing physical detail and show superior understanding of the TRPS signals compared to the semi-analytic model, which is conventionally used in the TRPS field. The physical phenomena considered included o -axis trajectories, particle-field interactions for both fluid and electric fields, and the non-homogeneous distribution of ions close to the charged membrane and particle interfaces. Several effects which have been observed experimentally could be explained, including the intrinsic pulse height distribution, the current rectification, and the occurrence of bi-phasic pulses, demonstrating the benefits of FEM methods for RPS.</p>


2021 ◽  
Author(s):  
◽  
Peter Hauer

<p>The detection and characterisation of micro- and nanoscale particles has become increasingly important in many scientific fields, spanning from colloidal science to biomedical applications. Resistive Pulse Sensing (RPS) and its derivative Tuneable Resistive Pulse Sensing (TRPS), which both use the Coulter principle, have proven to be useful tools to detect and analyse particles in solution over a wide range of sizes. While RPS uses a fixed size pore, TRPS uses a dynamically stretchable pore in a polyurethane membrane, which has the advantages that the pore geometry can be tuned to increase the device's sensitivity and range of detection. The technique has been used to accurately determine the size, concentration and charge of many different analytes.  However, the information obtained using TRPS does not give any insight into the particle's composition. In an attempt to overcome this, an experimental technique was developed in order to obtain simultaneous, time-resolved, high-resolution optical spectra of particles passing through the pore. Due to the ordered and controllable fashion in which the particles are guided through the sensing region, this approach has an advantage over diffusion based optical techniques. The experimental setup for the coordinated electrical and optical measurements involves many underlying physical phenomena, e.g. microuidics, electrokinetic effects, and Gaussian beam optics. A significant proportion of this work was therefore devoted to the development and the optimisation of the experimental setup by adapting a commercial TRPS device and a spectrometer with an attached microscope. Methods to engineer the spot size of a Gaussian beam to account for the different pore diameters, and the development of algorithms to filter, analyse and coordinate the recorded data are essential to the technique.  The results using fluorescently labelled polystyrene particle sets with diameters from 190nm to 2 µm show that matching rates between the electrical and optical measurements of over 90% can repeatedly be achieved. Mixtures of particle species with similar diameters but with different fluorescent labels were used to demonstrate the technique's capability to characterise the analyte on a particle-by-particle basis and extend the information that can be obtained by TRPS alone. It was also shown that the data acquired with the electrical and optical measurements complement each other and can be used to better understand the TRPS technique itself. The influence of experimental parameters, such as the particle velocity, the beam size and the optical detection volume, on the intensity of the optical signals and the matching rates was studied intensively. These studies showed that the technique requires a careful experimental design to achieve the best results. Overall, the developed technique enhances the particle-by-particle specificity of conventional RPS measurements, and could be useful for a range of particle characterization and bio-analysis applications.  Alongside the experiments, semi-analytic modelling and simulations using the Finite Element Method (FEM) were used to understand the particle motion through the pores, to interpret the experimental data, and predict the optical signals. The models were also used to assist the design and the optimization of the experiments. The FEM models were implemented with increasing physical detail and show superior understanding of the TRPS signals compared to the semi-analytic model, which is conventionally used in the TRPS field. The physical phenomena considered included o -axis trajectories, particle-field interactions for both fluid and electric fields, and the non-homogeneous distribution of ions close to the charged membrane and particle interfaces. Several effects which have been observed experimentally could be explained, including the intrinsic pulse height distribution, the current rectification, and the occurrence of bi-phasic pulses, demonstrating the benefits of FEM methods for RPS.</p>


2008 ◽  
Vol 22 (4) ◽  
pp. 213-221 ◽  
Author(s):  
Priscilla Ward ◽  
Chengdong Huang ◽  
Monimoy Banerjee ◽  
Smita Mohanty

Glutaminase interacting protein (GIP), a PDZ domain containing protein, mediates the distribution and clustering of proteins/peptides in membranes, acting as a scaffold where signaling molecules are linked to a multi-protein complex. GIP has been shown to play a key role in the glutamate signaling system. Some metals, particularly Pb2+, Cu2+and Zn2+, have been implicated in a wide range of neurological disorders including Alzheimer's disease and Parkinson's disease, whose etiologies have been associated with dysfunction of the glutamate signaling system. Here, for the first time, the effects of lead, copper, and zinc on GIP were determined by using circular dichroism and fluorescence spectroscopy. All three metal ions significantly affected the conformational properties of GIP. The deconvolution of CD data showed that, with increasing amounts of Pb2+/Cu2+/Zn2+, theα-helix percentage decreased while theβ-sheet content increased. The binding constants of GIP to Pb2+, Cu2+and Zn2+determined by fluorescence were found to be 1.4, 2.38 and 2.85 μM respectively, which indicated strong bindings between GIP and all three metal ions. We propose that the metal ion binding site of GIP is located onα-2 helix, where residues His90, Asp91 and Arg94 may coordinate the metal ions. The conformational change of GIP upon metal ion binding possibly results from the disruption of a salt bridge between Asp91 and Arg94.


Polymers ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1314
Author(s):  
Alan F. Y. Matsushita ◽  
María José Tapia ◽  
Alberto A. C. C. Pais ◽  
Artur J. M. Valente

The interaction between polyelectrolytes and metal ions is governed by different types of interactions, leading to the formation of different phases, from liquid state to weak gels, through an appropriate choice of metal ion/polyelectrolyte molar ratio. We have found that lanthanide ions, europium(III) and terbium(III), are able to form polymer composites with poly(sodium acrylate). That interaction enhances the luminescent properties of europium(III) and terbium(III), showing that Eu3+/poly(sodium acrylate) (PSA) and Tb3+/PSA composites have a highly intense red and green emission, respectively. The effect of cations with different valences on the luminescent properties of the polymer composites is analyzed. The presence of metal ions tends to quench the composite emission intensity and the quenching process depends on the cation, with copper(II) being by far the most efficient quencher. The interaction mechanism between lanthanoid ions and PSA is also discussed. The composites and their interactions with a wide range of cations and anions are fully characterized through stationary and non-stationary fluorescence, high resolution scanning electronic microscopy and X-ray diffraction.


2019 ◽  
Vol 4 (3) ◽  
pp. 616-625
Author(s):  
A. K. Singha Deb ◽  
P. Sahu ◽  
Sk. M. Ali

Crown ethers are very useful for metal ion recognition due to their nanocavity based specific ion selectivity, which on functionalization with carbon nanotubes (CNTs) can be employed as specific metal ion filters by exploiting their different interactions with metal ions.


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