Cocaine detection via rolling circle amplification of short DNA strand separated by magnetic beads

A novel and sensitive fluorescence biosensor based on aptamer and rolling circle amplification for the determination of cocaine was developed in the present work. Here cocaine aptamers immobilized onto Au nanoparticles modified magnetic beads hybridized with short DNA strand. In the presence of cocaine, the short DNA strand was displaced from aptamer owing to cocaine specially binding with aptamer. Next, the short DNA strand was separated by magnetic beads and used to originate rolling circle amplification as primer. The end products of rolling circle amplification were detected by fluorescence signal generation upon molecular beacons hybridizing with the end products of rolling circle amplification. With rolling circle amplification and the separation by magnetic beads reducing the background signal, the new strategy was suitable for the detection of as low as 0.48 nM cocaine. Compared with reported cocaine sensors, our method exhibited excellent sensitivity. Our new strategy may provide a platform for numerous proteins and low molecular weight analytes to highly sensitively detect by DNA amplification.     

A nanoparticle-based immobilization assay for prion-kinetics study

Magnetic and gold coated magnetic nanoparticles were synthesized by co-precipitation of ferrous and ferric chlorides, and by the micromicelles method, respectively. Synthesized nanoparticles were functionalized to bear carboxyl and amino acid moieties and used as prion protein carriers after carbodiimide activation in the presence of N-hydroxysuccinimide. The binding of human recombinant prion protein (huPrPrec) to the surface of these nanoparticles was confirmed by FTIR and the size and structures of the particles were characterized by transmission electron microscopy. Findings indicate that the rate of prion binding increased only slightly when the concentration of prion in the reaction medium was increased. Rate constants of binding were very similar on Fe₃O₄@Au and Fe₃O₄-LAA when the concentrations of protein were 1, 2, 1.5, 2.25 and 3.57 μg/ml. For a 5 μg/ml concentration of huPrPrec the binding rate constant was higher for the Fe₃O₄-LAA particles. This study paves the way towards the formation of prion protein complexes onto a 3-dimensional structure that could reveal obscure physiological and pathological structure and prion protein kinetics.     

The antitumor effect of magnetic nanodisks and DNA aptamer conjugates

Here we describe a method of forming large arrays (up to 10⁹ pieces) of free magnetic Ni-nanodisks 50 nm thick coated on both sides with layers of 5 nm thick Au. The antitumor effect of the magnetic nickel gold-coated nanodisks and DNA aptamer conjugates was evaluated in vivo and in vitro. Under the influence of rotating magnetic field, the studied nanodisks can cause the death of Ehrlich ascites carcinoma cells.     

Anti-prion activity of an RNA aptamer and its structural basis

Prion proteins (PrPs) cause prion diseases, such as bovine spongiform encephalopathy. The conversion of a normal cellular form (PrP^C) of PrP into an abnormal form (PrP^Sc) is thought to be associated with the pathogenesis. An RNA aptamer that tightly binds to and stabilizes PrP^C is expected to block this conversion and to thereby prevent prion diseases. Here, we show that an RNA aptamer comprising only 12 residues, r(GGAGGAGGAGGA) (R12), reduces the PrP^Sc level in mouse neuronal cells persistently infected with the transmissible spongiform encephalopathy agent. Nuclear magnetic resonance analysis revealed that R12, folded into a unique quadruplex structure, forms a dimer and that each monomer simultaneously binds to two portions of the N-terminal half of PrP^C, resulting in tight binding. Electrostatic and stacking interactions contribute to the affinity of each portion. Our results demonstrate the therapeutic potential of an RNA aptamer as to prion diseases.     

Anti-bovine prion protein RNA aptamer containing tandem GGA repeat interacts both with recombinant bovine prion protein and its �� isoform with high affinity

In order to obtain RNA aptamers against bovine prion protein (bPrP), we carried out in vitro selection from RNA pools containing a 55-nucleotide randomized region to target recombinant bPrP. Most of obtained aptamers contained conserved GGA tandem repeats (GGA)₄ and aptamer #1 (apt #1) showed a high affinity for both bPrP and its β isoform (bPrP-β). The sequence of apt #1 suggested that it would have a G-quadruplex structure, which was confirmed using CD spectra in titration with KCl. A mutagenic study of this conserved region, and competitive assays, showed that the conserved (GGA)₄ sequence is important for specific binding to bPrP and bPrP-β. Following 5′-biotinylation, aptamer #1 specifically detected PrP^c in bovine brain homogenate in a Northwestern blotting assay. Protein deletion mutant analysis showed that the bPrP aptamer binds within 25–131 of the bPrP sequence. Interestingly, the minimized aptamer #1 (17 nt) showed greater binding to bPrP and bPrP-β as compared to apt #1. This minimized form of aptamer #1 may therefore be useful in the detection of bPrP, diagnosis of prion disease, enrichment of bPr and ultimately in gaining a better understanding of prion diseases.Key words: RNA aptamer, prion protein, SELEX, GGA repeat, G-quadruplex     

Anti-bovine Prion protein RNA aptamer containing tandem GGA repeat interacts both with recombinant bovine prion protein and its β isoform with high affinity

In order to obtain RNA aptamers against bovine prion protein (bPrP), we carried out in vitro selection from RNA pools containing a 55-nucleotide randomized region to target recombinant bPrP. Most of obtained aptamers contained conserved GGA tandem repeats (GGA)4 and aptamer #1 (apt #1) showed a high affinity for both bPrP and its β isoform (bPrP-β). The sequence of apt #1 suggested that it would have a G-quadruplex structure, which was confirmed using CD spectra in titration with KCl. A mutagenic study of this conserved region, and competitive assays, showed that the conserved (GGA)4 sequence is important for specific binding to bPrP and bPrP-β. Following 5′-biotinylation, aptamer #1 specifically detected PrPc in bovine brain homogenate in a Northwestern blotting assay. Protein deletion mutant analysis showed that the bPrP aptamer binds within 25-131 of the bPrP sequence. Interestingly, the minimized aptamer #1 (17nt) showed greater binding to bPrP and bPrP-β as compared to apt #1. This minimized form of aptamer #1 may therefore be useful in the detection of bPrP, diagnosis of prion disease, enrichment of bPrP, and ultimately in gaining a better understanding of prion diseases.     

Single-step purification of recombinant Thermus aquaticus DNA polymerase using DNA-aptamer immobilized novel affinity magnetic beads

A DNA aptamer specific for Thermus aquaticus DNA polymerase (Taq-polymerase) was immobilized on magnetic beads, which were prepared in the presented study. The effect of various parameters including pH, temperaturem and aptamer concentration on the immobilization of 5'-thiol labeled DNA-aptamer onto glutaric dialdhyde activated magnetic beads was evaluated. The binding conditions of Taq-polymerase on the aptamer immobilized magnetic beads were studied using commercial Taq-polymerase to characterize the surface complexation reaction. Efficiency of affinity magnetic beads in the purification of recombinant Taq-polymerase from crude extracts was also evaluated. For this case, the enzyme "recombinant Taq-DNA polymerase" was cloned and expressed using an Amersham E. coli GST-Gene Fusion Expression system. Crude extracts were in contact with affinity magnetic beads for 30 min and were collected by magnetic field application. The purity of the eluted Tag-polymerase from the affinity beads, as determined by HPLC, was 93% with a recovery of 89% in a one-step purification protocol. Apparently, the system was found highly effective as one step for the low-cost purification of Taq-polymerase in bacterial crude extract.     

Activity of glucose oxidase functionalized onto magnetic nanoparticles

BACKGROUND: Magnetic nanoparticles have been significantly used for coupling with biomolecules, due to their unique properties. METHODS: Magnetic nanoparticles were synthesized by thermal co-precipitation of ferric and ferrous chloride using two different base solutions. Glucose oxidase was bound to the particles by direct attachment via carbodiimide activation or by thiophene acetylation of magnetic nanoparticles. Transmission electron microscopy was used to characterize the size and structure of the particles while the binding of glucose oxidase to the particles was confirmed using Fourier transform infrared spectroscopy. RESULTS: The direct binding of glucose oxidase via carbodiimide activity was found to be more effective, resulting in bound enzyme efficiencies between 94-100% while thiophene acetylation was 66-72% efficient. Kinetic and stability studies showed that the enzyme activity was more preserved upon binding onto the nanoparticles when subjected to thermal and various pH conditions. The overall activity of glucose oxidase was improved when bound to magnetic nanoparticles CONCLUSION: Binding of enzyme onto magnetic nanoparticles via carbodiimide activation is a very efficient method for developing bioconjugates for biological applications.     

A fluorescent aptasensor for analysis of adenosine triphosphate based on aptamer–magnetic nanoparticles and its single‐stranded complementary DNA labeled carbon dots

A new fluorimetric aptasensor was designed for the determination of adenosine triphosphate (ATP) based on magnetic nanoparticles (MNPs) and carbon dots (CDs). In this analytical strategy, an ATP aptamer was conjugated on MNPs and a complementary strand of the aptamer (CS) was labeled with CDs. The aptamer and its CS were hybridized to form a double helical structure. The hybridized aptamers could be used for the specific recognition of ATP in a biological complex matrix using a strong magnetic field to remove the interfering effect. In the absence of ATP, no CDs–CS could be released into the solution and this resulted in a weak fluorescence signal. In the presence of ATP, the target binds to its aptamer and causes the dissociation of the double helical structure and liberation of the CS, such that a strong fluorescence signal was generated. The increased fluorescence signal was proportional to ATP concentration. The limit of detection was estimated to be 1.0 pmol L^–1 with a dynamic range of 3.0 pmol L^–1 to 5.0 nmol L^–1. The specific aptasensor was applied to detect ATP in human serum samples with satisfactory results. Moreover, molecular dynamic simulation (MDS) studies were used to analyze interactions of the ATP molecule with the aptamer.     

Preparation and characterization of YADH-bound magnetic nanoparticles

The covalently binding of yeast alcohol dehydrogenase (YADH) to magnetic nanoparticles via carbodiimide activation was studied. The magnetic nanoparticles Fe₃O₄ with a mean diameter of 10.6 nm were prepared by co-precipitating Fe²⁺ and Fe³⁺ ions in an ammonia solution and treating under hydrothermal conditions. Transmission electron microscopy (TEM) micrographs showed that the magnetic nanoparticles remained discrete and had no significant change in size after binding YADH. X-ray diffraction (XRD) patterns indicated both the magnetic nanoparticles before and after binding YADH were pure Fe₃O₄. Magnetic measurement revealed the resultant magnetic nanoparticles were superparamagnetic characteristics, and their saturation magnetization was reduced only slightly after enzyme binding. The analysis of Fourier transform infrared (FTIR) spectroscopy confirmed the binding of YADH to magnetic nanoparticles and suggested a possible binding mechanism. In addition, the measurement of protein content revealed that the maximum weight ratio of YADH bound to magnetic nanoparticles was 0.125, below which the binding efficiency of YADH was almost 100%. The kinetic measurements indicated the bound YADH retained 62% of its original activity and exhibited a 10-fold improved stability than did the free enzyme. The maximum specific activities and Michaelis constants were also determined.     

Direct binding and characterization of lipase onto magnetic nanoparticles

Lipase was covalently bound onto Fe(3)O(4) magnetic nanoparticles (12.7 nm) via carbodiimide activation. The Fe(3)O(4) magnetic nanoparticles were prepared by coprecipitating Fe(2+) and Fe(3+) ions in an ammonia solution and treating under hydrothermal conditions. The analyses of transmission electron microscopy (TEM) and X-ray diffraction (XRD) showed that the size and structure of magnetic nanoparticles had no significant changes after enzyme binding. Magnetic measurement revealed the resultant lipase-bound magnetic nanoparticles were superparamagnetic with a saturation magnetization of 61 emu/g (only slightly lower than that of the naked ones (64 emu/g)), a remanent magnetization of 1.0 emu/g, and a coercivity of 7.5 Oe. The analysis of Fourier transform infrared (FTIR) spectroscopy confirmed the binding of lipase onto magnetic nanoparticles. The binding efficiency of lipase was 100% when the weight ratio of lipase bound to Fe(3)O(4) nanoparticles was below 0.033. Compared to the free enzyme, the bound lipase exhibited a 1.41-fold enhanced activity, a 31-fold improved stability, and better tolerance to the variation of solution pH. For the hydrolysis of pNPP by bound lipase at pH 8, the activation energy within 20-35 degrees C was 6.4 kJ/mol, and the maximum specific activity and Michaelis constant at 25 degrees C were 1.07 micromol/min mg and 0.4 mM, respectively. It revealed that the available active sites of lipase and their affinity to substrate increased after being bound onto magnetic nanoparticles.     

Integrating the QCM detection with magnetic separation for on-line analysis

We investigate the feasibility of coupling the quartz crystal microbalance (QCM) with magnetic separation for on-line analysis. A flow cell was integrated with QCM and magnetic force for the analysis of magnetic and nonmagnetic samples. The resonant frequency change (Deltaf) of QCM was related to the amount of deposited magnetic nanoparticles. This experiment demonstrates that QCM can be used as an on-line detector for magnetic separation. The QCM also gives a characteristic response of the binding between the streptavidin and biotin labeled on the magnetic nanoparticles. Biotin-labeled magnetic nanoparticles were flowed through a gold electrode of QCM to deposit as a matrix for selective capturing streptavidin. The resonant frequency change of QCM was proportional to the amounts of streptavidin captured by biotin. This technique can provide a simple, economic, and automatic method for on-line detection of biomarkers.     

A colorimetric detection method of pesticide acetamiprid by fine-tuning aptamer length

This work investigates the effect of shortening aptamer sequences on the colorimetric detection of acetamiprid using aptamer-wrapped gold nanoparticles (AuNPs). Truncated 37-mer and 25-mer aptamers were generated by deleting excess flanking nucleotides from parental 49-mer acetamiprid-target aptamer. In comparing the responses of the three sequences, truncated aptamers did not improve the ability to discriminate against other tested pesticides. However, comparison between 49-mer and other shorter aptamers showed that shortening aptamer sequences through removing excess flanking nucleotides outsides of binding region improved colorimetric sensitivity for acetamiprid by 3.3 fold. Due to excess bases, the target-bound aptamer might still adhere to AuNPs, resulting in incomplete dissociation of aptamer from AuNPs and therefore the suppression of aggregation responses. This work provides further insight to the effects of aptamer structure on detection of the target, as well as a method by fine-tuning aptamer length for rapid detection of pesticide residues in environments or food.     

Different approaches for the detection of thrombin by an electrochemical aptamer-based assay coupled to magnetic beads

Different assay formats based on the coupling of magnetic beads with electrochemical transduction were compared here for the detection of thrombin by using a thrombin specific aptamer. By using the thrombin-binding aptamer, a direct and an indirect competitive assay for thrombin have been developed by immobilising the aptamer or the protein, respectively. Moreover, another strategy was based on the direct measurement of the enzymatic product of thrombin captured by the immobilised aptamer. All the assays were developed by coupling the electrochemical transduction with the innovative and advantageous use of magnetic beads.

The assays based on the immobilisation of the protein were not successful since no binding was recorded between thrombin and its aptamer. With the direct competitive assay, when the aptamer was immobilised onto the magnetic beads, a detection limit of 430 nM for thrombin was achieved. A lower detection limit for the protein (175 nM) was instead obtained by detecting the product of the enzymatic reaction catalysed by thrombin. All these assays were finally compared with a sandwich assay which reached a detection limit of 0.45 nM of thrombin demonstrating the best analytical performances.

With this comparison the importance of a deep study on the different analytical approaches for thrombin detection to reach the performances of the best assay configuration has been demonstrated.     

Detection system based on the conformational change in an aptamer and its application to simple bound/free separation

Aptamers are good molecular recognition elements for biosensors. Especially, their conformational change, which is induced by the binding to the target molecule, enables the development of several types of useful detection systems. We applied this property to bound/free separation, which is a crucial process for highly sensitive detection. We designed aptamers which change their conformation upon binding to the target molecule and thereby expose a single-strand bearing the complementary sequence to the capture probe immobilized onto the support. We named the designed aptamers "capturable aptamers" and the capture probe "capture DNA". Three capturable aptamers were designed based on the PrP aptamer, which binds to prion protein. One of these capturable aptamers was demonstrated to recognize prion protein and change its conformation upon binding to it. A detection system using this designed capturable aptamer for prion protein was developed. Capturable aptamers and capture DNA allow us to perform simple bound/free separation with only one target ligand.     

The synthesis of doxorubicin-conjugated magnetite nanoparticles and their magnetic resonance and cytotoxic properties

The possibility of increasing the effectiveness of antitumor drugs such as doxorubicin by preparing its complex with ultrafine magnetic iron oxide nanoparticles is considered. A method for binding doxorubicin molecules to magnetic nanoparticles via citric acid is proposed. The main magnetic properties of the obtained conjugates were studied by proton relaxometry and Mössbauer spectroscopy, while their cytotoxic activity was evaluated via spectrophotometric MTT assay in HeLa cells. It was shown that the conjugates of magnetite nanoparticles with doxorubicin are characterized by a high level of contrast in magnetic resonance imaging. The magnetic properties of doxorubicin-free and bound magnetite nanoparticles are mainly determined by the average size of nanoobjects and the phase composition and slightly depend on the composition of the stabilizing shell. The cytotoxic effect of the synthesized conjugates of magnetite nanoparticles with doxorubicin is higher than that of unbound doxorubicin. This makes it possible to increase the antitumor effect of doxorubicin and control the dynamics of its delivery in the form of a conjugate into the disease focus due to the magnetic contrast properties of nanoparticles.     

Use of magnetic beads in selection and detection of biotoxin aptamers by electrochemiluminescence and enzymatic methods.

Systematic evolution of ligands by exponential enrichment (SELEX) was used to develop DNA ligands (aptamers) to cholera whole toxin and staphylococcal enterotoxin B (SEB). Affinity selection of aptamers was accomplished by conjugating the biotoxins to tosyl-activated magnetic beads. The use of magnetic beads reduces the volumes needed to perform aptamer selection, thus obviating alcohol precipitation and allowing direct PCR amplification from the bead surface. Following five rounds of SELEX, 5'-biotinylated aptamers were bound to streptavidin-coated magnetic beads and used for the detection of ruthenium trisbypyridine [Ru(bpy)3(2+)]-labeled cholera toxin and SEB by an electrochemiluminescence methodology. A comparison of control (double-stranded) aptamer binding was made with aptamers that were heat denatured at 96 degrees C (single-stranded) and allowed to cool (conform) in the presence of biotoxin-conjugated magnetic beads. Results suggest that control aptamers performed equally well when compared to heat-denatured DNA aptamers in the cholera toxin electrochemiluminescence assay and a colorimetric microplate assay employing peroxidase-labeled cholera toxin and 5'-amino terminated aptamers conjugated to N-oxysuccinimide-activated microtiter wells. Interestingly, however, in the SEB electrochemiluminescence assay, double-stranded aptamers exceeded the performance of single-stranded aptamers. The detection limits of all aptamer assays were in the low nanogram to low picogram ranges.     

Additional hydrogen bonds and base-pair kinetics in the symmetrical AMP-DNA aptamer complex.

The solution structure of an adenosine monophosphate (AMP)-DNA aptamer complex has been determined previously [Lin, C. H., and Patel, D. J. (1997) Chem. Biol. 4:817-832]. On a symmetrical aptamer complex containing the same binding loop, but with better resolved spectra, we have identified two additional hydrogen bond-mediated associations in the binding loop. One of these involves a rapidly exchanging G imino proton. The phosphate group of the AMP ligand was identified as the acceptor by comparison with other aptamer complexes. Imino proton exchange measurements also yielded the dissociation constants of the stem and binding loop base pairs. This study shows that nuclear magnetic resonance-based imino proton exchange is a good probe for detection of weak hydrogen-bond associations.     

Preparation and characterization of Saccharomyces cerevisiae alcohol dehydrogenase immobilized on magnetic nanoparticles

The covalently immobilized of Saccharomyces cerevisiae alcohol dehydrogenase (SCAD) to magnetic Fe(3)O(4) nanoparticles via glutaraldehyde coupling reaction was studied. The magnetic Fe(3)O(4) nanoparticles were prepared by hydrothermal method using H(2)O(2) as an oxidizer. Functionalization of surface-modified magnetic particles was performed by the covalent binding of chitosan onto the surface. The amino functional group on the magnetic Fe(3)O(4)-chitosan particles surface and the amino group of the dehydrogenase were coupled with glutaraldehyde. The immobilization process did not affect the size and structure of magnetic nanoparticles. For the reduction of phenylglyoxylic acid by immobilized SCAD, the kinetic analysis data indicated that the immobilized SCAD retained 48.77% activity of its original activity. The activation energy within 20-40 degrees C, the maximum specific activity and the Michaelis constants for phenylglyoxylic acid were 7.79 KJ mol(-1), 279.33 nmol min(-1) and 37.77 mmol l(-1), respectively. Furthermore, the immobilized SCAD enhanced thermal stability and good durability in the repeated use after recovered by magnetic separations.     

Optimization of the covalent coupling and ionic adsorption of magnetic nanoparticles on Flavobacterium ATCC 27551 using the Taguchi method

Abstract

Flavobacterium ATCC 27551 was used as a model system for the preparation of magnetic biocatalysts. The magnetic modification was carried out by covalently binding carboxylate- and amino-modified magnetic nanoparticles onto cells. Magnetic Fe₃O₄ nanoparticles were also used for ionic adsorption on the cell surface. Magnetically modified cells were concentrated using a magnet and exhibited organophosphate hydrolyzing activity. The Taguchi method was used to optimize the binding of the magnetic nanoparticles on the cell surface. SEM image analyses demonstrated good linkage of the magnetic nanoparticles over the Flavobacterium ATCC 27551 cell surface. Under optimal conditions, the magnetic cells displayed specific activity ratios of 93%, 89% and 95%, compared with untreated cells, after the covalent coupling with carboxylate- and amino-modified magnetic nanoparticles and the ionic adsorption of magnetic Fe₃O₄ nanoparticles, respectively.