QCM DNA biosensor for the diagnosis of a fish pathogenic virus VHSV

Viral haemorrhagic septicaemia (VHS) is one of the most serious viral diseases damaging both fresh and marine fish species. VHS caused by VHSV and diagnosis of VHSV has been dependent on the conventional methods, such as cell culture and RT-PCR, which takes a few days or several hours. This study demonstrates a rapid and sensitive QCM biosensor for diagnosis of VHSV infection in fish. The QCM biosensor was developed to detect a main viral RNA encoding G protein in VHSV using the specific DNA probe. To maximize the sensitivity of the biosensor, we prepared three different DNA probes which modified 3′ end of DNA by thiol, amine, or biotin and compared three different immobilisation methods on quartz surface coated with gold: immobilisation of thiol labelled probe DNA on naked gold surface, immobilisation of amino labelled probe DNA on gold surface prepared as carboxyl chip using MPA followed by EDC/NHS activation, and immobilisation of biotin labelled probe DNA on gold surface after immobilising avidin on carboxyl chip prior to biotin. As a result, immobilisation method using avidin-biotin interaction was most efficient to immobilise probe DNA and to detect target DNA. The QCM biosensor system using biotinylated probe DNA was stable enough to withstand 32 times of repeated regenerations and the detection limit was 0.0016 μM. Diagnosis using the QCM biosensor system was more sensitive and much faster than a conventional RT-PCR analysis in detecting the viral RNA.     

Aptamer-based biosensors for the detection of HIV-1 Tat protein

Two biosensors have been constructed using an RNA aptamer as biorecognition element. The aptamer, specific for HIV-1 Tat protein, has been immobilised on the gold surface of piezoelectric quartz crystals or surface plasmon resonance (SPR) chips to develop a quartz crystal microbalance (QCM)-based and an SPR-based biosensor, respectively. Both the biosensors were modified with the same immobilisation chemistry based on the binding of a biotinylated aptamer on a layer of streptavidin. The binding between the immobilised aptamer and its specific protein has been evaluated with the two biosensors in terms of sensitivity, reproducibility and selectivity. A protein very similar to Tat, Rev protein, has been used as negative control. The two biosensors both were very reproducible in the immobilisation and the binding steps. The selectivity was high in both cases.     

Adsorption of differently charged forms of horseradish peroxidase on metal electrodes of different nature: effect of surface charges

The adsorption and bioelectrocatalytical activity in the reaction of H(2)O(2) reduction of two forms of horseradish peroxidase (HRP) offering different surface charges at pH 6.0 were studied on gold and silver electrodes. Positively charged HRP was assessed at pH 6.0 for the case of native HRP (isoenzyme C, pI=8.8), and negatively charged HRP for the case of native HRP exposed to previous oxidation of carbohydrate residues and further introduction of sulfonate groups (pI=5.0). Under oxidative pretreatment, the gold electrode surface was considered to be negatively charged. Data on the direct immobilisation of HRPs on the bare gold surfaces were estimated with quartz crystal microbalance and data on bioelectrocatalytical activity of peroxidases on gold and silver electrodes were obtained in the course of direct and mediated amperometric detection of H(2)O(2). The presented results demonstrate that the surface charges of both the enzyme and the electrode play a dominant role in the immobilisation and, thereby, in the efficiency of the bioelectrocatalytical processes.     

SPR imaging as a tool for detecting mucin – anti-mucin interaction. Outline of the development of a sensor for near-patient testing for mucin

Sensors able to provide ‘yes’/‘no’ answers have become of interest in recent years, especially in the fields of environmental research and healthcare. We describe a procedure based on surface plasmon resonance imaging (SPRI) to investigate the interaction between mucin and anti-mucin antibody, and we outline the development of an alarm sensor for the protein mucin, whose high concentration in saliva, blood or tissue is related to illnesses such as gingivitis, peridontitis or even cancer. Anti-mucin gastric antibodies are immobilised onto a gold surface. The immobilisation is evaluated for neat gold chips and for polymer-modified gold surfaces. We found that two different pHs are required, one for the immobilisation of the antibodies on gold (pH 5.5) and a different one for optimal interaction between the sample and the antibody layer (pH 7.0). Finally, we briefly demonstrate the application of the sensor to real saliva samples, both mucin-less and mucin-containing, evaluating the potential of the sensor to discriminate between healthy and ill.     

Microgravimetric flow analysis of nucleic acid based on adsorption of nanoparticle-bioconjugate

A novel nanoparticle-bioconjugate has been prepared by specific hybridization of the target with complementary thiol-labeled and nanoparticle-labeled probes. The rapid adsorption of the nanoparticle-bioconjugate onto a gold surface via a thiol-gold reaction was monitored in real-time using a quartz crystal microbalance, and used to perform microgravimetric flow analysis of nucleic acid for the first time. This innovative assay is highly reproducible and sensitive, and shows great promise for clinical applications.     

Colloidal gold-polystyrene bead hybrid for chemiluminescent detection of sequence-specific DNA

A sensitive chemiluminescent (CL) detection of sequence-specific DNA has been developed by taking advantage of a magnetic separation/mixing process and the amplification feature of colloidal gold labels. In this protocol, the target oligonucleotides are hybridized with magnetic bead-linked capture probes, followed by the hybridization of the biotin-terminated amplifying DNA probes and the binding of streptavidin-coated gold nanoparticles; the nanometer-sized gold tags are then dissolved and quantified by a simple and sensitive luminol CL reaction. The proposed CL protocol is evaluated for a 30-base model DNA sequence, and the amount as low as 0.01 pmol of DNA is determined, which exhibits a 150 x enhancement in sensitivity over previous gold dissolution-based electrochemical formats and an enhancement of 20 x over the ICPMS detection. Further signal amplification is achieved by the assembly of biotinylated colloidal gold onto the surface of streptavidin-coated polystyrene beads. Such amplified CL transduction allows detection of DNA targets down to the 100 amol level, and offers great promise for ultrasensitive detection of other biorecognition events.     

Synthetic oligonucleotides: AFM characterisation and electroanalytical studies

One of the most important steps in designing more sensitive and stable DNA based biosensors is the immobilisation procedure of the nucleic acid probes on the transducer surface, while maintaining their conformational flexibility. MAC Mode AFM images in air demonstrated that the oligonucleotide sequences adsorb spontaneously on the electrode surface, showing the existence of pores in the adsorbed layer that reveal big parts of the electrode surface, which enables non-specific adsorption of other molecules on the uncovered areas. The electrostatic immobilisation onto a glassy carbon electrode followed by hybridisation with a complementary sequence and control with a non-complementary sequence was studied using differential pulse voltammetry and electrochemical impedance spectroscopy. Changes in the oxidation currents of guanosine and adenosine were observed after hybridisation events as well as after control experiments. Modification of the double layer capacitance that took place after hybridisation or control experiments showed that non-specific adsorption of complementary or non-complementary sequences occur allowing the formation of a mixed multilayer.     

Immobilization of RNase S-Peptide on a single-stranded DNA-fixed gold surface and effective masking of its surface by an acridinyl poly(ethylene glycol)

Oligonucleotide-peptide conjugate was synthesized by coupling of RNase S-peptide to a 24-mer single-stranded DNA (ssDNA) oligonucleotide to be immobilized on its complementary ssDNA oligonucleotide-fixed gold surface of sensor chip or electrode. Immobilization of on the ssDNA-fixed gold surface through DNA duplex formation was confirmed by quartz crystal microbalance (QCM) and electrochemical measurements. After treating with a synthetic acridinyl poly(ethylene glycol) (APEG), specific interaction of S-protein with the S-peptide immobilized on the gold surface was demonstrated by QCM without nonspecific adsorption of unrelated proteins such as BSA and RNase A at the surfaces. This result suggested that the acridine parts of APEG could bind to the DNA duplex on the gold surface and the poly(ethylene glycol) parts were fastened on the surface to resist the adsorption of proteins. Thus, the combination of oligonucleotide-peptide conjugate, ssDNA-fixed chip and APEG with effective masking property provides a new tool for the analysis of specific peptide-protein interactions without disturbance by other unrelated proteins.     

Quartz crystal microbalance genosensor for sequence specific detection of attomolar DNA targets

A mass sensitive quartz crystal microbalance (QCM) based genosensor has been developed using breast cancer 1 (BRCA1) gene as a model gene. We modified the traditional sandwich assay by conjugating reporter probe DNA (DNA-r) with an assembly of gold nanoparticles leading to an increased mass on the surface, which enhanced the sensitivity to few orders of magnitude. The unique cleavage function of endonuclease is used for achieving the selectivity to complementary DNA over mismatched DNA. With this combination, the sensor exhibited excellent sensitivity with a detection limit of 10 aM BRCA1 gene and it showed good selectivity for even single base mismatch DNA targets. This ultrasensitive and cost-effective DNA detection protocol can be extended to the direct analysis of any non-amplified genomic DNA.     

Non-covalent monolayer-piercing anchoring of lipophilic nucleic acids: preparation, characterization, and sensing applications

Functional interfaces of biomolecules and inorganic substrates like semiconductor materials are of utmost importance for the development of highly sensitive biosensors and microarray technology. However, there is still a lot of room for improving the techniques for immobilization of biomolecules, in particular nucleic acids and proteins. Conventional anchoring strategies rely on attaching biomacromolecules via complementary functional groups, appropriate bifunctional linker molecules, or non-covalent immobilization via electrostatic interactions. In this work, we demonstrate a facile, new, and general method for the reversible non-covalent attachment of amphiphilic DNA probes containing hydrophobic units attached to the nucleobases (lipid-DNA) onto SAM-modified gold electrodes, silicon semiconductor surfaces, and glass substrates. We show the anchoring of well-defined amounts of lipid-DNA onto the surface by insertion of their lipid tails into the hydrophobic monolayer structure. The surface coverage of DNA molecules can be conveniently controlled by modulating the initial concentration and incubation time. Further control over the DNA layer is afforded by the additional external stimulus of temperature. Heating the DNA-modified surfaces at temperatures >80 °C leads to the release of the lipid-DNA structures from the surface without harming the integrity of the hydrophobic SAMs. These supramolecular DNA layers can be further tuned by anchoring onto a mixed SAM containing hydrophobic molecules of different lengths, rather than a homogeneous SAM. Immobilization of lipid-DNA on such SAMs has revealed that the surface density of DNA probes is highly dependent on the composition of the surface layer and the structure of the lipid-DNA. The formation of the lipid-DNA sensing layers was monitored and characterized by numerous techniques including X-ray photoelectron spectroscopy, quartz crystal microbalance, ellipsometry, contact angle measurements, atomic force microscopy, and confocal fluorescence imaging. Finally, this new DNA modification strategy was applied for the sensing of target DNAs using silicon-nanowire field-effect transistor device arrays, showing a high degree of specificity toward the complementary DNA target, as well as single-base mismatch selectivity.     

Self-assembly of acetylcholinesterase on gold nanoparticles electrodeposited on graphite

The immobilisation of AChE enzyme through chemisorption on Au-modified graphite was examined with view of its prospective application in the design of membraneless electrochemical biosensors for the assay of enzyme inhibitors. The developed immobilisation protocol has been based on a two-stage procedure, comprising i) electrodeposition of gold nanostructures on spectroscopic graphite; followed by ii) chemisorption of the enzyme onto gold nanoparticles. Both the coverage of the electrode surface with Au nanostructures and the conditions for enzyme immobilisation were optimised. The proposed electrode architecture together with the specific type of enzyme immobilisation allow for a long-term retaining of the enzyme catalytic activity. The extent of inhibition of the immobilised acetylcholinesterase enzyme by the organophosphorous compound monocrotophos has been found to depend linearly on its concentration over the range from 50 to 400 nmol mL^?1 with sensitivity 77.2% inhibition per 1 µmol mL^?1 of monocrotophos.      

Highly sensitive biomolecule detection on a quartz crystal microbalance using gold nanoparticles as signal amplification probes.

We report here a novel strategy for the high-sensitive detection of target biomolecules with very low concentrations on a quartz crystal microbalance (QCM) device using gold nanoparticles as signal enhancement probes. By employing a streptavidin-biotin interaction as a model system, we could prepare biotin-conjugated gold nanoparticles maintaining good dispersion and long-term stability by controlling the biotin density on the surface of gold nanoparticles that have been investigated by UV-vis spectra and AFM images. These results showed that 10 microM N-(6-[biotinamido]hexyl)-3'-(2'-pyridyldithio)propionamide (biotin-HPDP) was the critical concentration to prevent the nonspecific aggregation of gold nanoparticles in this system. For sensing streptavidin target molecules by QCM, biotinylated BSA was absorbed on the Au surface of the QCM electrode and subsequent coupling of the target streptavidin to the biotin in the sensing interface followed. Amplification of the sensing process was performed by the interaction of the target streptavidin on the sensing surface with gold nanoparticles modified with 10 microM biotin-HPDP. The biotinylated gold nanoparticles were used as signal amplification probes to improve the detection limit, which was 50 ng/ml, of the streptavidin detection system without signal enhancement, and the calibration curve determined for the net frequency changes showed good linearity over a wide range from 1 ng/ml to 10 microg/ml for the quantitative streptavidin target molecule analysis. In addition, the measured dissipation changes suggested that the layer of biotin-BSA adsorbed on the Au electrode and the streptavidin layer assembled on the biotin-BSA surface were highly compact and rigid. On the other hand, the structure formed by the biotinylated gold nanoparticles on the streptavidin layer was flexible and dissipative, being elongated outward from the sensing surface.     

Direct application strategy to immobilise a thioctic acid self-assembled monolayer on a gold electrode

Immobilisation of a self-assembled monolayer (SAM) onto an electrode surface is often achieved by immersing it in a solution for over 24 h. A biological or biologically derived recognition component can then be linked to the SAM in fabricating a biosensor. This time consuming immobilisation step can be a drawback in biosensor development, especially when repeated preparations of the biosensor are required. In this work, an alternative immobilisation strategy involving the direct application of a known quantity of the ethanolic solution of the alkanethiol, thioctic acid, on a gold electrode surface was studied. The solution was left to dry at room temperature for approximately 20 min. Comparable results including the relative percentage decrease in double layer capacitance, the surface coverage and the percentage of binding to the bacterial protein, Protein A, were obtained relative to those obtained with SAM formed by the immersion method. Shewhart’s statistical analysis technique was applied to examine the stability in terms of the relative percentage decrease in double layer capacitance. In these tests, within 99.7% confidence control limits, only a 1% deterioration was observed over a 3-month period. Therefore, all these results have demonstrated that the direct application method yields a stable thioctic acid SAM on a gold electrode surface with characteristics similar to those obtained with an immersion method. However, formation of a SAM using direct application can be achieved within a significantly shorter period of time compared to immersion method.     

Application of diazo-thiourea and gold nano-particles in the design of a highly sensitive and selective DNA biosensor

An effective procedure for constructing a DNA biosensor is developed based on covalent immobilization of NH_2 labeled,single strand DNA(NH_2-ssDNA) onto a self-assembled diazo-thiourea and gold nanoparticles modified Au electrode(diazo-thiourea/GNM/Au).Gold nano-particles expand the electrode surface area and increase the amount of immobilized thiourea and single stranded DNA(ssDNA) onto the electrode surface.Diazo-thiourea film provides a surface with high conductibility for electron transfer and a bed for the covalent coupling of NH_2-ssDNA onto the electrode surface.The immobilization and hybridization of the probe DNA on the modified electrode is studied by differential pulse voltammetry(DPV) using methylene blue(MB) as a well-known electrochemical hybridization indicator.The linear range for the determination of complementary target ssDNA is from 9.5(±0.1) × 10~(-13) mol/L to1.2(±0.2) x 10~(-9) mol/L with a detection limit of 1.2(±0.1) 10~(-13) mol/L.     

A simple method of surface functionalisation for immuno-specific immobilisation of proteins

We present a new and advanced methodology, developed for surface functionalisation of gold and to study immobilisation of an immuno-specific system of proteins. A combination of electrochemical quartz crystal microbalance and Raman spectroscopy techniques allowed a complete understanding of the system starting from surface functionalisation and progressing to the functional structure analysis of immobilised proteins. A simple electrochemical procedure was formulated to prepare sulphonyl chloride terminated gold surfaces that form a strong sulphonamide bond with the receptor protein staphylococcal protein A (SpA). On the SpA grafted surfaces, the immobilisation of a human IgG and consecutive binding of an immuno-specific anti-human IgG was observed. The surface functional groups form a strong interaction with SpA without disturbing its functional properties. The native functional structure of SpA and also the IgGs was found to be retained in their immobilised state.     

Electrochemical Detection of FAM134B Mutations in Oesophageal Cancer Based on DNA‐Gold Affinity Interactions

Inexpensive, simple and rapid DNA sensors capable of accurate and sensitive detection of cancer specific point mutations in DNA biomarkers are crucial for the routine screening of genetic mutations in cancer. Conventional approaches based on sequencing, mass spectroscopy, and fluorescence are highly effective, but they are tedious, slow and require labels and expensive equipment. Recent electrochemistry based approaches mostly rely on conventional DNA biosensing using recognition and transduction layers, and hence limited by the complicated steps of sensor fabrication associated with surface cleaning, self‐assembled monolayer formation, and target hybridization. Herein we report a relatively simple and inexpensive method for detecting point mutation in cancer by using the direct adsorption of purified DNA sequences onto an unmodified gold surface. The method relies on the base dependent affinity interaction of DNA with gold. Since the affinity interaction (adsorption) trend of DNA bases follows as adenine (A) > cytosine (C) > guanine (G)> thymine (T), two DNA sequences with different DNA base compositions (i. e., amplified mutated sequences will be distinctly different than its original sequence) will have different adsorption affinity towards gold. The amount of mutation sites on a DNA sequence is quantified by monitoring the electrochemical current as a function of the relative adsorption level of DNA samples onto a bare gold electrode. This method can successfully distinguish single point mutation in DNA from oesophageal cancer. We demonstrated the clinical utility of this approach by detecting different levels of mutations in tissue samples (n=9) taken from oesophageal cancer patients. Finally, the method was validated with High Resolution Melt (HRM) curve analysis and Sanger Sequencing.     

Surface-enhanced Raman nanoparticle beacons based on bioconjugated gold nanocrystals and long range plasmonic coupling

We have developed a new class of surface-enhanced Raman scattering beacons (SERS beacons) that can be turned on and off by long-range plasmonic coupling, induced by biomolecular recognition and binding events. The beacons are based on colloidal gold nanocrystals in two sizes (40 and 60 nm) and are prepared by spectral encoding with a Raman reporter molecule, functionalized with thiolated DNA probes, and stabilized and protected by low molecular weight poly(ethylene glycol)s (PEGs). The results show the SERS signal intensities increase by 40-200-fold when the nanoparticle beacons are activated by plasmonic coupling, much higher than the bright-to-dark intensity ratios reported for traditional molecular beacons. Multivalent gold nanoparticles also have exquisite specificity and are able to recognize single-base mismatches or mutations. This class of SERS nanoparticle beacons has novel mechanisms for molecular detection and signal amplification, and its long-range coupling nature raises new opportunities in developing plasmonic probes to detect proteins, cells, and intact viruses.     

High affinity capture surface for matrix-assisted laser desorption/ionisation compatible protein microarrays

A surface for the capture of biotin-tagged proteins on matrix-assisted laser desorption/ionisation (MALDI) targets has been investigated. Binding of a poly-L-lysine poly(ethylene glycol)-biotin polymer to glass and gold surfaces has been demonstrated using dual wavelength interferometry. Biotinylated proteins were captured onto this surface using tetrameric neutravidin as a multivalent bridging molecule. Biotin tagging of proteins was achieved by chemical biotinylation or by expressing a protein with a biotinylation consensus sequence in E. coli. The specificity of the surface for biotin-tagged proteins allowed the purification of biotin-tagged glutathione-S-transferase from a bacterial lysate directly onto a MALDI target. Subsequently, the protein was digested on the MALDI target and a protein fingerprint analysis confirmed its presence directly, but no E. coli proteins were detected. Therefore, we conclude that this surface is highly specific for the capture of biotin-labelled proteins and has low non-specific binding properties for non-biotinylated proteins. Furthermore, protein-protein interactions using biotinylated lectins were investigated, and the selective capture of the glycoprotein fetuin with wheat germ agglutinin was demonstrated. Also, immobilised Arachis hypogea agglutinin recognised a minor asialo component of this glycoprotein on the array. The high affinity immobilisation of proteins onto this surface allowed effective desalting procedures to be used which improved the desorption of high molecular weight proteins. Another aspect of this surface is that a highly ordered coupling of the analyte can be achieved which eliminates the search for the sweet spot and allows the creation of densely packed protein microarrays for use in mass spectrometry.     

A generic platform for the addressable functionalisation of electrode surfaces through self-induced "electroclick"

A novel and general strategy for the immobilisation of functional objects onto electrodes is described. The concept is based on the addition of two pendant ethynyl groups onto a bis(pyridyl)amine derivative, which acts as a molecular platform. This platform is pre-functionalised with an N(3)-tagged object of interest by Huisgen cycloaddition to one of the ethynyl groups in biphasic conditions. Hence, when complexed by Cu(II) , this molecular-object holder can be immobilised, by a "self-induced electroclick", through the second ethynyl group onto N(3)-alkanethiol self-assembled monolayers on a gold electrode. Two different functional groups, a redox innocent ((CH(2))(3)-Ph) and an electrochemical probe (ferrocene), were immobilised by following this strategy. The in situ electrochemical grafting showed, for both systems, that the kinetics of immobilisation is fast. The voltammetric characterisation of the surface-tagged functionalised copper complexes indicated that a good surface coverage was achieved and that a moderately fast electron-transfer reaction occurs. Remarkably, in the case of the redox-active ferrocenyl-immobilised system, the electrochemical response highlighted the involvement of the copper ion of the platform in the kinetics of the electron transfer to the ferrocene moiety. This platform is a promising candidate for applications in surface addressing in areas as diverse as biology and materials.     

Anisotropic orientation of horseradish peroxidase by reconstitution on a thiol-modified gold electrode

Horseradish peroxidase (HRP) was reconstituted on the surface of a gold electrode that was modified first with a hemin-carbon-chain-thiol derivative followed by addition of the apo protein to the contacting solution. To facilitate the reconstitution of the holo enzyme, the hemin needs to be immobilised on a carbon-chain spacer arm. To achieve this, an immobilisation protocol was developed that is based on the initial formation of a mixed self-assembled monolayer on the gold surface consisting of 3-carboxypropyl disulphide and an activated disulphide (3,3'-dithiodipropionic acid di-(N-succinimidyl ester)) followed by binding of a diaminoalkane to the activated disulphide. The hemin was then coupled to the second amino group of the diaminoalkane by means of a carbodiimide coupling reagent. Finally, the enzyme was reconstituted on the hemin-modified surface by immersion of the electrode in a solution containing apo-HRP. The advantage of this method is that the length of the spacer arm can be changed easily, because diaminoalkanes of different chain lengths are available. The electrochemistry of the hemin and the reconstituted HRP electrodes was studied by means of cyclic voltammetry and differential-pulse voltammetry. The catalytic ability for reduction of hydrogen peroxide was investigated for both direct and mediated electrochemistry with a soluble electron donor (ortho-phenylenediamine).