Improved procedures for immobilisation of oligonucleotides on gold-coated piezoelectric quartz crystals

Analysis of nestin protein in the aqueous humor as biomarker of open angle glaucoma

Primary open angle glaucoma (POAG) is a progressive optic nerve degeneration, leading to irreversible visual damage. Alterations of the aqueous humor (AH), the biological fluid filling both the anterior and the posterior chambers of the eye, play a pathogenic role in POAG. AH protein composition is altered during glaucoma progression. Nestin protein was found to be differentially expressed in the AH of glaucomatous patients compared to unaffected matched controls.

METHODS

Nestin was analyzed by an open quartz crystal microbalance (QCM) in the AH of 21 glaucomatous patients compared to nine unaffected controls. The surface of the electrode used in the QCM was coated with an analyte-specific recognition layer.

RESULTS

Positive nestin values were recorded in the AH collected from POAG patients; negative values of nestin detection were obtained by analyzing the AH collected from non-POAG glaucomatous patients and unaffected controls.

CONCLUSION

The present study proposes and validates a new clinically applicable approach to analyze biological markers in AH for POAG diagnosis.

Detecting Escherichia coli Biofilm Development Stages on Gold and Titanium by Quartz Crystal Microbalance

Bacterial biofilms are responsible for persistent infections and biofouling, raising serious concerns in both medical and industrial processes. These motivations underpin the need to develop methodologies to study the complex biological structures of biofilms and prevent their formation on medical implants, tools, and industrial apparatuses. Here, we report the detailed comparison of Escherichia coli biofilm development stages (adhesion, maturation, and dispersion) on gold and titanium surfaces by monitoring the changes in both frequency and dissipation of a quartz crystal microbalance (QCM) device, a cheap and reliable microgravimetric sensor which allows the real-time and label-free characterization of various stages of biofilm development. Although gold is the most common electrode material used for QCM sensors, the titanium electrode is also readily available for QCM sensors; thus, QCM sensors with different metal electrodes serve as a simple platform to probe how pathogens interact with different metal substrates. The QCM outcomes are further confirmed by atomic force microscopy and crystal violet staining, thus validating the effectiveness of this surface sensitive sensor for microbial biofilm research. Moreover, because QCM technology can easily modify the substrate types and coatings, QCM sensors also provide well-controlled experimental conditions to study antimicrobial surface treatments and eradication procedures, even on mature biofilms.

Detecting Gold Biomineralization by Delftia acidovorans Biofilms on a Quartz Crystal Microbalance

The extensive use of gold in sensing, diagnostics, and electronics has led to major concerns in solid waste management since gold and other heavy metals are nonbiodegradable and can easily accumulate in the environment. Moreover, gold ions are extremely reactive and potentially harmful for humans. Thus, there is an urgent need to develop reliable methodologies to detect and possibly neutralize ionic gold in aqueous solutions and industrial wastes. In this work, by using complementary measurement techniques such as quartz crystal microbalance (QCM), atomic force microscopy, crystal violet staining, and optical microscopy, we investigate a promising biologically induced gold biomineralization process accomplished by biofilms of bacterium Delftia acidovorans. When stressed by Au³⁺ ions, D. acidovorans is able to neutralize toxic soluble gold by excreting a nonribosomal peptide, which forms extracellular gold nanonuggets via complexation with metal ions. Specifically, QCM, a surface-sensitive transducer, is employed to quantify the production of these gold complexes directly on the D. acidovorans biofilm in real time. Detailed kinetics obtained by QCM captures the condition for maximized biomineralization yield and offers new insights underlying the biomineralization process. To the best of our knowledge, this is the first study providing an extensive characterization of the gold biomineralization process by a model bacterial biofilm. We also demonstrate QCM as a cheap, user-friendly sensing platform and alternative to standard analytical techniques for studies requiring high-resolution quantitative details, which offers promising opportunities in heavy-metal sensing, gold recovery, and industrial waste treatment.

Recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview

Waterborne diseases have emerged as global health problems and their rapid and sensitive detection in environmental water samples is of great importance. Bacterial identification and enumeration in water samples is significant as it helps to maintain safe drinking water for public consumption. Culture‐based methods are laborious, time‐consuming, and yield false‐positive results, whereas viable but nonculturable (VBNCs) microorganisms cannot be recovered. Hence, numerous methods have been developed for rapid detection and quantification of waterborne pathogenic bacteria in water. These rapid methods can be classified into nucleic acid‐based, immunology‐based, and biosensor‐based detection methods. This review summarizes the principle and current state of rapid methods for the monitoring and detection of waterborne bacterial pathogens. Rapid methods outlined are polymerase chain reaction (PCR), digital droplet PCR, real‐time PCR, multiplex PCR, DNA microarray, Next‐generation sequencing (pyrosequencing, Illumina technology and genomics), and fluorescence in situ hybridization that are categorized as nucleic acid‐based methods. Enzyme‐linked immunosorbent assay (ELISA) and immunofluorescence are classified into immunology‐based methods. Optical, electrochemical, and mass‐based biosensors are grouped into biosensor‐based methods. Overall, these methods are sensitive, specific, time‐effective, and important in prevention and diagnosis of waterborne bacterial diseases.

Bio-mimetic sensors based on molecularly imprinted membranes

An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. By means of this technology, selective molecular recognition sites are introduced in a polymer, thus conferring it bio-mimetic properties. The potential applications of these systems include affinity separations, medical diagnostics, drug delivery, catalysis, etc. Recently, bio-sensing systems using molecularly imprinted membranes, a special form of imprinted polymers, have received the attention of scientists in various fields. In these systems imprinted membranes are used as bio-mimetic recognition elements which are integrated with a transducer component. The direct and rapid determination of an interaction between the recognition element and the target analyte (template) was an encouraging factor for the development of such systems as alternatives to traditional bio-assay methods. Due to their high stability, sensitivity and specificity, bio-mimetic sensors-based membranes are used for environmental, food, and clinical uses. This review deals with the development of molecularly imprinted polymers and their different preparation methods. Referring to the last decades, the application of these membranes as bio-mimetic sensor devices will be also reported.

Hydrogel based QCM aptasensor for detection of avian influenza virus

The objective of this study was to develop a quartz crystal microbalance (QCM) aptasensor based on ssDNA crosslinked polymeric hydrogel for rapid, sensitive and specific detection of avian influenza virus (AIV) H5N1. A selected aptamer with high affinity and specificity against AIV H5N1 surface protein was used, and hybridization between the aptamer and ssDNA formed the crosslinker in the polymer hydrogel. The aptamer hydrogel was immobilized on the gold surface of QCM sensor using a self-assembled monolayer method. The hydrogel remained in the state of shrink if no H5N1 virus was present in the sample because of the crosslinking between the aptamer and ssDNA in the polymer network. When it exposed to target virus, the binding reaction between the aptamer and H5N1 virus caused the dissolution of the linkage between the aptamer and ssDNA, resulting in the abrupt swelling of the hydrogel. The swollen hydrogel was monitored by the QCM sensor in terms of decreased frequency. Three polymeric hydrogels with different ratio (100:1 hydrogel I, 10:1 hydrogel II, 1:1 hydrogel III) of acrylamide and the aptamer monomer were synthesized, respectively, and then were used as the QCM sensor coating material. The results showed that the developed hydrogel QCM aptasensor was capable of detecting target H5N1 virus, and among the three developed aptamer hydrogels, hydrogel III coated QCM aptasensor achieved the highest sensitivity with the detection limit of 0.0128 HAU (HA unit). The total detection time from sampling to detection was only 30 min. In comparison with the anti-H5 antibody coated QCM immunosensor, the hydrogel QCM aptasensor lowered the detection limit and reduced the detection time.

Biosensing technologies for Mycobacterium tuberculosis detection: status and new developments

Biosensing technologies promise to improve Mycobacterium tuberculosis (M. tuberculosis) detection and management in clinical diagnosis, food analysis, bioprocess, and environmental monitoring. A variety of portable, rapid, and sensitive biosensors with immediate "on-the-spot" interpretation have been developed for M. tuberculosis detection based on different biological elements recognition systems and basic signal transducer principles. Here, we present a synopsis of current developments of biosensing technologies for M. tuberculosis detection, which are classified on the basis of basic signal transducer principles, including piezoelectric quartz crystal biosensors, electrochemical biosensors, and magnetoelastic biosensors. Special attention is paid to the methods for improving the framework and analytical parameters of the biosensors, including sensitivity and analysis time as well as automation of analysis procedures. Challenges and perspectives of biosensing technologies development for M. tuberculosis detection are also discussed in the final part of this paper.

Quartz crystal microbalance-based biosensor for the detection of α-thalassemia 1 (SEA deletion)

BACKGROUND

DNA piezoelectric biosensors have become a promising tool in molecular medicine since they do not require any label or staining. Here, a DNA piezoelectric biosensor based on a quartz crystal microbalance (QCM) was created to identify abnormal genes causing α-thalassemia 1 (SEA deletion).

METHODS

The functionalized gold electrode of the quartz crystal was coated with avidin and the biotinylated DNA probe was attached. The target gene causing α-thalassemia 1 was amplified and hybridized with the immobilized probe. DNA hybridization was indicated by changes in the quartz resonance frequencies. Diagnostic ability of the new α-thalassemia 1 biosensor was validated using both known and unknown blood samples. Specificity was tested using samples of β-thalassemia and α-thalassemia 2. Stability of the sensor was also evaluated.

RESULTS

The new biosensor could clearly identify α-thalassemia 1 (SEA deletion), both carrier and disease states, from the normal genotype. Identification accuracy was compatible to the standard gel electrophoresis. It was specific only to α-thalassemia 1 since no cross reaction was found with β-thalassemia and α-thalassemia 2. The sensor could be kept at room temperature up to 6 months with consistent identification accuracy.

CONCLUSIONS

The label free QCM based biosensor was successfully developed to diagnose an abnormal human globin gene causing α-thalassemia 1 (SEA deletion). Its accuracy, specificity and sensitivity were comparable to the standard method. Its stable diagnostic potency up to 6 months implied its field application in thalassemic control program.

Diagnosis and genotyping of Plasmodium falciparum by a DNA biosensor based on quartz crystal microbalance (QCM)

Malaria infection with

A label-free DNA biosensor based on quartz crystal microbalance (QCM) to diagnose and genotype

The newly developed QCM was tested for its diagnosis ability using both malaria laboratory strains and clinical isolates. The biosensor was sensitive at the sub-nanogram level, specific for only

The dual function QCM was successfully developed with high sensitivity and specificity, and was cost-effective, stable and field adaptable.

Label-free electrical detection of DNA hybridization using carbon nanotubes and graphene

The interface between biosystems and nanomaterials is emerging for detection of various biomolecules and subtle cellular activities. In particular, the development of cost-effective and sequence-selective DNA detection is urgent for the diagnosis of genetic or pathogenic diseases. Graphene-based nanocarbon materials, such as carbon nanotubes and thin graphene layers, have been employed as biosensors because they are biocompatible, extraordinarily sensitive, and promising for large-area detection. Electrical and label-free detection of DNA can be achieved by monitoring the conductance change of devices fabricated from these carbon materials. Here, the recent advances in this research area are briefly reviewed. The key issues and perspectives of future development are also discussed.

Development of a quartz crystal microbalance biosensor with aptamers as bio-recognition element

The ultimate goal in any biosensor development project is its use for actual sample detection. Recently, there has been an interest in biosensors with aptamers as bio-recognition elements, but reported examples all deal with standards, not human serum. In order to verify the differences of aptamer-based biosensor and antibody-based biosensor in clinical detection, a comparison of the performance of aptamer-based and antibody-based quartz crystal microbalance (QCM) biosensors for the detection of immunoglobulin E (IgE) in human serum was carried out. Aptamers (or antibodies) specific to IgE were immobilized on the gold surface of a quartz crystal. The frequency shifts of the QCM were measured. The linear range with the antibody (10–240 μg/L) compared to that of the aptamer (2.5–200 μg/L), but a lower detection limit could be observed in the aptamer-based biosensor. The reproducibility of the two biosensors was comparable. The aptamers were equivalent or superior to antibodies in terms of specificity and sensitivity. In addition, the aptamer receptors could tolerate repeated affine layer regeneration after ligand binding and recycling of the biosensor with little loss of sensitivity. When stored for three weeks, the frequency shifts of the aptamer-coated crystals were all greater than 90% of those on the response at the first day.

Protein-diazonium adduct direct electrografting onto SPRi-biochip

A direct protein immobilization method for surface plasmon resonance imaging (SPRi) gold chip arraying is exposed. The biomolecule electroaddressing strategy, previously demonstrated by our team on carbon surfaces, is here valuably involved and adapted to create a straightforward and efficient protein immobilization process onto SPRi-biochips. The proteins, modified with an aryl-diazonium adduct, are addressed to the SPRi chip surface through the electroreduction of the aryl-diazonium. The biomolecule deposition was followed through SPRi live measurements during the electrografting process. A specially designed setup enabled us to directly observe the mass increasing at the sensor surface while the proteins were electrografted. A pin electrospotting method, allowing the achievement of distinct sensing layers on gold SPRi-biochips, was used to generate microarray biochips. The integrity of the immobilized proteins and the specificity of the detection, based on antigen/antibody interactions, were demonstrated for the detection of specific antibodies and ovalbumin. The SPRi detection limit of ovalbumin using the electroaddressing of anti-ovalbumin IgG was compared with two other immobilization procedures, cystamine-glutaraldehyde self-assembled monolayer and pyrrole, and was found to be a decade lower than these ones (100 ng/mL, i.e., 2 nM).

A method of layer-by-layer gold nanoparticle hybridization in a quartz crystal microbalance DNA sensing system used to detect dengue virus

Dengue virus (DENV) is nowadays the most important arthropod-spread virus affecting humans existing in more than 100 countries worldwide. A rapid and sensitive detection method for the early diagnosis of infectious dengue virus urgently needs to be developed. In the present study, a circulating-flow quartz crystal microbalance (QCM) biosensing method combining oligonucleotide-functionalized gold nanoparticles (i.e. AuNP probes) used to detect DENV has been established. In the DNA-QCM method, two kinds of specific AuNP probes were linked by the target sequences onto the QCM chip to amplify the detection signal, i.e. oscillatory frequency change (DeltaF) of the QCM sensor. The target sequences amplified from the DENV genome act as a bridge for the layer-by-layer AuNP probes' hybridization in the method. Besides being amplifiers of the detection signal, the specific AuNP probes used in the DNA-QCM method also play the role of verifiers to specifically recognize their target sequences in the detection. The effect of four AuNP sizes on the layer-by-layer hybridization has been evaluated and it is found that 13 nm AuNPs collocated with 13 nm AuNPs showed the best hybridization efficiency. According to the nanoparticle application, the DNA-QCM biosensing method was able to detect dengue viral RNA in virus-contaminated serum as plaque titers being 2 PFU ml(-1) and a linear correlation (R(2) = 0.987) of DeltaF versus virus titration from 2 x 10(0) to 2 x 10(6) PFU ml(-1) was found. The sensitivity and specificity of the present DNA-QCM method with nanoparticle technology showed it to be comparable to the fluorescent real-time PCR methods. Moreover, the method described herein was shown to not require expensive equipment, was label-free and highly sensitive.

Rapid detection of human papilloma virus using a novel leaky surface acoustic wave peptide nucleic acid biosensor

A novel leaky surface acoustic wave (LSAW) bis-peptide nucleic acid (bis-PNA) biosensor with double two-port resonators has been constructed successfully for the quantitative detection of human papilloma virus (HPV). The bis-PNA probe can directly detect HPV genomic DNA without polymerase chain reaction (PCR) amplification, and it can bind to the target DNA sequences more effectively and specifically than a DNA probe. When the concentrations varied from 1 pg/L to 1000 microg/L, with 100 microg/L being the optimal, a typical linearity was found between the quantity of target and the phase shifts. The detection limit was 1.21 pg/L and the clinical specificity was 97.22% of that of real-time PCR. The bis-PNA probe was able to distinguish sequences that differ only in one base. Both the intraassay and interassay coefficients of variance (CVs) were <10%, and the biosensor can be regenerated for ten times without appreciable loss of activity. Therefore, this technical platform of LSAW biosensor can be applied to clinical samples for direct HPV detection.

Hydrogel-Coated Streptavidin Piezoelectric Biosensors and Applications to Selective Detection of Strep-Tag Displaying Cells

Two different hydrogel-coated streptavidin (SAv) piezoelectric chips were investigated. One was directly prepared by immobilizing SAv molecules covalently onto a dextran-modified crystal, and the other one was indirectly prepared by physically adsorbing SAv onto a biotin-linked dextran surface. The covalent preparation yielded 80% more SAv-binding and better subsequent adsorption of biotinylated bovine serum albumin (bBSA). Both chips displayed the best binding affinity with bBSA at pH 5.0 in a flow injection analysis and exhibited reproductive real-time response during layer-by-layer assembly of a bBSA and SAv multilayer film. In the multilayer assembly, approximately 3-7 SAv molecules were captured by each immobilized bBSA, and the estimated apparent KD values of the binding of flowing bBSA with surface SAv were 0.24 and 0.11 microM in the first two cycles of the covalently prepared chip, respectively. Two Escherichia coli cells, each flagellum-displaying Strep-tag I and Strep-tag II, respectively, were selectively detected by both kinds of SAv chips. These studies suggest the potential application of both chips in real-time screening SAv affinity ligands from a cell-display random peptide library.

Modification of carbon electrode with aryl groups having an aliphatic amine by electrochemical reduction of in situ generated diazonium cations

The electrochemically induced functionalization of glassy carbon electrode by aryl groups having an aliphatic amine group was achieved by reduction of in situ generated diazonium cations in aqueous media. The corresponding diazonium cations of 4-aminobenzylamine, 2-aminobenzylamine, 4-(2-aminoethyl)aniline, N-methyl-1,2-phenylenediamine, and N, N-dimethyl- p-phenylenediamine were generated in situ with sodium nitrite in aqueous HCl. The kinetics of electrochemical grafting were investigated with electrochemical impedance spectroscopy and electrochemical quartz crystal microbalance measurements (with carbon-coated quartz crystal), and the barrier properties of the grafted layers were evaluated by cyclic voltammetry in the presence of electroactive redox probes such as Fe(CN)6 3-/4- and Ru(NH 3)6 (3+). The grafting efficiency of aryl groups was found to depend on the nature of the amine (primary, secondary, and tertiary), the chain length of the alkyl substituent, and the substitution position on the aromatic ring. The nitrosation of the "aliphatic" amine, in the case of secondary and tertiary amines, was also evidenced by X-ray photoelectron spectroscopy.

Using oligonucleotide-functionalized Au nanoparticles to rapidly detect foodborne pathogens on a piezoelectric biosensor

A circulating-flow piezoelectric biosensor, based on an Au nanoparticle amplification and verification method, was used for real-time detection of a foodborne pathogen, Escherichia coli O157:H7. A synthesized thiolated probe (Probe 1; 30-mer) specific to E. coli O157:H7 eaeA gene was immobilized onto the piezoelectric biosensor surface. Hybridization was induced by exposing the immobilized probe to the E. coli O157:H7 eaeA gene fragment (104-bp) amplified by PCR, resulting in a mass change and a consequent frequency shift of the piezoelectric biosensor. A second thiolated probe (Probe 2), complementary to the target sequence, was conjugated to the Au nanoparticles and used as a "mass enhancer" and "sequence verifier" to amplify the frequency change of the piezoelectric biosensor. The PCR products amplified from concentrations of 1.2 x 10(2) CFU/ml of E. coli O157:H7 were detectable by the piezoelectric biosensor. A linear correlation was found when the E. coli O157:H7 detected from 10(2) to 10(6) CFU/ml. The piezoelectric biosensor was able to detect targets from real food samples.

Aspects of recent development of immunosensors

This chapter focuses on the recent developments in the field of immunosensors. Immunosensors incorporate the specific immunochemical reaction with the modern transducers including electrochemical (potentiometric, conductometric, capacitative, impedance, amperometric), optical (fluorescence, luminescence, refractive index), and microgravimetric transducers. These immunosensor devices with dramatic improvements in the sensitivity and selectivity possess the abilities to investigate the reaction dynamics of antibody–antigen binding and the potential to revolutionize conventional immunoassay techniques. With the rapid development of immunological reagents and detection equipments, immunosensors have allowed an increasing range of analytes to be identified and quantified and in particular, simple-to-use, inexpensive, and reliable immunosensing systems have been developed for areas such as outpatient monitoring, large screening programs, and remote environmental surveillance. Immunosensors with lowered detection limits and increased sensitivities have been developed in various fields, particularly in clinical analysis. A noticeable development trend is also observed in the development of immunosensors combining with other techniques such as flow injection analysis (FIA) or capillary electrophoretic (CE) analysis, which complement and improve the present immunoassay methods. Belov et al. have proposed a novel immunophenotyping method for leukemias which uses a cluster of differentiation antibody microarray, and a microarray of enzyme-linked immunosorbent assay has been developed for autoimmune diagnosis of systematic rheumatic disease. Development of microfluidic immunosensor systems for proteomics and drug discovery have also been reported in recent years where the microfluidic system integrates multiple processes in a single device to improve analytical performance by reducing the reagent consumption and the analysis time, and increasing reliability and sensitivity through automation.

Analysis of C-reactive protein on amide-linked N-hydroxysuccinimide-dextran arrays with a spectral surface plasmon resonance biosensor for serodiagnosis

A new label-free array system using amide-linked (AL) NHS-dextran and a spectral SPR biosensor are presented for the high-throughput analysis of C-reactive protein (CRP) in human sera. The AL NHS-dextran layer on the surface of gold arrays was composed of an amide linkage between NHS-modified carboxymethyl-dextran and amine-modified 11-mercaptoundecanoic acid. The topology of the AL NHS-dextran layer was analyzed by atomic force microscopy, and it was found to be superior to the previously used epoxide-linked carboxymethyl-dextran layer in its immobilization of proteins. Specific immunoreactions and a dose-dependent increase of SPR signals were demonstrated on the AL NHS-dextran layer. Then, the label-free array system was successfully applied to the rapid analysis of CRP in 120 human sera. CRP levels in human sera determined by the array-based spectral SPR biosensor showed a good correlation with those determined by the latex-enhanced turbidimetry immunoassay (n = 120, r = 0.945, p < 0.0001). Thus, the array-based spectral SPR biosensor based on the AL NHS-dextran surface is a potential system for rapid and label-free serodiagnosis of human diseases.

Analytical performances of aptamer-based sensing for thrombin detection

Aptamer-based assays represent a modern and attractive approach in bioanalytical chemistry. The DNA thrombin aptamer has been extensively investigated, and the coupling of this aptamer to different transduction principles has demonstrated the wide applicability of aptamers as bioreceptors in bioanalytical assays. The goal of this work was to critically evaluate all the parameters that can influence the sensor performances by using the thrombin aptamer immobilized onto piezoelectric quartz crystals. The optimization of the immobilization and the binding protocol was of paramount importance, and improvements in analytical performances could be obtained by optimizing simple steps in immobilization and assay conditions. Moreover, the work demonstrated the possibility of using aptamer-based sensors in complex matrixes, opening the possibility of a real application to diagnostics or medical investigation.

Label-free voltammetric detection of single-nucleotide mismatches recognized by the protein MutS

MutS, a protein involved in DNA mismatch repair, recognizes mispaired and unpaired bases in duplex DNA. We have previously used MutS in an electrochemical double-surface technique (DST) for in-vitro detection of point mutations in DNA. The DST involved binding of unlabeled MutS to DNA heteroduplexes at the surface of magnetic beads followed by a highly sensitive electrochemical determination of the protein by measurement of a catalytic protein signal (peak H) at mercury electrodes. Detection of MutS using a peak resulting from oxidation of tyrosine and tryptophan residues of the protein at a carbon-paste electrode (CPE) was also possible but was approximately three orders of magnitude less sensitive. In this work we present an optimized technique for ex-situ voltammetric determination of MutS at a CPE. Choice of optimum experimental conditions (pH of supporting electrolyte, square-wave voltammetry settings, etc.) resulted in substantial improvement of the sensitivity of the assay, enabling detection of approximately 140 pg (1.6 fmol protein monomer) MutS in a 5-microL sample. The sensitivity was increased further by acid hydrolysis of the protein before measurement. The hydrolyzed protein was detectable down to 5 pg (approx. 56 amol) MutS in 5 microL solution. By using the DST combined with determination of the bound unlabeled MutS at the CPE we demonstrated selective interactions of the protein with single-base mismatches and discrimination among different base mispairs in 30-mer or 95-mer DNA duplexes. In agreement with previous studies, binding of the protein to the 30-mer substrates followed the trend G:T>>C:A>A:A>C:T>homoduplex. The electrochemical data were confirmed by use of an independent technique-a quartz-crystal microbalance for real-time monitoring of MutS interactions with DNA duplexes containing different base mispairs. By using the electrochemical DST a G:T mismatch was detectable in up to 1000-fold excess of homoduplex DNA.

Nucleic acid sensing by regenerable surface-associated isothermal rolling circle amplification

A novel method for regenerating biosensors has been developed in which the highly specific detection of nucleic acid sequences is carried out using molecular padlock probe (MPP) technology and surface-associated rolling circle amplification (RCA). This technique has a low occurrence of false positive results when compared to polymerase chain reaction, and is an isothermal reaction, which is advantageous in systems requiring low power consumption such as remote field sensing applications. Gold-sputtered 96-well polystyrene microplates and a fluorescent label were used to explore the detection limits of the surface-associated RCA technique, specificity for different MPP, conditions for regeneration of the biomolecular sensing surface, and reproducibility of measurements on regenerated surfaces. The technique was used to create highly selective biomolecular surfaces capable of discriminating between DNA oligonucleotides with sequences identical to RNA from infectious salmon anemia (ISA) and infectious hematopoietic necrosis (IHN) virus. As little as 0.6 fmol of circularized MPP was detectable with this fluorimetric assay. The sensing layers could be reused for at least four cycles of amplification using thermal denaturation, with less than 33% decrease in RCA response over time. Because the nucleic acid product of the test is attached to a surface during amplification, the technique is directly applicable to a variety of existing sensing platforms, including acoustic wave and optical devices.

A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions

The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally 'bulk acoustic wave' (BAW), 'thickness shear mode' (TSM) sensors or 'quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed.

DNA immobilisation procedures for surface plasmon resonance imaging (SPRI) based microarray systems

Two different surface chemistries have been studied for the development of surface plasmon resonance imaging (SPRI) based DNA microarray affinity sensors: (1) 11-mercaptoundecanoic acid-poly(ethylenimine) (MUA-PEI) and (2) dextran procedures. The MUA-PEI method consists of assembling a multilayer on the basis of electrostatic interactions formed with: 11-mercaptoundecanoic acid (MUA), poly(ethylenimine) (PEI) and extravidin layers. The dextran procedure involves assembling a multilayer formed with 11-mercaptoundecanol, dextran and streptavidin layers, which are linked by covalent bonds. The oligonucleotide probes are immobilised onto the sensor surface as spots forming a matrix 14x14, which is spotted by a robot, while the target sequences are free in solution. The system allows the interaction (hybridisation) monitoring, in real-time and in parallel, of unlabeled oligonucleotide solution targets to oligonucleotide probes immobilised on a 196 spots matrix. Using oligonucleotides as probes and targets, both functionalised surfaces have been evaluated in view of their application to the diagnosis of gene mutations involved in human diseases. In particular, we demonstrate the ability to detect, in parallel, several mutations causing human cystic fibrosis (CF), which lie within exon 10 of the human cystic fibrosis transmembrane conductance regulator (CFTR) gene. The immobilised probes were complementary to sequences corresponding the mutant or wild type alleles. Two deletions of three bases (DeltaF508 and DeltaI507) and four single nucleotide polymorphisms (M470V, Q493X, V520F and 1716 G>A) were investigated. In both functionalised surfaces, the system showed the capacity to discriminate normal and mutant sequences differing by a single base.

Point-of-care biosensor systems for cancer diagnostics/prognostics

With the growing number of fatalities resulting from the 100 or so cancer-related diseases, new enabling tools are required to provide extensive molecular profiles of patients to guide the clinician in making viable diagnosis and prognosis. Unfortunately with cancer-related diseases, there is not one molecular marker that can provide sufficient information to assist the clinician in making effective prognoses or even diagnoses. Indeed, large panels of markers must typically be evaluated that cut across several different classes (mutations in certain gene fragments--DNA; over/under-expression of gene activity as monitored by messenger RNAs; the amount of proteins present in serum or circulating tumor cells). The classical biosensor format (dipstick approach for monitoring the presence of a single element) is viewed as a valuable tool in many bioassays, but possesses numerous limitations in cancer due primarily to the single element nature of these sensing platforms. As such, if biosensors are to become valuable tools in the arsenal of the clinician to manage cancer patients, new formats are required. This review seeks to provide an overview of the current thinking on molecular profiling for diagnosis and prognosis of cancers and also, provide insight into the current state-of-the-art in the biosensor field and new strategies that must be considered to bring this important technology into the cancer field.

Surface plasmon resonance imaging as a multidimensional surface characterization instrument--application to biochip genotyping

Surface plasmon resonance imaging (SPRI) sensors allow the characterization of a metal/dielectric interface. Providing proper biochemical functionalization and spatial structuration of the functionalized surface, an optical biochip system--label free and real time--can be achieved. We study the impact of the different physical parameters on the quality of the measurements. Such a SPRI system has a great sensitivity to small variations of the physical parameters (layer optical index, thickness, etc.) occurring at the sensor surface. Precision and reliability of the measurements are provided by a multidimensional approach (4D i.e. spatial coordinates x-y, time t, angle of incidence theta) allowing multiple self-calibration procedures. Such apparatus has already been successfully applied in genomics and proteomics, studying DNA:DNA and oligosaccharide:protein interactions. In this article, we illustrate the advantages of the SPRI setup applied to the detection of gene mutations, using as a model the genetic disease Cystic Fibrosis. The results demonstrate that the system is able to monitor and analyse the interaction under investigation, allowing the diagnosis of genetic single nucleotide polymorphisms by exploiting only a part of the multidimensional potential (x, y, t, theta).

Investigating oligonucleotide hybridization at subnanomolar level by surface plasmon resonance biosensor method

We have optimized surface plasmon resonance (SPR) biosensor technology for a rapid, direct, and low-consumption label-free multianalyte screening of synthetic oligonucleotides (ONs) with modified internucleotide linkages potentially applicable in antisense therapy. Monitoring of the ONs hybridization is based on the formation of complex between the natural oligonucleotide probe immobilized on the sensor surface and the ON in solution in contact with the sensor surface. An immobilization chemistry utilizing the streptavidin-biotin interaction was employed to obtain desired ligand density and high hybridization efficiency. It was demonstrated that the sensor is capable of detecting complementary 23-mer ONs in concentrations as low as 0.1 nM with high specificity and reproducibility.

Oriented immobilization of antibodies by a self-assembled monolayer of 2-(biotinamido)ethanethiol for immunoarray preparation

Orientation of antibodies is very important in the preparation of immunoarrays to keep the activity of antibodies on solid surfaces. Thus, we synthesized a new bifunctional compound, 2-(biotinamido)ethanethiol, and investigated whether the thiol compound is useful to analyze antibody-antigen interactions on immunoarrays with a spectral SPR biosensor. The synthesized organic thiol was characterized by nuclear magnetic resonance spectroscopy and mass spectrometry. 2-(Biotinamido)ethanethiol formed a monolayer on a gold surface and properly immobilized antibodies via streptavidin and biotinylated protein G. Optimal molar ratio of 2-(biotinamido)ethanethiol and mercaptohexanol for antigen-antibody interactions was 1:2. Thus, 2-(biotinamido)ethanethiol is an useful bifunctional linker in the preparation of immunoarrays on gold surfaces.

A nanoparticle amplification based quartz crystal microbalance DNA sensor for detection of Escherichia coli O157:H7

A quartz crystal microbalance (QCM) DNA sensor, based on the nanoparticle amplification method, was developed for detection of Escherichia coli O157:H7. A thiolated single-stranded DNA (ssDNA) probe specific to E. coli O157:H7 eaeA gene was immobilized onto the QCM sensor surface through self-assembly. The hybridization was induced by exposing the ssDNA probe to the complementary target DNA, and resulted in the mass change and therefore frequency change of the QCM. Streptavidin conjugated Fe(3)O(4) nanoparticles (average diameter=145 nm) were used as "mass enhancers" to amplify the frequency change. Synthesized biotinylated oligonucleotides as well as E. coli O157:H7 eaeA gene fragments (151 bases) amplified using asymmetric PCR with biotin labeled primers were tested. As low as 10(-12)M synthesized oligonucleotides and 2.67 x 10(2) colony forming unit (CFU)/ml E. coli O157:H7 cells can be detected by the sensor. Linear correlation between frequency change and logarithmic number of bacterial cell concentration was found for E. coli O157:H7 from 2.67 x 10(2) to 2.67 x 10(6)CFU/ml.

Multi-analyte surface plasmon resonance biosensing

Surface plasmon resonance (SPR) biosensors are affinity sensing devices exploiting a special mode of electromagnetic field-surface plasmon-polariton-to detect the binding of analyte molecules from a liquid sample to biomolecular recognition elements immobilized on the surface of the sensor. In this paper, we review advances of SPR biosensor technology towards detection systems for the simultaneous detection of multiple analytes (multi-analyte detection). In addition, we report application of a recently developed multichannel SPR sensor based on spectroscopy of surface plasmons and wavelength division multiplexing of sensing channels to multi-analyte detection.

Piezoelectric biosensors: Strategies for coupling nucleic acids to piezoelectric devices

The development of a piezoelectric biosensor based on nucleic acids interaction is presented focusing on the methodology for probe immobilization. This is a key step in any DNA biosensor development. Often, the detection limits and, in general, the analytical performances of the biosensor can be improved by optimizing the immobilization of the receptor on the transducer surface. DNA must be attached to the solid support, retaining native conformation, and binding activity. This attachment must be stable over the course of a binding assay and, in addition, sufficient binding sites must be presented to the solution phase to interact with the analyte. In this paper, the optimization of the coating of the gold quartz crystal surface, to immobilize an oligonucleotide probe, is reported. Two immobilization procedures are illustrated in details with a comparison regarding the immobilization of the probe, the detection of the hybridization reaction, and the possibility of regeneration. The two procedures are based on the use of biotinylated or thiolated DNA probes. Specific applications will be also presented.

Direct electrochemical detection of oligonucleotide hybridization on poly(5-hydroxy-1,4-naphthoquinone- co-5-hydroxy-3-thioacetic acid-1,4-naphthoquinone) film

We describe the construction of a new DNA-modified electrode based on an electroactive film. 5-Hydroxy-1,4-naphthoquinone is coelectrooxidized with 5-hydroxy-3-thioacetic acid-1,4-naphthoquinone to give a copolymer, presenting both electroactive and chemically reactive groups. The carboxylic function acts as a precursor for the covalent grafting of ODN probes while the quinone group acts as the transduction element of hybridization. Electrochemical detection was performed by differential pulse voltammetry in the electroactivity domain of the quinone group (i.e., at very low potentials, 0 to -0.8 V vs SCE). A very clear modification of the redox activity is observed between unmodified and probe-modified films and especially upon addition of target ODN.

Electrogenerated chemiluminescence. 72. Determination of immobilized DNA and C-reactive protein on Au(111) electrodes using tris(2,2'-bipyridyl)ruthenium(II) labels

Anodic electrogenerated chemiluminescence (ECL) with tri-n-propylamine (TPrA) as a coreactant was used to determine DNA and C-reactive protein (CRP) by immobilizations on Au(111) electrodes using tris(2,2'-bipyridyl)ruthenium(II) (Ru(bpy)(3)(2+)) labels. A 23-mer synthetic single-stranded (ss) DNA derived from the Bacillus anthracis with an amino-modified group at the 5' end position was covalently attached to the Au(111) substrate precoated with a self-assembled thiol monolayer of 3-mercaptopropanoic acid (3-MPA) in the presence of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDAC) and then hybridized with a target ssDNA tagged with Ru(bpy)(3)(2+) ECL labels. Similarly, biotinylated anti-CRP species were immobilized effectively onto the Au(111) substrate precovered with a layer of avidin linked covalently via the reaction between avidin and a mixed thiol monolayer of 3-MPA and 16-mercaptohexadecanoic acid on Au(111) in the presence of EDAC and N-hydroxysuccinimide. CRP and anti-CRP tagged with Ru(bpy)(3)(2+) labels were then conjugated to the surface layer. ECL responses were generated from the modified electrodes described above by immersing them in a TPrA-containing electrolyte solution. A series of electrode treatments, including blocking free -COOH groups with ethanol amine, pinhole blocking with bovine serum albumin, washing with EDTA/NaCl/Tris buffer, and spraying with inert gases, were used to reduce the nonspecific adsorption of the labeled species. The ECL peak intensity was linearly proportional to the analyte CRP concentration over the range 1-24 microg/mL. CRP concentrations of two unknown human plasma/serum specimens were measured by the standard addition method based on this technique.