Oligonucleotides form a duplex with non-helical properties on a positively charged surface

RNA therapeutics-An evaluation of potential occupational health hazards and a strategy to establish occupational exposure limits (OELs)

RNA therapeutics represent a rapidly expanding and innovative group of pharmaceuticals. These new modalities necessitate the establishment of Occupational Exposure Limits (OELs) to ensure safe occupational handling. While there is an established methodology for setting OELs for small molecule therapeutics, this methodology is not readily applicable to large molecule RNA therapeutics that deserve additional considerations in their safety assessment, particularly for aspects related to their unique modes of action. This research, which involves an extensive review of the data available for RNA therapeutics to derive substance-specific OELs and to propose a strategy for low-characterized RNA therapeutics, fills this crucial gap. It is recommended to apply an activity correction factor (ACF) in the OEL formula for large molecules, as representative of the "α" in the OEL formula for small molecules, considering differences in route of administration, critical effects, mechanism of action, and the RNA delivery platform. Additionally, it is proposed to consider lower OEL values for mRNA vaccines as compared to other RNA therapeutics. Finally, it is suggested that the exposure assessment experience that has already been acquired when handling therapeutic proteins can also be used to define containment strategies for RNA therapeutics.

Evaluation of covalent coupling strategies for immobilizing ligands on silica colloidal crystal films by optical interferometry

Immobilizing ligands is a crucial part of preparing optical sensors and directly connected to the sensitivity, stability, and other characteristics of sensors. In this work, an ordered porous layer interferometry (OPLI) system that can monitor the covalent coupling process of ligands in real time was developed. Films of silica colloidal crystal (SCC), as optical interference substrates, were surface modified by three different reagents: chloroacetic acid, glutaric anhydride, and carboxymethyl dextran. Staphylococcus aureus protein A (SPA), the ligand, was immobilized on SCC films. The covalent coupling process of SPA and SCC films can be dynamically monitored by the OPLI system. In addition, the three different strategies were evaluated by comparing the efficiency of the sensors prepared by different methods for binding Immunoglobulin G (IgG). The glutaric anhydride-modified sensor offers apparent advantages in terms of bound IgG quantity and affinity. This system provides a simple and intuitive way to determine the efficiency of different covalent coupling strategies. Furthermore, the sensor covalently coupled with SPA also excels in the determination of IgG content in complex systems such as milk. At the same time, the covalent coupling gives the sensor the ability to be stored stably over time.

DNA Electrochemistry and Electrochemical Sensors for Nucleic Acids

Sensitive, specific, and fast analysis of nucleic acids (NAs) is strongly needed in medicine, environmental science, biodefence, and agriculture for the study of bacterial contamination of food and beverages and genetically modified organisms. Electrochemistry offers accurate, simple, inexpensive, and robust tools for the development of such analytical platforms that can successfully compete with other approaches for NA detection. Here, electrode reactions of DNA, basic principles of electrochemical NA analysis, and their relevance for practical applications are reviewed and critically discussed.

Covalent linker-free immobilization of conjugatable oligonucleotides on polypropylene surfaces

A novel plasma treatment method was used to activate a polymer surface for oligonucleotide immobilization.

Surface Modification Chemistries of Materials Used in Diagnostic Platforms with Biomolecules

Biomolecules including DNA, protein, and enzymes are of prime importance in biomedical field. There are several reports on the technologies for the detection of these biomolecules on various diagnostic platforms. It is important to note that the performance of the biosensor is highly dependent on the substrate material used and its meticulous modification for particular applications. Therefore, it is critical to understand the principles of a biosensor to identify the correct substrate material and its surface modification chemistry. The imperative surface modification for the attachment of biomolecules without losing their bioactivity is a key to sensitive detection. Therefore, finding of a modification method which gives minimum damage to the surface as well as biomolecule is highly inevitable. Different surface modification technologies are invented according to the type of a substrate used. Surface modification techniques of the materials used as platforms in the fabrication of biosensors are reviewed in this paper.

Surface state of the dopamine RNA aptamer affects specific recognition and binding of dopamine by the aptamer-modified electrodes

Specific monitoring of dopamine, in the presence of structurally related neurotransmitters, is critical for diagnosis, treatment and mechanistic understanding of a variety of human neuropathologies, but nevertheless the proper tools are scarce. Recently, an electrochemical aptasensor for specific analysis of dopamine, exploiting dopamine biorecognition by the RNA aptamer electrostatically adsorbed onto a cysteamine-modified electrode, has been reported (Analytical Chemistry 85 (2013) 121). However it was not clear which way dopamine biorecognition and binding by such aptamer layers proceed and if they can be improved. Here, we show that the aptamer surface state, in particular the aptamer surface density, in a bell-shaped manner affects the dopamine binding, being maximal for the 3.5 ± 0.3 pmol cm(-2) monolayer coverage of the aptamer molecules lying flat on the surface. Therewith, the aptamer affinity for dopamine increases one order of magnitude due to electrostatically regulated immobilization, with the aptamer-dopamine dissociation constant of 0.12 ± 0.01 μM versus 1.6 ± 0.17 μM shown in solution. Under optimal conditions, 0.1-2 μM dopamine was specifically and 85.4 nA μM(-1) cm(-2) sensitively detected, with no interference from structurally related catecholamines. The results allow improvement of the robustness of dopamine monitoring by aptamer-modified electrodes in biological systems, within the 0.01-1 μM dopamine fluctuation range.

Novel Approaches and Technologies in Molecular HLA Typing

The invention of the Polymerase Chain Reaction (PCR) has revolutionized molecular biology enabling gene isolation and characterization in hours rather than days. Scientists working in transplant diagnostics have proven to be pioneers in adapting this molecular technique to the clinical needs of histocompatibility testing. This chapter describes a number of novel genotyping technologies which have been used to address the challenges posed by genetic diversity seen in the extensive polymorphism in HLA genes. These novel approaches include single-stranded and duplex conformational analyses, real-time PCR, microarray hybridization, RNA-based sequencing, and the present day Next Generation Sequencing. The chapter concludes with a brief look at a possible next, Next Generation Sequencing system.

Immobilization techniques for microarray: challenges and applications

The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.

9G DNAChip Technology: Self-Assembled Monolayer (SAM) of ssDNA for Ultra-Sensitive Detection of Biomarkers

A 9G DNAChip obtained by allowing the formation of a self-assembled monolayer (SAM) of oligonucleotides appended with nine consecutive guanines on the chip surface has been applied in the detection of biomarkers. Using a 9G DNAChip, biomarker in the concentration range of 4 pg/mL to 40 fg/mL can be easily differentiated in the buffer matrix. Moreover, it is the first time that a biomarker with a concentration of 40 fg/mL has been detected in a mixture of proteins without use of any signal amplification technique.

RNA aptamer-based electrochemical biosensor for selective and label-free analysis of dopamine

The inherent redox activity of dopamine enables its direct electrochemical in vivo analysis ( Venton , B. J.; Wightman, M. R. Anal. Chem. 2003, 75, 414A). However, dopamine analysis is complicated by the interference from other electrochemically active endogenous compounds present in the brain, including dopamine precursors and metabolites and other neurotransmitters (NT). Here we report an electrochemical RNA aptamer-based biosensor for analysis of dopamine in the presence of other NT. The biosensor exploits a specific binding of dopamine by the RNA aptamer, immobilized at a cysteamine-modified Au electrode, and further electrochemical oxidation of dopamine. Specific recognition of dopamine by the aptamer allowed a selective amperometric detection of dopamine within the physiologically relevant 100 nM to 5 μM range in the presence of competitive concentrations of catechol, epinephrine, norepinephrine, 3,4-dihydroxy-phenylalanine (L-DOPA), 3,4-dihydroxyphenylacetic acid (DOPAC), methyldopamine, and tyramine, which gave negligible signals under conditions of experiments (electroanalysis at 0.185 V vs Ag/AgCl). The interference from ascorbic and uric acids was eliminated by application of a Nafion-coated membrane. The aptasensor response time was <1 s, and the sensitivity of analysis was 62 nA μM(-1) cm(-2). The proposed design of the aptasensor, based on electrostatic interactions between the positively charged cysteamine-modified electrode and the negatively charged aptamer, may be used as a general strategy not to restrict the conformational freedom and binding properties of surface-bound aptamers and, thus, be applicable for the development of other aptasensors.

Development of an electrochemical DNA biosensor with the DNA immobilization based on in situ generation of dithiocarbamate ligands

In this article, a simple and effective strategy for DNA immobilization on gold electrode surface is developed. The amine-modified oligonucleotide was firstly reacted with CS(2) and then in situ generated dithiocarbamate group functionalized probe DNA (DTC-DNA) was directly attached onto the gold surface by bidentate anchoring points. The DNA biosensor fabrication process was characterized by cyclic voltammetry and electrochemical impedance spectroscopy with the use of Fe(CN)(6)(3-/4-) as a redox indicator. The hybridization of DTC-DNA with complementary target DNA could be well distinguished with the use of Co(phen)(3)(3+) as an electrochemical indicator. The fabricated electrochemical DNA biosensor could achieve a detection limit of about 0.1nM toward complementary target DNA. Also, the current strategy is readily operated with less time consumed and lower cost compared with those commonly used strategies.

Human leucocyte antigen typing: techniques and technology, a critical appraisal

Methods for the identification of Human Leukocyte Antigens (HLA) have changed significantly since this group of polymorphic proteins were first characterized by serological reagents in the 1960s and 1970s. The invention and development of the Polymerase Chain Reaction (PCR) has been key in the progress of methods for HLA genotyping. As the complexity of HLA polymorphism has unravelled so it has exposed the weaknesses in techniques such as PCR - Restriction Fragment Length Polymorphism (RFLP) and Reference Strand Mediated Conformation Analysis (RSCA), which are no longer in use today. Methods which have been considered routine laboratory tools in recent years, such as Sequence-Specific Primer - PCR and Sequencing Based Typing (SBT) are now also threatened with extinction, not only because of the depth of HLA variation but also because of the rapid development of Next Generation Sequencing and technologies which will follow this. This review describes the merits and disadvantages of current technologies available to HLA Typing laboratories, future trends and the problems posed by new alleles.

RECENT TRENDS IN DNA BIOSENSING TECHNOLOGIES

Recent development and challenges in DNA biosensing technology for the detection of DNA hybridization are reviewed with respect to their abilities to achieve lower detection limit and higher selectivity. Researchers exploit a range of different chemistries for the development of DNA hybridization biosensors, however all the designs take advantage of heterogenous hybridization between the surface-bound DNA (the probe) and the DNA sample (target) in the solution. The detection protocols include using optical, microgravimetry, and electrochemical-based device to transduce DNA hybridization by observing changes in light, mass/frequency, and current/charge, respectively, upon exposure to the sample. The pros and cons of these biosensor designs are discussed with illustrative examples.

Oblique-Incidence Reflectivity Difference and Fluorescence Imaging of Oligonucleotide and IgG Protein Microarrays

We have constructed an oblique-incidence reflectivity difference (OI-RD) microscope for fluorescent label-free imaging of DNA and protein microarrays on standard glass substrates. Using both OI-RD and fluorescence images, we demonstrate a difference in wetting behavior of labeled and unlabeled IgG protein molecules deposited on an aldehyde-derivatized glass surface. The potential of fluorescent labeling agents to influence the properties of proteins highlights the need for label-free microarray detection techniques to supplement existing fluorescence methods. We also present OI-RD images of an oligonucleotide microarray after printing and washing procedures to demonstrate the use of OI-RD for non-destructive monitoring of changes in the optical properties of microarrays during processing.

Gold nanoparticle-assisted single base-pair mismatch discrimination on a microfluidic microarray device

Two simple gold nanoparticle (GNP)-based DNA analysis methods using a microfluidic device are presented. In the first method, probe DNA molecules are immobilized on the surface of a self-assembled submonolayer of GNPs. The hybridization efficiency of the target oligonulceotides was improved due to nanoscale spacing between probe molecules. In the second method, target DNA molecules, oligonulceotides or polymerase chain reaction (PCR) amplicons, are first bound to GNPs and then hybridized to the immobilized probe DNA on a glass slide. With the aid of GNPs, we have successfully discriminated, at room temperature, between two PCR amplicons (derived from closely related fungal pathogens, Botrytis cinerea and Botrytis squamosa) with one base-pair difference. DNA analysis on the microfluidic chip avoids the use of large sample volumes, and only a small amount of oligonucelotides (8 fmol) or PCR products (3 ng), was needed in the experiment. The whole procedure was accomplished at room temperature in 1 h, and apparatus for high temperature stringency was not required.

The detection of DNA hybridization on phosphorus dendrimer multilayer films by surface plasmon field enhanced-fluorescence spectroscopy

Dendrimer multilayers on gold substrates prepared via layer-by-layer (LbL) assembly technique were characterized and used as substrates for DNA immobilization/hybridization. The multilayers, built using alternately polycationic and polyanionic phosphorus dendrimers of generation 4, were studied by surface plasmon resonance (SPR) spectroscopy. By varying the concentration of NaCl, the optimized optical thickness of a single dendrimer layer (about 4.5 nm) was achieved. Using the multilayers as the substrate, a high loading of DNA probes was obtained through covalent coupling of probe DNA on dendrimer multilayer film. The following hybridization of Cy5-dye labeled complementary target DNA with immobilized probe DNA was detected by surface plasmon field-enhanced fluorescence spectroscopy (SPFS). The limit of detection of target DNA upon hybridization reached 50 pM and 30 pM on 1 bilayer and 4 bilayers, respectively. The phosphorus dendrimer multilayer films display high stability during repeated regeneration and hybridization cycles. The sensitive platforms based on dendrimer multilayers deposited in the presence of NaCl make them attractive candidates for application in DNA sensing.

Patterned and switchable surfaces for biomolecular manipulation

The interactions of biomolecules and cells with solid interfaces play a pivotal role in a range of biomedical applications and have therefore been studied in great detail. An improved understanding of these interactions results in the ability to manipulate DNA, proteins and other biomolecules, as well as cells, spatially and temporally at surfaces with high precision. This in turn engenders the development of advanced devices, such as biosensors, bioelectronic components, smart biomaterials and microarrays. Spatial control can be achieved by the production of patterned surface chemistries using modern high-resolution patterning technologies based on lithography, microprinting or microfluidics, whilst temporal control is accessible through the application of switchable surface architectures. The combination of these two surface properties offers unprecedented control over the behaviour of biomolecules and cells at the solid-liquid interface. This review discusses the behaviour of biomolecules and cells at solid interfaces and highlights fundamental and applied research exploring patterned and switchable surfaces.

Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips

The reliable interpretation of Affymetrix GeneChip data is a multi-faceted problem. The interplay between biophysics, bioinformatics and mining of GeneChip surveys is leading to new insights into how best to analyse the data. Many of the molecular processes occurring on the surfaces of GeneChips result from the high surface density of probes. Interactions between neighbouring adjacent probes affect their rate and strength of hybridization to targets. Competing targets may hybridize to the same probe, and targets may partially bind to more than one probe. The formation of these partial hybrids results in a number of probes not reaching thermodynamic equilibrium during hybridization. Moreover, some targets fold up, or cross-hybridize to other targets. Furthermore, probes may fold and can undergo chemical saturation. There are also sequence-dependent differences in the rates of target desorption during the washing stage. Improvements in the mappings between probe sequence and biological databases are leading to more accurate gene expression profiles. Moreover, algorithms that combine the intensities of multiple probes into single measures of expression are increasingly dependent upon models of the hybridization processes occurring on GeneChips. The large repositories of GeneChip data can be searched for systematic effects across many experiments. This data mining has led to the discovery of a family of thousands of probes, which show correlated expression across thousands of GeneChip experiments. These probes contain runs of guanines, suggesting that G-quadruplexes are able to form on GeneChips. We discuss the impact of these structures on the interpretation of data from GeneChip experiments.

Manipulating the salt and thermal stability of DNA multilayer films via oligonucleotide length

DNA films are promising materials for diverse applications, including sensing, diagnostics, and drug/gene delivery. However, the ability to tune the stability of DNA films remains a crucial aspect for such applications. Herein, we examine the role of oligonucleotide length on the formation, and salt and thermal stability, of DNA multilayer films using oligonucleotides of homopolymeric diblocks (polyAG and polyTC), with each block (A, G, T, or C) ranging from 5 to 30 bases (10-, 20-, 30-, 40-, and 60-mer). Using a combination of quartz crystal microgravimetry, dual polarization interferometry, and flow cytometry, we demonstrate that at least 10 bases per hybridizing block in the DNA diblocks (that is, 20-mer) are required for successful hybridization and, hence, DNA multilayer film formation. Films assembled using longer oligonucleotide blocks were more stable in low salt conditions, with the DNA multilayer films assembled from the 60-mer oligonucleotides remaining intact in solutions of about 25 mM NaCl. A systematic increase in film melting temperature ( T m) was observed for the DNA multilayer films (assembled on colloids) with increasing oligonucleotide length, ranging from 38.5 degrees C for the 20-mer films to 53 degrees C for the 60-mer films. Further, an alternating trend in T m of the DNA multilayer films was observed with layer number (AG or TC); DNA multilayer films terminated with an AG layer exhibited a higher T m (44-49 degrees C) than films with an outermost TC layer (ca. 38 degrees C), suggesting a rearrangement of the film structure upon hybridization of the outermost layer. This work shows that the stability of DNA multilayer films can be tuned by varying the length of the oligonucleotide building blocks, thus providing a versatile means to tailor the salt and thermal stability of DNA films, which is necessary for the application of such films.

Label-free DNA sensor by boron-doped diamond electrode using an ac impedimetric approach

An electrochemical biosensor using a boron-doped diamond (BDD) electrode is described for differentiating between gene sequences according to DNA hybridization events using an ac impedimetric approach. BDD electrodes were dipped into a 1% solution of polyethylenimine (PEI) to adsorb a thin layer of positively charged PEI on the surface of BDD, then PEI-modified BDD electrodes were used to immobilize negatively charged single-stranded PCR fragments from Exon 7 of human p53 gene. Alternating current impedimetric measurements were first performed on these systems in phosphate buffered saline (PBS) and then upon exposure to single-stranded DNA (ssDNA). When the ssDNA-immobilized BDD electrode and solution ssDNA were completely complementary, a large drop in impedance was measured. Complementary DNA could be clearly detected at concentrations down to 10 (-19) g mL (-1) at a fixed frequency (10 Hz). Higher concentrations of DNA gave faster hybridization with saturation occurring at levels above 1.0 pg mL (-1.) Responses were much lower upon exposure to noncDNA, even at higher concentrations. The results show it is possible to directly detect target DNA at a fixed frequency and without additional labeling.

The study of genomic DNA adsorption and subsequent interactions using total internal reflection ellipsometry

The adsorption of genomic DNA and subsequent interactions between adsorbed and solvated DNA was studied using a novel sensitive optical method of total internal reflection ellipsometry (TIRE), which combines spectroscopic ellipsometry with surface plasmon resonance (SPR). Single strands of DNA of two species of fish (herring and salmon) were electrostatically adsorbed on top of polyethylenimine films deposited upon gold coated glass slides. The ellipsometric spectra were recorded and data fitting utilized to extract optical parameters (thickness and refractive index) of adsorbed DNA layers. The further adsorption of single stranded DNA from an identical source, i.e. herring ss-DNA on herring ss-DNA or salmon ss-DNA on salmon ss-DNA, on the surface was observed to give rise to substantial film thickness increases at the surface of about 20-21 nm. Conversely adsorption of DNA from alternate species, i.e. salmon ss-DNA on herring ss-DNA or herring ss-DNA on salmon ss-DNA, yielded much smaller changes in thickness of 3-5 nm. AFM studies of the surface roughness of adsorbed layers were in line with the TIRE data.

An introduction to electrochemical DNA biosensors

Electrochemical DNA biosensors exploit the affinity of single-stranded DNA for complementary strands of DNA and are used in the detection of specific sequences of DNA with a view towards developing portable analytical devices. Great progress has been made in this field but there are still numerous challenges to overcome. This review for researchers new to the field describes the components of electrochemical DNA biosensors and the important issues in their design. Methods of transducing DNA binding events are discussed along with future directions for DNA biosensors.

Quantitative real-time measurements of DNA hybridization with alkylated nonoxidized silicon nanowires in electrolyte solution

The quantitative, real-time detection of single-stranded oligonucleotides with silicon nanowires (SiNWs) in physiologically relevant electrolyte solution is demonstrated. Debye screening of the hybridization event is circumvented by utilizing electrostatically adsorbed primary DNA on an amine-terminated NW surface. Two surface functionalization chemistries are compared: an amine-terminated siloxane monolayer on the native SiO2 surface of the SiNW, and an amine-terminated alkyl monolayer grown directly on a hydrogen-terminated SiNW surface. The SiNWs without the native oxide exhibit improved solution-gated field-effect transistor characteristics and a significantly enhanced sensitivity to single-stranded DNA detection, with an accompanying 2 orders of magnitude improvement in the dynamic range of sensing. A model for the detection of analyte by SiNW sensors is developed and utilized to extract DNA-binding kinetic parameters. Those values are directly compared with values obtained by the standard method of surface plasmon resonance (SPR) and demonstrated to be similar. The nanowires, however, are characterized by higher detection sensitivity. The implication is that SiNWs can be utilized to quantitate the solution-phase concentration of biomolecules at low concentrations. This work also demonstrates the importance of surface chemistry for optimizing biomolecular sensing with silicon nanowires.

Surface modification of titanium-based alloys with bioactive molecules using electrochemically fixed nucleic acids

A new method of surface modification for titanium (alloys) with bioactive molecules was developed with the intention of providing a new basis of implant adaptation for particular requirements of certain medical indications. Nucleic acid single strands are fixed electrochemically via their termini (regiospecifically) by growing an oxide layer on Ti6Al7Nb anodically. It could be shown that they are accessible to subsequent hybridization with complementary strands at physiological pH. Amount of nucleic acids immobilized and hybridized were determined radioanalytically using 32P-labelled nucleic acids. Stable fixation was attained at and above potentials of 4 V(SCE). Up to 4 pmol/cm2 of nucleic acid single strands could be immobilized and hybridization efficiencies up to 1.0 were reached. Hybridization efficiency was found to depend on surface density of immobilized oligonucleotides, while hybridization rates increased when MgCl2 was added. A conjugate consisting of an oligonucleotide complementary to the immobilized strand and the hexapeptide GRGDSP with RGD as an integrin recognition site was synthesized. This conjugate was able to bind to integrins on osteoblasts. It was shown that this conjugate binds to the anchor strand fixed on Ti6Al7Nb to an extent comparable with the unconjugated complementary strand.

Single Gene Differentiation by DNA-Modified Carbon Electrodes Using an AC Impedimetric Approach

A simple and novel electrochemical biosensor is described for differentiating between differing gene sequences on the basis of DNA hybridization events. Polyethylenimine-modified screen-printed carbon electrodes were used to immobilize single-stranded PCR fragments from plasmid DNA from the gene for pyruvate kinase. AC impedimetric measurements were first performed on these systems in buffer and then upon exposure to single-stranded DNA. When the electrode and solution DNA were complementary, a large drop in impedance was measured. Complementary DNA could be clearly detected at concentrations down to 1 fg/mL. Higher concentrations gave faster hybridization with saturation occurring at levels above 1 ng/mL. Responses were much lower upon exposure to noncomplementary DNA, even at higher concentrations, with the sensor showing a high degree of selectivity. This sensor format offers great promise for many DNA hybridization applications and lends itself to mass fabrication.

Introduction: array technology - an overview

Microarray technology has its roots in high-throughput parallel synthesis of biomacromolecules, combined with combinatorial science. In principle, the preparation of arrays can be performed either by in situ synthesis of biomacromolecules on solid substrates or by spotting of ex situ synthesized biomacromolecules onto the substrate surface. The application of microarrays includes spatial addressing with target (macro) molecules and screening for interactions between immobilized probe and target. The screening is simplified by the microarray format, which features a known structure of every immobilized library element. The area of nucleic acid arrays is best developed, because such arrays are allowed to follow the biosynthetic pathway from genes to proteins, and because nucleic acid hybridization is a most straightforward screening tool. Applications to genomics, transcriptomics, proteomics, and glycomics are currently in the foreground of interest; in this postgenomic phase they are allowed to gain new insights into the molecular basis of cellular processes and the development of disease.

Surface Modification for DNA and Protein Microarrays

Microarrays of biomolecules are emerging as powerful tools for genomics, proteomics, and clinical assays, since they make it possible to screen biologically important binding events in a parallel and high throughput fashion. Because the microarrays are fabricated on a solid support, coating of the surface and immobilization strategy of the biomolecules are major issues for successful microarray fabrication. This review deals with both DNA microarrays and protein microarrays, and focuses on the various modification approaches for the two-dimensional surface materials and three-dimensional ones. In addition, the immobilization strategies including adsorption, covalent attachment, physical entrapment, and affinity attachment of the biomolecules are summarized, and advantage and limitation of representative efforts are discussed.

Magnetic Nanoparticles Applied in Electrochemical Detection of Controllable DNA Hybridization

Electrochemical detection of hybridized DNA strands was achieved with a magnetic nanoparticle modified electrode and the commonly used electrochemical couple K3[Fe(CN)6]/K4[Fe(CN)6]. The detection proved to be fast and very simple. Furthermore, magnetic nanoparticles could be employed to control the DNA hybridization process. An inhibited or an enhanced degree of hybridizing could be produced.

DNA recognition interfaces: the influence of interfacial design on the efficiency and kinetics of hybridization

The effect of the surface chemistry of DNA recognition interfaces on DNA hybridization at a gold surface was investigated using both electrochemistry and the quartz crystal microbalance (QCM) technique. Different DNA recognition interfaces were prepared using a two-component self-assembled monolayer consisting of thiolated 20-mer probe single-stranded DNA (ss-DNA) containing either a 3'-mercaptopropyl or a 3'-mercaptohexyl linker group and an alcohol-terminated diluent layer with 2-, 6-, or 11-carbon length. The influence of the interfacial design on the hybridization efficiency, the affinity constant (Ka) describing hybridization, and the kinetics of hybridization was assessed. It was found that the further the DNA was above the surface defined by the diluent layer the higher the hybridization efficiency and Ka. The kinetics of DNA hybridization was assessed using both a QCM and an electrochemical approach to ascertain the influence of the interface on both the initial binding of target DNA to the surface and the formation of a complete duplex. These measurements showed that the length of the diluent layer has a large impact on the time taken to form a perfect duplex but no impact on the initial recognition of the target DNA by the immobilized probe DNA.

Species differentiation by DNA-modified carbon electrodes using an ac impedimetric approach

A simple and novel electrochemical biosensor based approach is described for differentiating between differing species of fish on the basis of DNA hybridisation events. Screen-printed carbon electrodes modified with a variety of polymers were used to immobilise commercially available DNA in a single-stranded form. AC impedimetric measurements were firstly carried out on these systems and then upon exposure to single-stranded DNA solutions. When the electrode and solution DNA were complementary, a large drop in impedance was measured; this did not occur for non-matching DNA exposures. DNA hybridisation sensors for closely related species of fish were in the first instance developed as a demonstration for this approach. Species of fish such as herrings and salmon could be differentiated by this method. This sensor format offers great promise for many DNA hybridisation applications and lends itself to mass fabrication due to the simplicity and inexpensiveness of the materials and methods used. The hybridisation results were confirmed by use of ellipsometry to measure the characteristics of similar films deposited on silicon substrates.

Molecular biology and DNA microarray technology for microbial quality monitoring of water

Public concern over polluted water is a major environmental issue worldwide. Microbial contamination of water arguably represents the most significant risk to human health on a global scale. An important challenge in modern water microbial quality monitoring is the rapid, specific, and sensitive detection of microbial indicators and waterborne pathogens. Presently, microbial tests are based essentially on time-consuming culture methods. Rapid microbiological analyses and detection of rare events in water systems are important challenges in water safety assessment since culture methods present serious limitations from both quantitative and qualitative points of view. To circumvent lengthy culture methods, newer enzymatic, immunological, and genetic methods are being developed as an alternative. DNA microarray technology is a new and promising tool that allows the detection of several hundred or even thousands DNA sequences simultaneously. Recent advances in sample processing and DNA microarray technologies provide new perspectives to assess microbial water quality. The aims of this review are to (1) summarize what is currently known about microbial indicators, (2) describe the most important waterborne pathogens, (3) present molecular methods used to monitor the presence of pathogens in water, and (4) show the potential of DNA microarrays in water quality monitoring.

Fabrication of DNA microarrays on nanoengineered polymeric ultrathin film prepared by self-assembly of polyelectrolyte multilayers

Microarray-based technology is in need of flexible and cost-effective chemistry for fabrication of oligonucleotide microarrays. We have developed a novel method for the fabrication of oligonucleotide microarrays with unmodified oligonucleotide probes on nanoengineered three-dimensional thin films that are deposited on glass slides by consecutive layer-to-layer adsorption of polyelectrolytes. Unmodified oligonucleotide probes were spotted and immobilized on these multilayered polyelectrolyte thin films (PET) by electrostatic adsorption and entrapment on the porous structure of the PET film. The PET provides higher probe binding capacity and thus higher hybridization signal than that of the traditional two-dimensional aminosilane and poly-L-lysine coated slides. Immobilized probe densities of 3.4 x 10(12)/cm2 were observed for microarray spots on PET with unmodified 50-mer oligonucleotide probes, which is comparable to the immobilized probe densities of alkyamine-modified 50-mer probes end-tethered on an aldehyde-functionalized slide. The study of hybridization efficiency showed that 90% of immobilized probes on PET film are accessible to target DNA to form duplex format in hybridization. The DNA microarray fabricated on PET film has wider dynamic range (about 3 orders of magnitude) and lower detection limit (0.5 nM) than the conventional amino- and aldehyde-functionalized slides. Oligonucleotide microarrays fabricated on these PET-coated slides also had consistent spot morphology. In addition, discrimination of single nucleotide polymorphism of 16S rRNA genes was achieved with the PET-based oligonucleotide microarrays. The PET microarrays constructed by our self-assembly process is cost-effective, versatile, and well suited for immobilizing many types of biological active molecules so that a wide variety of microarray formats can be developed.

Label-free detection of microarrays of biomolecules by oblique-incidence reflectivity difference microscopy

We developed an oblique-incidence reflectivity difference (OI-RD) scanning microscope for label-free imaging of microarrays of biomolecules upon solid substrates. We demonstrate that hybridization reactions in an oligonucleotide microarray fabricated upon a glass slide can be detected by such an OI-RD microscope.

Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios

BACKGROUND

DNA microarrays are now routinely used to monitor the transcript levels of thousands of genes simultaneously. However, the array fabrication method, hybridization conditions, and oligodeoxyribonucleotide probe length can impact the performance of a DNA microarray platform.

RESULTS

We demonstrate solution-phase hybridization behavior of probe:target interactions by showing a strong correlation between the effect of mismatches in probes attached to a three dimensional matrix of a microarray and solution-based, thermodynamic duplex melting studies. The effects of mismatches in the probes attached to the microarray also demonstrate that most, if not all, of the oligodeoxyribonucleotide is available for hybridization. Kinetic parameters were also investigated. As anticipated, hybridization signals increased in a transcript concentration-dependent manner, and mismatch specificity increased with hybridization time. Unexpectedly, hybridization time increased the accuracy of fold changes by relieving the compression observed in expression ratios, and this effect may be more dramatic for larger fold changes.

CONCLUSIONS

Taken together, these studies demonstrate that a three-dimensional surface may enable use of shorter oligodeoxyribonucleotide probes and that hybridization time may be critical in improving the accuracy of microarray data.

Expression profiling with oligonucleotide arrays: technologies and applications for neurobiology

DNA microarrays have been used in applications ranging from the assignment of gene function to analytical uses in prognostics. However, the detection sensitivity, cross hybridization, and reproducibility of these arrays can affect experimental design and data interpretation. Moreover, several technologies are available for fabrication of oligonucleotide microarrays. We review these technologies and performance attributes and, with data sets generated from human brain RNA, present statistical tools and methods to analyze data quality and to mine and visualize the data. Our data show high reproducibility and should allow an investigator to discern biological and regional variability from differential expression. Although we have used brain RNA as a model system to illustrate some of these points, the oligonucleotide arrays and methods employed in this study can be used with cell lines, tissue sections, blood, and other fluids. To further demonstrate this point, we provide data generated from total RNA sample sizes of 200 ng.