DNA Biosensors and Microarrays

Prospects of Nanobiomaterials for Biosensing

Progress and development in biosensor development will inevitably focus upon the technology of the nanomaterials that offer promise to solve the biocompatibility and biofouling problems. The biosensors using smart nanomaterials have applications for rapid, specific, sensitive, inexpensive, in-field, on-line and/or real-time detection of pesticides, antibiotics, pathogens, toxins, proteins, microbes, plants, animals, foods, soil, air, and water. Thus, biosensors are excellent analytical tools for pollution monitoring, by which implementation of legislative provisions to safeguard our biosphere could be made effectively plausible. The current trends and challenges with nanomaterials for various applications will have focus biosensor development and miniaturization. All these growing areas will have a remarkable influence on the development of new ultrasensitive biosensing devices to resolve the severe pollution problems in the future that not only challenges the human health but also affects adversely other various comforts to living entities. This review paper summarizes recent progress in the development of biosensors by integrating functional biomolecules with different types of nanomaterials, including metallic nanoparticles, semiconductor nanoparticles, magnetic nanoparticles, inorganic/organic hybrid, dendrimers, and carbon nanotubes/graphene.

DNA detection using functionalized conducting polymers

A well-defined DNA bioconjugated surface is a key component in the development of efficient biosensor platforms for diseases, ranging from point-of-care detection of pathogens and viruses to personalized diagnostics and medication, as well as for drug discovery, forensics, and food technology. We herein describe a universal and rapid methodology to construct such surfaces based on functionalized conducting polymer thin films. The conducting polymers combine sensing properties with the ability to act as signal transducers for the biorecognition event. We have shown that biosensor designs based on conducting polymers display a number of advantageous features, such as a long-term stability, label-free sensing, fast analysis, and the capability to apply both electrochemical and fluorescent protocols for DNA detection.

Conjugation polymer nanobelts: a novel fluorescent sensing platform for nucleic acid detection

In this article, we report on the facile and rapid synthesis of conjugation polymer poly(p-phenylenediamine) nanobelts (PNs) via room temperature chemical oxidation polymerization of p-phenylenediamine monomers by ammonium persulfate in aqueous medium. We further demonstrate the proof-of-concept that PNs can be used as an effective fluorescent sensing platform for nucleic acid detection for the first time. The general concept used in this approach lies in the facts that the adsorption of the fluorescently labeled single-stranded DNA probe by PN leads to substantial fluorescence quenching, followed by specific hybridization with the complementary region of the target DNA sequence. This results in desorption of the hybridized complex from PN surface and subsequent recovery of fluorescence. We also show that the sensing platform described herein can be used for multiplexing detection of nucleic acid sequences.

Microfluidic DNA microarray analysis: a review

Microarray DNA hybridization techniques have been used widely from basic to applied molecular biology research. Generally, in a DNA microarray, different probe DNA molecules are immobilized on a solid support in groups and form an array of microspots. Then, hybridization to the microarray can be performed by applying sample DNA solutions in either the bulk or the microfluidic manner. Because the immobilized probe DNA binds and retains its complementary target DNA, detection is achieved through the read-out of the tagged markers on the sample target molecules. The recent microfluidic hybridization method shows the advantages of less sample usage and reduced incubation time. Here, sample solutions are confined in microfabricated channels and flow through the probe microarray area. The high surface-to-volume ratio in microchannels of nanolitre volume greatly enhanced the sensitivity as obtained with the bulk solution method. To generate nanolitre flows, different techniques have been developed, and this including electrokinetic control, vacuum suction and syringe pumping. The latter two are pressure-driven methods which are more flexible without the need of considering the physicochemical properties of solutions. Recently, centrifugal force is employed to drive liquid movement in microchannels. This method utilizes the body force from the liquid itself and there are no additional solution interface contacts such as from electrodes or syringes and tubing. Centrifugal force driven flow also features the ease of parallel hybridizations. In this review, we will summarize the recent advances in microfluidic microarray hybridization and compare the applications of various flow methods.

Hybridization efficiency of molecular beacons bound to gold nanowires: effect of surface coverage and target length

Surface-bound nucleic acid probes designed to adopt specific secondary structures are becoming increasingly important in a range of biosensing applications but remain less well characterized than traditional single-stranded probes, which are typically designed to avoid secondary structure. We report the hybridization efficiency for surface-immobilized hairpin DNA probes. Our probes are molecular beacons, carrying a 3' dye moiety and a 5' thiol for attachment to gold nanowires, which serve as both scaffolds for probe attachment and quenchers. Hybridization efficiency was dependent on probe surface coverage, reaching a maximum of ∼90% at intermediate coverages of (1-2) × 10(12) probes/cm(2) and dropping to ≤20% at higher or lower coverages. Fluorescence intensity did not track with the number of target molecules bound, and was highest for high probe coverage despite the lower bound targets per square centimeter. Backfilling with short thiolated oligoethylene glycol spacers increased hybridization efficiency at low hairpin probe coverages (∼(3-4) × 10(11) probes/cm(2)), but not at higher probe coverages (1 × 10(12)/cm(2)). We also evaluated the effect of target length by adding up to 50 nonhybridizing nucleotides to the 3' or 5' end of the complementary target sequence. Additional nucleotides on the 3' end of the complementary target sequence (i.e., the end near the nanowire surface) had a much greater impact on hybridization efficiency as compared to nucleotides added to the 5' end. This work provides guidance in designing sensors in which surface-bound probes designed to adopt secondary structures are used to detect target sequences from solution.

Silver ions-mediated conformational switch: facile design of structure-controllable nucleic acid probes

Conformationally constraint nucleic acid probes were usually designed by forming an intramolecular duplex based on Watson-Crick hydrogen bonds. The disadvantages of these approaches are the inflexibility and instability in complex environment of the Watson-Crick-based duplex. We report that this hydrogen bonding pattern can be replaced by metal-ligation between specific metal ions and the natural bases. To demonstrate the feasibility of this principle, two linear oligonucleotides and silver ions were examined as models for DNA hybridization assay and adenosine triphosphate detection. The both nucleic acids contain target binding sequences in the middle and cytosine (C)-rich sequences at the lateral portions. The strong interaction between Ag(+) ions and cytosines forms stable C-Ag(+)-C structures, which promises the oligonucleotides to form conformationally constraint formations. In the presence of its target, interaction between the loop sequences and the target unfolds the C-Ag(+)-C structures, and the corresponding probes unfolding can be detected by a change in their fluorescence emission. We discuss the thermodynamic and kinetic opportunities that are provided by using Ag(+) ion complexes instead of traditional Watson-Crick-based duplex. In particular, the intrinsic feature of the metal-ligation motif facilitates the design of functional nucleic acids probes by independently varying the concentration of Ag(+) ions in the medium.

Recent advancements in optical DNA biosensors: exploiting the plasmonic effects of metal nanoparticles

The emerging field of plasmonics, the study of electromagnetic responses of metal nanostructures, has revealed many novel signal enhancing phenomena. As applied to the development of label-free optical DNA biosensors, it is now well established that plasmon-based surface enhanced spectroscopies on nanostructured metal surfaces or metal nanoparticles can markedly improve the sensitivity of optical biosensors, with some showing great promise for single molecule detection. In this review, we first summarize the basic concepts of plasmonics in metal nanostructures, as well as the characteristic optical phenomena to which plasmons give rise. We will then describe recent advances in optical DNA biosensing systems enabled by metal nanoparticle-derived plasmonic effects, including the use of surface enhanced Raman scattering (SERS), colorimetric methods, "scanometric" processes, and metal-enhanced fluorescence (MEF).

Homogeneous assays using aptamers

Aptamers are DNA or RNA oligonucleotides that can bind with high affinity and specificity to a wide range of targets such as proteins, metal ions or pathogenic microorganisms. Soluble aptamers and aptazymes have been used as sensing elements for developing homogeneous assays in a solution phase, the whole sensing process being carried out in a homogeneous solution. Contrary to most conventional heterogeneous assays that are time-consuming and labor-intensive, aptamer-based homogeneous assays are simple, easy-to-perform, rapid and do not require immobilization nor washing steps. To our knowledge, this review is the first entirely dedicated to aptamer-based homogeneous assays. Optical detection appears as the most developed technique. Colorimetry represents the simplest sensing mode that occupies a very important position among aptamer-based assays, involving gold nanoparticle aggregation (with unmodified or aptamer-modified gold NPs), the formation of HRP-mimicking DNAzyme with hemin, dye displacement or interactions with a cationic polymer. Fluorescence that is highly sensitive offers the most developed detection mode. Aptamers can be labeled or not, to give rise to turn-on or usually less sensitive turn-off fluorescent assays. Newly reported and thus less developed non-conventional magnetic resonance imaging (MRI) and electrochemistry also recently appeared in the literature, thrombin still remains the main detected target. Homogeneous assays based on aptazyme, an aptamer sequence connected to a known ribozyme motif, are also described in this review, involving optical detection, by colorimetry or fluorescence.

Synthesis, DNA-binding and photocleavage of "light switch" complexes [Ru(bpy)2(pyip)]2+ and [Ru(phen)2(pyip)]2+

Two novel Ru(II) complexes [Ru(bpy)(2)(pyip)](2+)1 and [Ru(phen)(2)(pyip)](2+)2 (bpy=2,2'-bipyridine; phen=1,10-phenanthroline; pyip=2-(pyridine-2-yl)imidazo-[4,5-f][1,10]-phenanthroline), have been synthesized and characterized by elemental analysis, ES-MS, (1)H NMR, UV-Vis. The DNA-binding behaviors of both complexes were studied by spectroscopic methods and viscosity measurements. The results indicate that the two complexes can bind to CT-DNA in an intercalative mode, and also show that these two Ru(II) complexes can promote the photocleavage of pBR322 DNA. In addition, In the presence of Co(2+), the emission of DNA-[Ru(L)(2)pyip](2+) can be quenched, which exhibited the DNA "light switch" properties.

An electrostatic model for DNA surface hybridization

DNA hybridization at surfaces is a crucial process for biomolecular detection, genotyping, and gene expression analysis. However, hybridization density and kinetics can be strongly inhibited by electric fields from the negatively charged DNA as the reaction proceeds. Here, we develop an electrostatic model to optimize hybridization density and kinetics as a function of DNA surface density, salt concentrations, and applied voltages. The electrostatic repulsion from a DNA surface layer is calculated numerically and incorporated into a modified Langmuir scheme, allowing kinetic suppression of hybridization. At the low DNA probe densities typically used in assays (<10(13)/cm(2)), electrostatics effects are largely screened and hybridization is completed with fast kinetics. However, higher hybridization densities can be achieved at intermediate DNA surface densities, albeit with slower kinetics. The application of positive voltages circumvents issues resulting from the very high DNA probe density, allowing highly enhanced hybridization densities and accelerated kinetics, and validating recent experimental measurements.

Ultrasensitive nucleic acid biosensor based on enzyme-gold nanoparticle dual label and lateral flow strip biosensor

In this article, we describe an ultrasensitive nucleic acid biosensor (NAB) based on horseradish peroxidase (HRP)-gold nanoparticle (Au-NP) dual labels and lateral flow strip biosensor (LFSB). The results presented here expand on prior work (Mao et al., 2009a) by optimizing the preparation of HRP-Au-NP-DNA conjugates. It was found that sodium dodecyl sulfate (SDS) and the immobilization sequence of thiolated DNA and HRP on the Au-NP surface played very important roles to improve the sensitivity of the assay. After systematic optimization, the detection limit of current approach is 1000 times lower than that in prior work. Deposition of insoluble enzymatic catalytic product (red colored chromogen) on the captured Au-NPs at the test zone of LFSB offers a dramatic visual enhancement. Combining enzyme catalytic amplification with unique optical properties of Au-NPs, the NAB was capable of detecting of 0.01-pM target DNA without instrumentation. The NAB thus provides a rapid, sensitive, low-cost tool for the detection of nucleic acid samples. It shows great promise for in-field and point-of-care diagnosis of genetic diseases and for the detection of infectious agents.

DNA surface hybridization: comparison of theory and experiment

The design and interpretation of surface hybridization assays is complicated by poorly understood aspects of the interfacial environment that cause both kinetic and thermodynamic behaviors to deviate from those in solution. The origins of these differences lie in the additional interactions experienced by hybridizing strands at the surface. In this report, an analysis of surface hybridization equilibria is provided for end-tethered, single-stranded oligonucleotide "probes" hybridizing with similarly sized, single-stranded solution "target" molecules. Theoretical models by Vainrub and Pettitt (Phys. Rev. E 2002, 66, 041905) and by Halperin, Buhot, and Zhulina (Biophys. J. 2004, 86, 718), and an "extended" model that in addition includes a solution-like salt dependence of probe-target dimerization, are compared to experiments as a function of salt concentration and probe coverage. Good agreement with experiment is observed when the DNA volume fraction at the surface remains below approximately 0.25. None of the models, however, can account for strong suppression of hybridization when the volume fraction of DNA approaches 0.3, realizable in the limit of high buffer strength and densely tethered films. Under these conditions, hybridization yields become insensitive to increases in analyte concentration even though many probes remain available to bind targets. These observations are attributed to the onset of packing constraints which, interestingly, become limiting significantly below maximum DNA coverages estimated from ideally efficient hexagonal packing. By delineating conditions under which specific hybridization behaviors are observed, the results advance fundamental knowledge in support of DNA microarray and biosensor applications.

Effect of (L:D) Aspect Ratio on Single Polypyrrole Nanowire FET Device

Effect of different aspect ratio (length to diameter ratio, L:D) on single polypyrrole (Ppy) nanowire based field effect transistor (FET) sensor for real time pH monitoring was studied. Ppy nanowires with diameters of ~60, ~80 and ~200 nm were synthesized using electrochemical deposition inside anodized aluminium oxide (AAO) template and were assembled using AC dielectrophoretic alignment followed by maskless anchoring on a pair of gold electrodes separated with different gap lengths. Microfabricated gold electrode patterns with gap size between 1 - 4 μm were developed by means of MEMS technique (photolithography). Using field effect transistor geometry with pair of microfabricated gold contact electrodes serving as a source and a drain, and a platinum (Pt) mesh (anchored in a microfluidic channel) was used as a gate electrode. When effect of different aspect ratio of the nanowire were compared, higher sensitivity was recorded for higher aspect ratio. The sensitivity was further improved by modulating the gate potential. These FET sensors based on single polypyrrole nanowire exhibited excellent and tunable sensitivity towards pH variations.

Biomineralization-assisted ultrasensitive detection of DNA

The development of instrument-free, PCR-less, ultrasensitive and selective DNA detection methods is highly desired in chemical and life sciences. Herein we report on the utility of a biomineralization-assisted amplification methodology for the identification of DNA. Significantly, the diagnostic strategy has allowed the target detection at a concentration as low as 50 aM, equivalent to approximately 180 copies in the entire 6 microL sample. In addition, the DNA sequence with a single-base mismatch can be differentiated from the perfect target through a facile salt-based stringency wash. Substitution of the DNA structures with other recognition moieties should allow the translation of the strategy to the assay of different targets of interest. The visual readout format provides a sound basis for the broad applicability of the proposed strategy, especially in resource-poor settings.

Molecular mechanisms in morpholino-DNA surface hybridization

Synthetic nucleic acid mimics provide opportunity for redesigning the specificity and affinity of hybridization with natural DNA or RNA. Such redesign is of great interest for diagnostic applications where it can enhance the desired signal against a background of competing interactions. This report compares hybridization of DNA analyte strands with morpholinos (MOs), which are uncharged nucleic acid mimics, to the corresponding DNA-DNA case in solution and on surfaces. In solution, MO-DNA hybridization is found to be independent of counterion concentration, in contrast to DNA-DNA hybridization. On surfaces, when immobilized MO or DNA "probe" strands hybridize with complementary DNA "targets" from solution, both the MO-DNA and DNA-DNA processes depend on ionic strength but exhibit qualitatively different behaviors. At lower ionic strengths, MO-DNA surface hybridization exhibits hallmarks of kinetic limitations when separation between hybridized probe sites becomes comparable to target dimensions, whereas extents of DNA-DNA surface hybridization are instead consistent with limits imposed by buildup of surface (Donnan) potential. The two processes also fundamentally differ at high ionic strength, under conditions when electrostatic effects are weak. Here, variations in probe coverage have a much diminished impact on MO-DNA than on DNA-DNA hybridization for similarly crowded surface conditions. These various observations agree with a structural model of MO monolayers in which MO-DNA duplexes segregate to the buffer interface while unhybridized probes localize near the solid support. A general perspective is presented on using uncharged DNA analogues, which also include compounds such as peptide nucleic acids (PNA), in surface hybridization applications.

Increasing the sensitivity and single-base mismatch selectivity of the molecular beacon using graphene oxide as the "nanoquencher"

Here, we report a novel, highly sensitive, selective and economical molecular beacon using graphene oxide as the "nanoquencher". This novel molecular beacon system contains a hairpin-structured fluorophore-labeled oligonucleotide and a graphene oxide sheet. The strong interaction between hairpin-structured oligonucleotide and graphene oxide keep them in close proximity, facilitating the fluorescence quenching of the fluorophore by graphene oxide. In the presence of a complementary target DNA, the binding between hairpin-structured oligonucleotide and target DNA will disturb the interaction between hairpin-structured oligonucleotide and graphene oxide, and release the oligonucleotide from graphene oxide, resulting in restoration of fluorophore fluorescence. In the present study, we show that this novel graphene oxide quenched molecular beacon can be used to detect target DNA with higher sensitivity and single-base mismatch selectivity compared to the conventional molecular beacon.

Oligonucleotide microarrays with horseradish peroxidase-based detection for the identification of extended-spectrum β-lactamases

Production of extended-spectrum β-lactamases (ESBLs) is the one of most widespread and clinically significant mechanism of Enterobacteriaceae resistance towards modern β-lactam antibiotics. There are known 400 ESBLs, with the majority represented by the enzymes of TEM, SHV and CTX-M families. Oligonucleotide microarrays with colorimetric detection have been developed for the purposes of determination of ESBLs and inhibitor-resistant β-lactamases using horseradish peroxidase (HRP). Specific oligonucleotide probes have been designed for the identification of β-lactamase family and important SNPs responsible for the broadening of substrate specificity and tolerance to inhibitors. Multiplex PCR has been developed for simultaneous amplification and labeling of full-size genes of TEM-, SHV- and CTX-M-type β-lactamases with biotin. The labeled target DNA is then hybridized with specific oligonucleotide probes immobilized on a porous membrane support. After hybridization, biotin-labeled DNA duplexes are stained with the streptavidin-HRP conjugate detected colorimetrically. Design of oligonucleotide probes and optimization of hybridization conditions ensure the specificity of all control ESBLs identification. The newly developed method has been successfully used to identify bla(TEM), bla(SHV) and bla(CTX-M) genes in 90 clinical isolates of Enterobacteriaceae: 70% were found to carry bla(TEM), 50% bla(SHV), 50% bla(CTX-M); with the following distribution of CTX-M subclusters: 68% bla(CTX-M-1), 4% bla(CTX-M-2), and 14% bla(CTX-M-9). No ESBL of TEM-type and IRT phenotype assigned to TEM- or SHV-type β-lactamases had been detected; 24.6% of clinical samples show two types of ESBLs simultaneously. A mixture of CTX-M-1-like and SHV-5-like genes was the most abundant combination detected. Membrane microarray technique with colorimetric detection provides both high specificity and effectiveness of screening for ESBL- and IRT-producing samples.

Synthesis and application of a triazene-ferrocene modifier for immobilization and characterization of oligonucleotides at electrodes

A new DNA modifier containing triazene, ferrocene, and activated ester functionalities was synthesized and applied for electrochemical grafting and characterization of DNA at glassy carbon (GC) and gold electrodes. The modifier was synthesized from ferrocenecarboxylic acid by attaching a phenyltriazene derivative to one of the ferrocene Cp rings, while the other Cp ring containing the carboxylic acid was converted to an activated ester. The modifier was conjugated to an amine-modified DNA sequence. For immobilization of the conjugate at Au or GC electrodes, the triazene was activated by dimethyl sulfate for release of the diazonium salt. The salt was reductively converted to the aryl radical which was readily immobilized at the surface. DNA grafted onto electrodes exhibited remarkable hybridization properties, as detected through a reversible shift in the redox potential of the Fc redox label upon repeated hybridization/denaturation procedures with a complementary target DNA sequence. By using a methylene blue (MB) labeled target DNA sequence the hybridization could also be followed through the MB redox potential. Electrochemical studies demonstrated that grafting through the triazene modifier can successfully compete with existing protocols for DNA immobilization through the commonly used alkanethiol linkers and diazonium salts. Furthermore, the triazene modifier provides a practical one-step immobilization procedure.

Investigation of immobilization of functionalized magnetic nanobeads in rolling circle amplified DNA coils

Immobilization characteristics for single-stranded oligonucleotide-functionalized magnetic beads with nominal sizes of 40, 80, 130, and 250 nm in rolling circle amplified (RCA) DNA coils is investigated by employing complex magnetization measurements, dynamic light scattering and fluorescence microscopy. It was found that larger beads in a polydisperse bead size distribution more easily immobilize in the RCA DNA coils than do smaller beads. This may be related to a higher oligonucleotide surface coverage for the larger beads. Furthermore, it was concluded that both bead size and oligonucleotide surface coverage determine whether beads immobilize to give isolated coils with beads or larger clusters of beads and coils. A small bead size and a low oligonucleotide surface coverage favor the first kind of immobilization behavior, whereas a large bead size and a high oligonucleotide surface coverage favor the other. The present findings could be used to optimize both size and surface functionalization of beads employed in substrate-free magnetic biosensors.