Nucleic Acid Analysis

Marine Delivery Vehicles: Molecular Components and Applications of Bacterial Extracellular Vesicles

In marine ecosystems, communication among microorganisms is crucial since the distance is significant if considered on a microbial scale. One of the ways to reduce this gap is through the production of extracellular vesicles, which can transport molecules to guarantee nutrients to the cells. Marine bacteria release extracellular vesicles (EVs), small membrane-bound structures of 40 nm to 1 µm diameter, into their surrounding environment. The vesicles contain various cellular compounds, including lipids, proteins, nucleic acids, and glycans. EVs may contribute to dissolved organic carbon, thus facilitating heterotroph growth. This review will focus on marine bacterial EVs, analyzing their structure, composition, functions, and applications.

Monitoring Various Bioactivities at the Molecular, Cellular, Tissue, and Organism Levels via Biological Lasers

The laser is considered one of the greatest inventions of the 20th century. Biolasers employ high signal-to-noise ratio lasing emission rather than regular fluorescence as the sensing signal, directional out-coupling of lasing and excellent biocompatibility. Meanwhile, biolasers can also be micro-sized or smaller lasers with embedded/integrated biological materials. This article presents the progress in biolasers, focusing on the work done over the past years, including the molecular, cellular, tissue, and organism levels. Furthermore, biolasers have been utilized and explored for broad applications in biosensing, labeling, tracking, bioimaging, and biomedical development due to a number of unique advantages. Finally, we provide the possible directions of biolasers and their applications in the future.

A microfluidic chip for rapid analysis of DNA melting curves for BRCA2 mutation screening

A microfluidic chip integrated with a microheater and a luminescent temperature sensor for rapid, spatial melting curve analysis was developed and applied for the screening of a breast cancer gene fragment. The method could detect genetic differences in around 3 minutes total for the whole procedure, which is much faster than established procedures. A microfabrication technique was developed to allow for bonding of a temperature sensing thin film and a Pt microheater with PDMS and the chips could be employed to generate and measure thermal gradients and the fluorescence intensity of stained DNA through multispectral optical imaging. The sensing layer consisting of poly(styrene-co-acrylonitrile) and a tris(1,10-phenanthroline)ruthenium(ii) temperature probe was generated by blade coating on a glass substrate with an attached Pt microheater. Calibration of the temperature between 20 and 90 °C yielded an overall resolution of around 0.13 K. The chip was employed for the screening of the BRCA 2 breast cancer gene; BRCA2 exon 5 was differentiated by its mutant rs80359463 by a 1.1 K difference in melting temperature and two fragments of BRCA2 exon 11 were differentiated by their mutants rs276174826 and rs876660311 by 0.7 K and 2.0 K, respectively. The standard deviations were between 0.1 and 0.5 K. Capable of detecting fluorescence in the DNA and temperature simultaneously and being imaged in a customized assembly, this microchip can be used to screen for mutations in a variety of DNA samples in disease diagnosis and prognosis.

Digital DNA detection based on a compact optofluidic laser with ultra-low sample consumption

DNA lasers self-amplify optical signals from a DNA analyte as well as thermodynamic differences between sequences, allowing quasi-digital DNA detection. However, these systems have drawbacks, such as relatively large sample consumption and complicated dye labelling. Moreover, although the lasing signal can detect the target DNA, it is superimposed on an unintended fluorescence background, which persists for non-target DNA samples as well. From an optical point of view, it is thus not truly digital detection and requires spectral analysis to identify the target. In this work, we propose and demonstrate an optofluidic laser that has a single layer of DNA molecules as the gain material. A target DNA produces intensive laser emission comparable to existing DNA lasers, while any unnecessary fluorescence background is successfully suppressed. As a result, the target DNA can be detected with a single laser pulse, in a truly digital manner. Since the DNA molecules cover only a single layer on the surface of the laser microcavity, the DNA sample consumption is a few orders of magnitude lower than that of existing DNA lasers. Furthermore, the DNA molecules are stained by simply immersing the microcavity in the intercalating dye solution, and thus the proposed DNA laser is free of any complex dye-labelling process prior to analysis.

Nanoprobe-Initiated Enzymatic Polymerization for Highly Sensitive Electrochemical DNA Detection

Electrochemical DNA (E-DNA) sensors have been greatly developed and play an important role in early diagnosis of different diseases. To determine the extremely low abundance of DNA biomarkers in clinical samples, scientists are making unremitting efforts toward achieving highly sensitive and selective E-DNA sensors. Here, a novel E-DNA sensor was developed taking advantage of the signal amplification efficiency of nanoprobe-initiated enzymatic polymerization (NIEP). In the NIEP based E-DNA sensor, the capture probe DNA was thiolated at its 3'-terminal to be immobilized onto gold electrode, and the nanoprobe was fabricated by 5'-thiol-terminated signal probe DNA conjugated gold nanoparticles (AuNPs). Both of the probes could simultaneously hybridize with the target DNA to form a "sandwich" structure followed by the terminal deoxynucleotidyl transferase (TdT)-catalyzed elongation of the free 3'-terminal of DNA on the nanoprobe. During the DNA elongation, biotin labels were incorporated into the NIEP-generated long single-stranded DNA (ssDNA) tentacles, leading to specific binding of avidin modified horseradish peroxidase (Av-HRP). Since there are hundreds of DNA probes on the nanoprobe, one hybridization event would generate hundreds of long ssDNA tentacles, resulting in tens of thousands of HRP catalyzed reduction of hydrogen peroxide and sharply increasing electrochemical signals. By employing nanoprobe and TdT, it is demonstrated that the NIEP amplified E-DNA sensor has a detection limit of 10 fM and excellent differentiation ability for even single-base mismatch.

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.

Trinity DNA detection platform by ultrasmooth and functionalized PEDOT biointerfaces

An oligonucleotide-grafted poly(3,4-ethylenedioxythiophene) (PEDOT) thin film is developed for three DNA biosensor detection methods, including fluorescence, quartz crystal microbalance, and electrochemical methods. By electrocopolymerization of hydroxyl-functionalized EDOT and carboxylic-functionalized EDOT in microemulsion solutions, ultrasmooth films with a controlled surface density of carboxylic groups are created. The probe oligonucleotides are immobilized on PEDOT thin films by using a N-hydroxysuccinimide and 1-ethyl-3-[3-(dimethylamino)propyl]carbodiimide hydrochloride coupling method. By monitoring the DNA hybridization efficiency on thin films with different oligonucleotide densities, the optimized density for DNA hybridization is obtained. The feasibility and limitation of using this platform for electrochemical detection are also discussed.

Molecular beacon-functionalized gold nanoparticles as probes in dry-reagent strip biosensor for DNA analysis

The highly specific molecule recognition properties of molecular beacons (MB) are combined with the unique optical properties of gold nanoparticles (Au-NPs) for the development of a dry-reagent strip-type nucleic acid biosensor (DSNAB) that enables sensitive and low-cost detection of nucleic acid samples within 15 min.

Label-free detection of DNA hybridization at a liquid|liquid interface

A novel electrochemical approach for label-free detection of DNA primary sequence has been proposed. The flow of nonelectroactive ions across a liquid|liquid interface was used as an electrochemical probe for detection of DNA hybridization. Disposable graphite screen-printed electrodes shielded with a thin layer of inert polymer plasticized with water-immiscible polar organic solvent were modified by probe oligonucleotide and used as a DNA sensor. The specific DNA coupling has been detected with impedance spectroscopy by decrease of ion-transfer resistance. The detection limit was of 10-8 M of target oligonucleotide. The reported sensor was suitable for discrimination of a single mismatch oligonucleotide from the full complementary one. The reported DNA sensor was advantageous over known physicochemical approaches, providing the most significant changes in the measured parameters.

Quadruple-analyte chemiluminometric hybridization assay. Application to double quantitative competitive polymerase chain reaction

We developed a highly sensitive quadruple-analyte chemiluminometric hybridization assay for simultaneous quantification of four nucleic acid sequences. The targets are amplified by the polymerase chain reaction (PCR) and captured to microtiter wells coated with streptavidin. The immobilized fragments are hybridized with specific probes containing a sequence complementary to the target and a sequence or a hapten that allows linkage with a chemiluminescent reporter. We prepared a mixture of four reporters conjugated to complementary oligonucleotides or antihapten antibodies. The reporters were aequorin-(dT)(30), galactosidase-oligonucleotide, horseradish peroxidase-antifluorescein, and alkaline phosphatase-antidigoxigenin conjugates. The four chemiluminescent reactions were triggered sequentially. The signals were linearly related to the concentration of target sequences. The entire quadruple-analyte bioluminometric hybridization assay is complete in 75 min. We have demonstrated the applicability of the proposed assay to high-throughput quantitative competitive PCR of two target sequences in the presence of the corresponding competitors. The assay is universal since the same reporter conjugates can be used for multianalyte quantification of any sequences with properly designed probes.

Nanopore sensor for fast label-free detection of short double-stranded DNAs

Functionalizing surface enhanced the molecular sensing ability of a fabricated nanopore by increasing the translocation duration time for a short double-stranded DNA. The surface of nanopore was derivatized with gamma-aminopropyltriethoxysilane and the positively charged surface attracted DNA molecules when they were in the vicinity of nanopore. The translocation duration time of DNA increased due to the strong electrostatic interaction and it enabled us to detect a short double-stranded DNA (<1 kbp) that is under the size limit of a conventional solid state nanopore sensor. Both 539 and 910 bp double-stranded DNAs were analyzed with the surface functionalized nanopore and their translocation kinetics are presented in this work. The new feature of the surface modified nanopore that can detect short double-stranded DNA molecules could readily be applied for a rapid label-free diagnostic analysis in a Lab-On-a-Chip type DNA sensor.

Electronic deoxyribonucleic acid (DNA) microarray detection of viable pathogenic Escherichia coli, Vibrio cholerae, and Salmonella typhi

An electronic deoxyribonucleic acid (DNA) microarray technique was developed for detection and identification of viable Escherichia coli O157:H7, Vibrio cholerae O1, and Salmonella typhi. Four unique genes, the E. coli O157 lipopolysaccharide (LPS) gene (rfbE) and H7 flagellin gene (fliC), the V. cholerae O1 LPS gene (rfbE), and the S. typhi LPS gene (tyv), were chosen as the targets for detection. These targets were selectively amplified from mRNA of viable cells using reverse transcription polymerase chain reaction (RT-PCR) and detected using the electronic DNA microarray technique. Specific captures and reporters were designed and examined for selective detection and correct identification of the target pathogens. The technique was able to detect as few as 2-150 cells of E. coli O157:H7. The co-presence of six other common bacteria and a parasite at 10- and 1000-fold higher concentrations than the target E. coli O157:H7 did not interfere with the specific detection. Comparative analysis of live and heat-killed E. coli O157:H7 cells showed that the technique only responded to the viable cells and not to the dead cells. Thus, the integration of RT-PCR of specific mRNA with the electronic DNA microarray technique enables specific and sensitive detection of viable target cells. This technique is potentially useful for high throughput screening of multiple pathogenic bacteria in different samples.

Direct Detection of DNA with an Electrocatalytic Threading Intercalator

Herein we report the synthesis, intercalating properties, and analytical applications of an imidazole-substituted naphthalene diimide, N,N'-bis(3-propylimidazole)-1,4,5,8-naphthalene diimide (PIND), functionalized with electrocatalytic redox moieties. PIND was prepared in a single-step reaction from the corresponding dianhydride. Attachment of the redox moieties to PIND relied upon ligand exchange with one of the liable chloride ligands of an Os(bpy)2Cl2 (bpy = 2,2'-bipyridine) complex. The Os(bpy)2Cl2 complex was grafted onto PIND through coordinative bonds with the two imidazole groups at its termini, forming a PIND-[Os(bpy)2Cl]+ compound (PIND-Os). Gel electrophoretic studies revealed that PIND-Os binds more strongly to double-stranded DNA (ds-DNA) than its parent compound 1,4,5,8-naphthalene diimide. The naphthalene diimide group binds to ds-DNA in a "classical" threading intercalation mode, while the two Os(bpy)2Cl+ pendants interact with DNA via electrostatic interaction, reinforcing the intercalation by "locking up" the naphthalene diimide group in place. An electrochemical biosensor was fabricated using the redox-active and catalytic PIND-Os intercalator. An increase in sensitivity of 2500-fold over direct voltammetry was obtained in electrocatalytic amperometry, making this an interesting system for amperometric DNA sensing. Under optimized experimental conditions, the biosensor allowed the detection of a 50-mer target DNA in the range of 1.0-300 pM with a detection limit of 600 fM (1.5 amol, 23 fg).

Amperometric detection of nucleic acid at femtomolar levels with a nucleic acid/electrochemical activator bilayer on gold electrode

Cationic redox polymers containing osmium-bipyridine complexes strongly interact with anionic enzymes, such as glucose oxidase and peroxidases, and electrochemically "activate" the enzymes. On the basis of these observations, attempts were made to develop an ultrasensitive nucleic acid biosensor. A mixed monolayer of single-stranded oligonucleotide capture probe and 16-mercaptohexadecanoic acid was formed on a gold electrode through self-assembly. Following hybridization with a complementary nucleic acid and glucose oxidase labeled oligonucleotide detection probe, a cationic redox polymer (electrochemical activator) overcoating was applied to the electrode through layer-by-layer electrostatic self-assembly. The formation of an anionic-cationic bilayer brought the glucose oxidase in electrical contact with the redox polymer, making the bilayer an electrocatalyst for the oxidation of glucose. Thus, nucleic acid molecules were quantified amperometrically at femtomolar levels. The effect of experimental variables on the amperometric response was investigated and optimized to maximize the sensitivity and speed up the assay time. A detection limit of 1.0 fmol/L in 1.0-microL droplets and a linear current-concentration relationship up to 800 fmol/L were attained following a 30-min hybridization. The biosensor was applied to the detection of the 16S gene in a mixture of Escherichia coli 16S + 32S rRNA and a full-length rat housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), of a RT-PCR product.

Synthesis and hybridization properties of oligonucleotide-perylene conjugates: influence of the conjugation parameters on triplex and duplex stabilities

We report here the synthesis of oligo-2'-deoxyribonucleotides (ODNs) conjugated with perylene. Introduction of perylene, coupled either directly or via a propyl linker to the anomeric position of a 2'-deoxyribose residue, induces the formation of two anomers. Single incorporations of each pure anomer of these sugar-perylene units have been performed at either the 5'-end or an internal position of a pyrimidic pentadecamer. The binding properties of these modified ODNs with their single- and double-stranded DNA targets were studied by absorption spectroscopy. Double incorporations of the sugar-perylene unit most efficient at stabilizing the triplex and duplex structures (the beta-anomer involving the propyl linker) have been performed at both the 5'-end and at an internal position (or both the 5'- and 3'-ends) of the ODN chain. Comparison has been made with ODN-perylene conjugates involving either one or two perylenes attached via a longer polymethylene chain to either the 5'- or 3'- (or both the 5'-and 3'-) terminal phosphate groups. The ODNs involving two perylenes are more efficient at stabilizing the triplex and the duplex structures than the ODNs involving only one perylene and, among these, the ODN-perylene conjugate involving two sugar-perylene units attached at both termini is the most efficient. The results of the fluorescence studies have shown an important increase in the intensity of the fluorescent signal upon hybridization of the ODNs involving two perylenes with either the single- or the double-stranded targets. This increase in the intensity of the fluorescent signal could be used as proof of the hybridization.

Electrical frequency dependent characterization of DNA hybridization

The hybridization of oligomeric DNA was investigated using the frequency dependent techniques of electrochemical impedance spectroscopy (EIS) and quartz crystal microgravimetry (QCM). Synthetic 5'-amino terminated single stranded oligonucleotides (ssDNA) were attached to the exposed glass surface between the digits of microlithographically fabricated interdigitated microsensor electrodes using 3-glycidoxypropyl-trimethoxysilane. Similar ssDNA immobilization was achieved to the surface of the gold driving electrodes of AT-cut quartz QCM crystals using 3-mercaptopropyl-trimethoxysilane. Significant changes in electrochemical impedance values (both real and imaginary components) (11% increase in impedance modulus at 120 Hz) and resonant frequency values (0.004% decrease) were detected as a consequence of hybridization of the bound ssDNA upon exposure to its complement under hybridization conditions. Non-complementary (random) sequence sowed a modest decrease in impedance and a non-detectable change in resonant frequency. The possibility to detect the binding state of DNA in the vicinity of an electrode, without a direct connection between the measurement electrode and the DNA, has been demonstrated. The potential for development of label-free, low density DNA microarrays is demonstrated and is being pursued.

Frequency dependent and surface characterization of DNA immobilization and hybridization

The hybridization of oligomeric DNA was investigated using the frequency dependent techniques of quartz crystal microbalance (QCM) and electrochemical impedance spectroscopy (EIS). Synthetic 5'-amine-terminated single stranded oligonucleotides (ssDNA) were immobilized on the surface of the oxidized platinum driving electrodes of AT-cut quartz QCM crystals using 3-glycidoxypropyl-trimethoxysilane. Similar ssDNA coupling was accomplished on the exposed glass surface between the metallic digits of microlithographically fabricated interdigitated microsensor electrodes (IMEs). Confirmation of this covalent coupling surface chemistry was achieved using Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR). Substantial changes in resonant frequency values (0.012% decrease) and electrochemical impedance values (both real and imaginary components) (35.4 and 42.1% increase in impedance magnitude at 1.0 Hz in buffer and deionized water, respectively) were observed resulting from hybridization of the attached ssDNA upon exposure to its complement under appropriate hybridization conditions. Non-complementary (random) oligomer sequence demonstrated a modest change in resonant frequency and a non-detectable change in impedance. Microarray glass slide surfaces modified with 3-glycidoxypropyltrimethoxysilane (GPS), shown to be advantageous in the design and use of microarrays of amine-terminated ssDNA, is confirmed to arise from direct covalent coupling of the DNA to the surface with little non-specific adsorption. The possibility to detect the binding state of DNA in the vicinity of an electrode, without a direct connection between the measurement electrode and the DNA is hereby reported. The potential for development of label-free, low-density DNA microarrays is demonstrated and is being pursued.

A Robust Technique for Assembly of Nucleic Acid Hybridization Chips Based on Electrochemically Templated Chitosan

A nucleic acid hybridization assay was assembled onto a robust and readily addressable silicon-based chip using polysaccharide chitosan as a scaffold for the covalent coupling of probe DNA to the chip's surface. Chitosan is a unique polymer, ideally suited for this application because its net charge and solubility are pH dependent. Specifically in this work, gold-patterned electrodes were created using standard photolithographic techniques, chitosan was electrodeposited in a spatially resolved manner onto the polarized electrodes, probe DNA was covalently assembled onto the chitosan, and both DNA:DNA and DNA:mRNA hybridization detection schemes were evaluated. Hybridization of target nucleic acid was quantifiable, reproducible, and robust; the surface was regenerated and rehybridized up to eight times without loss of signal. Finally, transcriptional upregulation of the Escherichia coli chaperone, DnaK, which is an indicator of cellular stress, was observed using the hybridization chip sandwich assay. Thus, this method enables rapid and facile monitoring of gene expression in a format that is reusable and requires minimal reagent quantities.

Affinity capture-facilitated preparation of aequorin- oligonucleotide conjugates for rapid hybridization assays

We report a general procedure for the preparation of biomolecular conjugates that combine the molecular recognition properties of oligonucleotides with the high detectability of the photoprotein aequorin. Central to the conjugation protocols is the use of recombinant aequorin fused to a hexahistidine tag. In one protocol, an amino-modified oligonucleotide was treated with a homobifunctional cross-linker carrying two N-hydroxysuccinimide ester groups, and the derivative was allowed to react with (His)(6)-aequorin. A second strategy involved the introduction of protected sulfhydryl groups into (His)(6)-aequorin and subsequent reaction with a heterobifunctional linker containing a N-hydroxysuccinimide and a maleimide group. The strong, but reversible, binding of (His)(6)-aequorin to Ni(2+)-nitrilotriacetic acid agarose enabled the rapid and effective removal of the unreacted oligonucleotide, which otherwise diminishes the performance of the hybridization assay by competing with the conjugate for the complementary target sequence. Aequorin-oligo conjugates prepared by affinity capture showed similar performance with those purified by anion-exchange HPLC. The conjugates were applied to the development of rapid bioluminometric hybridization assays. The analytical range extended from 2 to 2000 pmol/L of target DNA. The reproducibility was less than 10%. The conjugate obtained from a reaction of 10 nmol of (His)(6)-aequorin is sufficient for about 5000 hybridization assays. The proposed conjugation strategy is general because a variety of reporter proteins can be fused to hexahistidine tag by using suitable vectors that are commercially available.

Multiplexed DNA quantification by spectroscopic shift of two microsphere cavities

We have developed a novel, spectroscopic technique for high-sensitivity, label-free DNA quantification. We demonstrate that an optical resonance (whispering gallery mode) excited in a micron-sized silica sphere can be used to detect and measure nucleic acids. The surface of the silica sphere is chemically modified with oligonucleotides. We show that hybridization to the target DNA leads to a red shift of the optical resonance wavelength. The sensitivity of this resonant technique is measured as 6 pg/mm(2) mass loading, higher as compared to most optical single-pass devices such as surface plasmon resonance biosensors. Furthermore, we show that each microsphere can be identified by its unique resonance wavelength. Specific, multiplexed DNA detection is demonstrated by using two microspheres. The multiplexed signal from two microspheres allows us to discriminate a single nucleotide mismatch in an 11-mer oligonucleotide with a high signal-to-noise ratio of 54. This all-photonic whispering gallery mode biosensor can be integrated on a semiconductor chip that makes it an easy to manufacture, analytic component for a portable, robust lab-on-a-chip device.

Electrochemical transducers based on surfactant bilayers for the direct detection of affinity interactions

The simple methods for the preparing of direct affinity sensors are proposed. The proposed method consists of the immobilizations of either oligonucleotide or antibodies as recognizing elements onto the surfactant bilayer. For DNA-sensor we propose to immobilize oligonucleotide by spontaneous infiltration of hydrocarbon chain bound to oligonucleotide pentadecathymidylate (dT(15)) into the hydrophobic region of surfactant bilayer. The adsorption of antibodies on bilayer surface has resulted in immunosensor development. The direct detection of affinity interactions in both cases has been investigated by impedance spectroscopy. At both studies the significant changes in impedance spectra have observed. The dynamics of response manifestation have been followed the specific DNA-coupling causing the decrease of real part of impedance, whereas the antibody-antigen interaction caused the increase of real part. The obtained results are promising for the development of impedimetric affinity sensors for clinical or environmental applications.

Oligonucleotide-Functionalized Gold Nanoparticles as Probes in a Dry-Reagent Strip Biosensor for DNA Analysis by Hybridization

The highly specific molecular recognition properties of oligonucleotides are combined with the unique optical properties of gold nanoparticles for the development of a dry-reagent strip-type biosensor that enables visual detection of double stranded DNA within minutes. The assay does not require instrumentation and avoids the multiple incubation and washing steps performed in most current assays. Gold nanoparticle reporters with oligo(dT) attached to their surface form an integral part of the strip. Biotinylated PCR products (233 bp or 495 bp) are hybridized (5 min) with a poly(dA)-tailed oligo and applied on the strip, which is then immersed in the appropriate buffer. As the buffer migrates upward, it rehydrates the nanoparticles that are linked to the target DNA through poly(dA)/(dT) hybridization. Capture of the hybrids by immobilized streptavidin in the test zone of the strip generates a characteristic red band. A second red band is formed, by hybridization, in the control zone of the strip to indicate proper test performance. The sensor offers at least 8 times higher detectability than ethidium bromide staining of agarose gels and provides confirmation of the amplified fragments. Quantitative data are obtained by densitometric analysis of the bands. As low as 2 fmol of amplified DNA were detectable by the strip sensor. Also, 500 copies of prostate-specific antigen cDNA were detected by combining PCR and the strip sensor. The sensor was used successfully for detection of hepatitis C virus in plasma samples from 20 patients. The strip detected 16 out of 16 positive samples and gave no signal for 4 samples that were negative for the virus. To our knowledge, this is the first dry-reagent system that makes use of oligonucleotide-conjugated gold nanoparticles as probes.

Microfabricated device for DNA and RNA amplification by continuous-flow polymerase chain reaction and reverse transcription-polymerase chain reaction with cycle number selection

We have developed a high-throughput microfabricated, reusable glass chip for the functional integration of reverse transcription (RT) and polymerase chain reaction (PCR) in a continuous-flow mode. The chip allows for selection of the number of amplification cycles. A single microchannel network was etched that defines four distinct zones, one for RT and three for PCR (denaturation, annealing, extension). The zone temperatures were controlled by placing the chip over four heating blocks. Samples and reagents for RT and PCR were pumped continuously through appropriate access holes. Outlet channels were etched after cycles 20, 25, 30, 35, and 40 for product collection. The surface-to-volume ratio for the PCR channel is 57 mm(-1) and the channel depth is 55 microm, both of which allow very rapid heat transfer. As a result, we were able to collect PCR product after 30 amplification cycles in only 6 min. Products were collected in 0.2-mL tubes and analyzed by agarose gel electrophoresis and ethidium bromide staining. We studied DNA and RNA amplification as a function of cycle number. The effect of the number of the initial DNA and RNA input molecules was studied in the range of 2.5 x 10(6) - 1.6 x 10(8) and 6.2 x 10(6) - 2 x 10(8), respectively. Successful amplification of a single-copy gene (beta-globin) from human genomic DNA was carried out. Furthermore, PCR was performed on three samples of DNA of different lengths (each of 2-microL reaction volume) flowing simultaneously in the chip, and the products were collected after various numbers of cycles. Reverse transcription was also carried out on four RNA samples (0.7-microL reaction volume) flowing simultaneously in the chip, followed by PCR amplification. Finally, we have demonstrated the concept of manually pumped injection and transport of the reaction mixture in continuous-flow PCR for the rapid generation of amplification products with minimal instrumentation. To our knowledge, this is the first report of a monolithic microdevice that integrates continuous-flow RT and PCR with cycle number selection.

Comparison of the separation of large DNA fragments in the presence and absence of electroosmotic flow at high pH

This paper describes the analysis of large DNA fragments at pH > 10.0 by capillary electrophoresis (CE) in the presence of electroosmotic flow (EOF) using hydroxyethylcellulose (HEC) solution. HEC solution in the anodic reservoir enters the capillaries filled with high-pH buffer by EOF after sample injection. With respect to resolution, sensitivity, and speed, separation conducted under discontinuous conditions (different pH values of HEC solutions and buffer filling the capillary) is appropriate. Using HEC solution at concentrations higher than its entanglement threshold ensures a good separation of large DNA fragments in the presence of EOF at high pH. In addition to pH and HEC, the electrolyte species, dimethylamine, methylamine, and piperidine, play different roles in determining the resolution. The separation of DNA fragments ranging in size from 5 to 40 kilo base pairs was completed in 6 min using 1.5% HEC prepared in 20 mM methylamine-borate, pH 12.0, and the capillary filled with 40 mM dimethylamine-borate, pH 10.0. In comparison, this method allows faster separations of large DNA fragments compared with that conducted in the absence of EOF using dilute HEC solutions.

Recombinant Gaussia luciferase. Overexpression, purification, and analytical application of a bioluminescent reporter for DNA hybridization

The cDNA for Gaussia luciferase (GLuc), the enzyme responsible for the bioluminescent reaction of the marine copepod Gaussia princeps, has been cloned recently. GLuc (MW = 19 900) catalyzes the oxidative decarboxylation of coelenterazine to produce coelenteramide and light. We report the first quantitative anaytical study of GLuc and examine its potential as a new reporter for DNA hybridization. A plasmid encoding both a biotin acceptor peptide-GLuc fusion protein as well as the enzyme biotin protein ligase (BPL) is engineered by using GLuc cDNA as a starting template. BPL catalyzes the covalent attachment of a single biotin to the fusion protein in vivo. Purification of GLuc is then accomplished by affinity chromatography using immobilized monomeric avidin. Moreover, the in vivo biotinylation enables subsequent complexation of GLuc with streptavidin (SA), thereby avoiding chemical conjugation reactions that are known to inactivate luciferases. Purified GLuc can be detected down to 1 amol with a signal-to-background ratio of 2 and a linear range extending over 5 orders of magnitude. The background luminescence of coelenterazine is the main limiting factor for even higher detectability of GLuc. Furthermore, the GLuc-SA complex is used as a detection reagent in a microtiter well-based DNA hybridization assay. The analytical range extends from 1.6 to 800 pmol/L of target DNA. Biotinylated GLuc produced from 1 L of bacterial culture is sufficient for 150,000 hybridization assays.

Voltammetric determination of underivatized oligonucleotides on graphite electrodes based on their oxidation products

A new electrochemical method to determine underivatized oligonucleotides is developed. The electro-oxidation of the adenine moieties of adsorbed oligonucleotides at elevated potentials on pyrolytic graphite electrodes (PGE) in neutral or alkaline media gives rise to electroactive products strongly adsorbed on the electrode surface. The extent of the redox processes of these products, with formal potential close to 0 V (vs Ag /AgCl) at pH 10, correlates well with the amount of parent oligonucleotide. Various electrochemical techniques have been compared and applied to the detection of specific DNA sequences and synthetic homopolynucleotides. Detection limits of 2 and 10 ng for (dA)20 and a 21-mer sequence of HIV-1, respectively, have been achieved using sample volumes of 10 microL. Moreover, the adsorbed oxidized oligonucleotide shows electrocatalytic activity toward the oxidation of NADH. The capability of the new method to detect DNA hybridization is discussed.

Classical dot-blot format implemented as an amperometric hybridisation genosensor

A new electrochemical hybridisation genosensor has been designed. This genosensor is based on a concept adapted from classical dot-blot DNA analysis, but implemented in an electrochemical biosensor configuration. The use of amperometric transduction and the enzyme label method--that increases the genosensor sensitivity--are the main features of this new approach. The analytical procedure consists of five steps: DNA target immobilisation by adsorption onto a nylon membrane, hybridisation between DNA target and biotin-DNA probe, complexation reaction between biotin-DNA probe and an enzyme (horseradish peroxidase) streptavidin conjugate; integration of the modified membrane onto an electrochemical transducer; and finally, amperometric detection using a suitable substrate for the enzyme labelled duplex. Besides the adapted dot-blot format, a competitive assay in which the target is in solution is reported as well. This procedure, based on amperometric transduction, represents certain advantages with respect to dot-blot analysis: labelled hybrid detection is far simpler, quicker and requires more ordinary or simple reactives; the response obtained is a direct analytical signal via low-cost instrumentation, a nonisotopic labelling is used, and the membranes can be reused. These characteristics are ideal in implementing the procedure developed in kit form.

Enzyme-modulated cleavage of dsDNA for supramolecular design of biosensors

Supramolecular docking and immobilization of biotinylated dsDNA onto a self-assembled monolayer of avidin have been measured using impedance spectroscopy and quartz crystal microbalance technique. The formation of the serial assembly was first achieved by linearizing circular plasmid dsDNA using BamH I endonuclease enzyme. This was followed by a bisulfite-catalyzed transamination reaction in order to biotinylate the dsDNA. The reaction is single-strand specific, and it specifically targets unpaired cytosine bases generated during the enzyme cleavage. The biotinylated dsDNA was then used as a ligand at a gold electrode containing avidin. The process was monitored by ac impedance spectroscopy that was used to probe the changes in interfacial electron-transfer resistance upon binding and a microgravimetric quartz crystal microbalance that reflected in situ mass changes on the dsDNA-functionalized substrates. Our results demonstrated that this approach could be employed for the determination of small-molecular-weight organics such as cisplatin, daunomycin, bisphenol A, chlorinated phenols, and ethidium bromide. A detection limit in the magnitude of ca. 10 nM was achieved. This immobilization technique provides a generic approach for dsDNA-based sensor development and for the monitoring of DNA-analyte interactions.

Recent advances in DNA sequencing by capillary and microdevice electrophoresis

A number of significant improvements in the electrophoretic performance and design of DNA sequencing devices have culminated in the introduction of truly industrial grade production scale instruments. These instruments have been the workhorses behind the massive increase in genomic sequencing data available in public and private databases. We highlight the recent progress in aspects of capillary electrophoresis (CE) that has enabled these achievements. In addition, we summarize recent developments in the use of microfabricated devices for DNA sequencing that promise to bring the next leap in productivity.

Gold nanoparticle-based quantitative electrochemical detection of amplified human cytomegalovirus DNA using disposable microband electrodes

An electrochemical DNA detection method has been developed for the sensitive quantification of an amplified 406-base pair human cytomegalovirus DNA sequence (HCMV DNA). The assay relies on (i) the hybridization of the single-stranded target HCMV DNA with an oligonucleotide-modified Au nanoparticle probe, (ii) followed by the release of the gold metal atoms anchored on the hybrids by oxidative metal dissolution, and (iii) the indirect determination of the solubilized AuIII ions by anodic stripping voltammetry at a sandwich-type screen-printed microband electrode (SPMBE). Due to the enhancement of the AuIII mass transfer by nonlinear diffusion during the electrodeposition time, the SPMBE allows the sensitive determination of AuIII in a small volume of quiescent solution. The combination of the sensitive AuIII determination at a SPMBE with the large number of AuIII released from each gold nanoparticle probe allows detection of as low as 5 pM amplified HCMV DNA fragment.