DNA biosensor for the detection of hydrazines

A double-stranded (ds) DNA-coated carbon paste electrode is employed as a remarkably sensitive biosensor for the detection of hydrazine compounds. The sensor relies on monitoring changes in the intrinsic anodic response of the surface-confined DNA resulting from its interaction with hydrazine compounds and requires no label or indicator. Short reaction times (1-10 min) are sufficient for monitoring part-per-billion levels of different hydrazines. Applicability to untreated natural water samples is illustrated. The response mechanism is discussed, along with prospects of using DNA biosensors for quantitaing other important molecules and elucidating DNA interactions and damage.     

Molecular beacon-based junction probes for efficient detection of nucleic acids via a true target-triggered enzymatic recycling amplification

This work reports the development of a new molecular beacon-based junction sensing system with highly sensitive DNA detection and a strong capability to identify SNPs. The single linear probe typically labels the midsection of the oligonucleotide, but our next-generation junction sensing system uses a hairpin-structured MB with labels on each end of the oligonucleotide to maintain the cleaving activity of our newly designed ssDNA-cleaved endonuclease, Nt.BbvCI, rather than the typical dsDNA-cleaved endonuclease. These design improvements guarantee a true and efficient target-triggered enzymatic recycling amplification process in our sensing system. They also afford a faster and more sensitive response toward target DNA than the first-generation junction sensing system.     

Selective enzymatic cleavage of gold nanoparticle-labelled DNA on a microarray

The use of the restriction enzyme EcoRI for the manipulation of double-stranded DNA on microarrays is introduced. Gold nanoparticles are attached to a microarray via base pairing between complementary DNA sequences on the array and on the particles. These particles could be detected by light scattering measurements following an enhancement step, in which silver islands were deposited on top of the gold particles. This deposition of silver could be completely suppressed if the particles were removed by enzymatic cleavage of their DNA linker molecules. This cleavage step critically depends on the presence of a specific enzyme recognition site.     

Unimolecular beacons for the detection of DNA-binding proteins

A new methodology for detecting sequence-specific DNA-binding proteins has been recently developed (Heyduk, T.; Heyduk, E. Nat. Biotechnol. 2002, 20, 171). The core feature of this methodology is protein-dependent association of two fluorochrome-labeled DNA fragments, which allows generation of a fluorescence signal reporting the presence of the target protein. Previous kinetic experiments identified the association of the two DNA fragments as the rate-limiting step of the assay. Here we report on a variant of the assay, in which components of the assay--fluorescent DNA fragments--were covalently tethered by a non-DNA linker with the goal of increasing the rate of association of the two fragments. We investigated the effect of the tether on the performance of the assay under a variety of conditions using a model DNA-binding protein. Quantitative titrations and rapid kinetic stopped-flow experiments were conducted to validate the molecular model that describes the two linked equilibria: oscillation of the tethered construct between the open and closed states and the exclusive association of the protein with the closed state. Experiments were also performed to demonstrate the ability of these tethered constructs to signal when attached to a solid surface. The major advantage of this new assay format is the faster response time for the detection allowing the higher throughput of the analysis. Additionally, it will be possible to attach tethered beacons to other solid surfaces, thus allowing the preparation of arrays containing molecular beacons for many different DNA-binding proteins.     

Peptide-nucleic acid-modified ion-sensitive field-effect transistor-based biosensor for direct detection of DNA hybridization

Here, we report the development of a peptide-nucleic acid (PNA)-modified ion-sensitive field-effect transistor (IS-FET)-based biosensor that takes advantage of the change in the surface potential upon hybridization of a negatively charged DNA. PNA was immobilized on a silicon nitride gate insulator by an addition reaction between a maleimide group introduced on the gate surface, the succinimide group of N-(6-maleimidocaproyloxy) succinimide, and the thiol group of the terminal cysteine in PNA. The surface was characterized after each step of the reaction by X-ray photoelectron spectroscopy analysis, and the kinetic analysis of the hybridization events was assessed by surface plasmon resonance. In addition, we measured the -potential before and after PNA-DNA hybridization in the presence of counterions to investigate the change in surface charge density at the surface-solution interface within the order of the Debye length. On the basis of the zeta-potential, the surface charge density, DeltaQ, calculated using the Grahame equation was approximately 4.0 x 10(-3) C/m2 and the estimated number of hybridized molecules was at least 1.7 x 10(11)/cm2. The I-V characteristics revealed that the PNA-DNA duplexes induce a positive shift in the threshold voltage, VT, and a decrease in the saturated drain current, ID. These results demonstrate that direct detection of DNA hybridization should be possible using a PNA-modified IS-FET-based biosensor. PNA is particularly advantageous for this system because it enables highly specific and selective binding at low ionic strength.     

Acetylcholinesterase liquid crystal biosensor based on modulated growth of gold nanoparticles for amplified detection of acetylcholine and inhibitor

A novel acetylcholinesterase (AChE) liquid crystal (LC) biosensor based on enzymatic growth of gold nanoparticles (Au NPs) has been developed for amplified detection of acetylcholine (ACh) and AChE inhibitor. In this method, AChE mediates the hydrolysis of acetylthiocholine (ATCl) to form thiocholine, and the latter further reduces AuCl(4)(-) to Au NPs without Au nanoseeds. This process, termed biometallization, leads to a great enhancement in the optical signal of the LC biosensor due to the large size of Au NPs, which can greatly disrupt the orientational arrangement of LCs. On the other hand, the hydrolysis of ATCl is inhibited in the presence of ACh or organophosphate pesticides (OPs, a AChE inhibitor), which will decrease the catalytic growth of Au NPs and, as a result, reduce the orientational response of LCs. On the basis of such an inhibition mechanism, the AChE LC biosensor can be used as an effective way to realize the detection of ACh and AChE inhibitors. The results showed that the AChE LC biosensor was highly sensitive to ACh with a detection limit of 15 μmol/L and OPs with a detection limit of 0.3 nmol/L. This study provides a simple and sensitive AChE LC biosensing approach and offers effective signal enhanced strategies for the development of enzyme LC biosensors.     

Graphene-DNAzyme based biosensor for amplified fluorescence "turn-on" detection of Pb2+ with a high selectivity

On the basis of the remarkable difference in affinity of graphene (GO) with ssDNA containing a different number of bases in length, we for the first time report a GO-DNAzyme based biosensor for amplified fluorescence "turn-on" detection of Pb(2+). A FAM-labeled DNAzyme-substrate hybrid acted as both a molecular recognition module and signal reporter and GO as a superquencher. By taking advantage of the super fluorescence quenching efficiency of GO, our proposed biosensor exhibits a high sensitivity toward the target with a detection limit of 300 pM for Pb(2+), which is lower than previously reported for catalytic beacons. Moreover, with the choice of a classic Pb(2+)-dependent GR-5 DNAzyme instead of 8-17 DNAzyme as the catalytic unit, the newly designed sensing system also shows an obviously improved selectivity than previously reported methods. Moreover, the sensing system was used for the determination of Pb(2+) in river water samples with satisfying results.     

Enhanced bacterial biosensor for fast and sensitive detection of oxidatively DNA damaging agents

A number of known and potential chemicals may cause substantial damage to genomic DNA, further inducing mutagenesis and carcinogenesis. To screen potentially genotoxic compounds from a multitude of chemicals, fast and senstive bioanalytical technologies are desirable. By taking advantage of the DNA damage-dependent SOS response (a regulatory signal initiated by damage to DNA or the physiological consequences of such damage in prokaryotes) in reactive oxygen species (ROS)-sensitive bacterium and the enhanced green fluorescent protein reporter, we constructed a composite bacterial biosensor for detection of DNA damage agents. The sensitivity of the bacterium to ROS induced DNA damage is 10-20-times enhanced by the knockout of one alkyl hydroperoxide reductase gene and two catalase genes. This biosensor can be used for fast and sensitive detection of DNA damaging agents among which some cannot be detected by previous bacterial biosensors, demonstrating the potential and promising applications for evaluation of DNA damage and for screening of DNA damaging agents in large scale.     

Enzymatically amplified surface plasmon resonance imaging detection of DNA by exonuclease III digestion of DNA microarrays

This paper describes a novel approach utilizing the enzyme exonuclease III in conjunction with 3'-terminated DNA microarrays for the amplified detection of single-stranded DNA (ssDNA) with surface plasmon resonance (SPR) imaging. When ExoIII and target DNA are simultaneously introduced to a 3'-terminated ssDNA microarray, hybridization adsorption of the target ssDNA leads to the direction-dependent ExoIII hydrolysis of probe ssDNA strands and the release of the intact target ssDNA back into the solution. Readsorption of the target ssDNA to another probe creates a repeated hydrolysis process that results over time in a significant negative change in SPR imaging signal. Experiments are presented that demonstrate the direction-dependent surface enzyme reaction of ExoIII with double-stranded DNA as well as this new enzymatically amplified SPR imaging process with a 16-mer target ssDNA detection limit of 10-100 pM. This is a 10(2)-10(3) improvement on previously reported measurements of SPR imaging detection of ssDNA based solely on hybridization adsorption without enzymatic amplification.     

Ultrasensitive detection of DNA sequences in solution by specific enzymatic labeling

We present a newly developed technique for the direct detection of very low concentrations of specific nucleic acid sequences in homogeneous solution based on a polymerase extension reaction. This method consists of synthesizing a highly fluorescent nucleic acid reporter molecule using a sequence of the target as a template. Synthesis of the reporter molecule is accomplished by hybridizing a short complementary oligonucleotide primer to the target and extending the reporter using a polymerase and free nucleotides. One of these nucleotides is partially labeled with a fluorophore. The reaction sample is then flowed through the capillary cell of a single molecule detector. Detection of the reporter signifies the presence of the target being sought. Under carefully selected conditions, fluorescence from the reporter molecule is much stronger than that of the free nucleotide background over the detection time. We have derived practical equations that allow us to determine an optimal range of values for the relative reporter and free-nucleotide concentrations. This method allows for the rapid, direct detection of individual targets at femtomolar concentrations without the use of an amplification procedure, such as the polymerase chain reaction.     

Amplified on-chip fluorescence detection of DNA hybridization by surface-initiated enzymatic polymerization

We describe the incorporation of multiple fluorophores into a single stranded DNA (ssDNA) chain using terminal deoxynucleotidyl transferase (TdT), a template-independent DNA polymerase that catalyzes the sequential addition of deoxynucleotides (dNTPs) at the 3'-OH group of an oligonucleotide primer; we term this methodology surface initiated enzymatic polymerization (SIEP) of DNA. We found that long (>1 Kb) ssDNA homopolymer can be grown by SIEP, and that the length of the ssDNA product is determined by the monomer to oligonucleotide initiator ratio. We observed efficient initiation (≥50%) and narrow polydispersity of the extended product when fluorescently labeled nucleotides are incorporated. TdT's ability to incorporate fluorescent dNTPs into a ssDNA chain was characterized by examining the effect of the molar ratios of fluorescent dNTP to natural dNTP on the degree of fluorophore incorporation and the length of the polymerized DNA strand. These experiments allowed us to optimize the polymerization conditions to incorporate up to ~50 fluorescent Cy3-labeled dNTPs per kilobase into a ssDNA chain. With the goal of using TdT as an on-chip labeling method, we also quantified TdT mediated signal amplification on the surface by immobilizing ssDNA oligonucleotide initiators on a glass surface followed by SIEP of DNA. The incorporation of multiple fluorophores into the extended DNA chain by SIEP translated to a ~45 fold signal amplification compared to the incorporation of a single fluorophore. SIEP was then employed to detect hybridization of DNA, by the posthybridization, on-chip polymerization of fluorescently labeled ssDNA that was grown from the 3'-OH of target strands that hybridized to DNA probes that were printed on a surface. A dose-response curve for detection of DNA hybridization by SIEP was generated, with a ~1 pM limit of detection and a linear dynamic range of 2 logs.     

Ultrasensitive aptamer-based multiplexed electrochemical detection by coupling distinguishable signal tags with catalytic recycling of DNase I

This work reports an aptamer-based, disposable, and multiplexed sensing platform for simultaneous electrochemical determination of small molecules, employing adenosine triphosphate (ATP) and cocaine as the model target analytes. The multiplexed sensing strategy is based on target-induced release of distinguishable redox tag-conjugated aptamers from a magnetic graphene platform. The electronic signal of the aptasensors could be further amplified by coupling DNase I with catalytic recycling of self-produced reactants. The assay was based on the change in the current at the various peak potentials in the presence of the corresponding signal tags. Experimental results revealed that the multiplexed electrochemical aptasensor enabled the simultaneous monitoring of ATP and cocaine in a single run with wide working ranges and low detection limits (LODs: 0.1 pM for ATP and 1.5 pM for cocaine). This concept offers promise for rapid, simple, and cost-effective analysis of biological samples.     

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.     

DNA biosensor for detection of Helicobacter pylori using phen-dione as the electrochemically active ligand in osmium complexes

A surface-based method for the study of the interactions of DNA with redox-active 1,10-phenantroline-5,6-dione (phen-dione) osmium complexes is described. The study was carried out using gold electrodes modified with DNA via adsorption and [Os(bpy)(2)(phe-dione)](3+/2+) (bpy = 2,2'-bipyridyl) or [Os(phen)(2)(phen-dione)](3+/2+) (phen = 1,10-phenantroline) as electrochemical reported molecules. The method, which is simple and reagent-saving, allows the accumulation of osmium complexes within the DNA layer. The amount of osmium complex bound by the adsorbed layer of DNA was determined from the voltammetric charge associated with the osmium redox process of the immobilized metal complex. The quinone moiety of the phen-dione ligand was useful as an indicator for electrochemical DNA sensing because of its redox response at low potentials. A thiol-linked single-stranded Helicobacter pylori DNA probe was immobilized, through S-Au bonds on to a gold electrode (density of modification 86 pmol/cm(2)). Following hybridization with the complementary DNA sequence, the osmium complex was electrochemically accumulated within the double-stranded DNA layer. Electrochemical detection was performed by differential pulse voltammetry over the potential range where the quinone moiety was redox active (i.e., at very low potentials, -0.020 V vs SSCE); with this approach, a sequence of the H. pylori could be quantified over the range from 5 to 20 pmol with a linear correlation of r = 0.9888 and a detection limit of approximately 6 pmol.     

Efficient fluorescence turn-on probe for zirconium via a target-triggered DNA molecular beacon strategy

It is well-known that Zr(4+) could selectively bind with two phosphate-functionalized molecules through a coordinate covalent interaction to form a sandwich-structured complex (-PO(3)(2-)-Zr(4+)-PO(3)(2-)-). In this paper, we for the first time converted such interaction into fluorescence sensing systems for Zr(4+) via a target-triggered DNA molecular beacon strategy. In the new designed sensing system, two phosphorylated and pyrene-labeled oligonucleotides were chosen as both recognition and reporter units, which will be linked by target Zr(4+) to form a hairpin structure and bring the two labeled pyrene molecules into close proximity, resulting in a "turn-on" excimer fluorescence signal. Moreover, γ-cyclodextrin was introduced to afford an amplified fluorescence signal and, therefore, provided an improved sensitivity for the target Zr(4+). This allows detection of Zr(4+) with high sensitivity (limit of detection, LOD = 200 nM) and excellent selectivity. The proposed sensing system has also been used for detection of Zr(4+) in river water samples with satisfactory result.     

Electrical detection of DNA hybridization based on enzymatic accumulation confined in nanodroplets

Electrical monitoring of DNA hybridization is one way to reduce the cost and size of the DNA chip reader in comparison with the more classical optical detection. Within electrical methods, electrochemical detection shows very high performances in terms of accuracy and sensitivity, especially when an enzymatic accumulation is used to amplify the signal. However, signal multiplexing for miniaturized systems based on both enzymatic accumulation and electrochemical detection remains challenging due to the Brownian diffusion of the detected product of the enzymatic reaction. We present here a DNA chip with electrical detection based on the following sequence: (i) hybridization of nucleic acids and washing in a liquid layer as usual, (ii) formation of independent nanodroplets on each detection site, (iii) enzymatic accumulation in each droplet avoiding cross-contamination between neighboring sites, and (iv) electrochemical detection of the product accumulated during the enzymatic reaction. The simple and fast transition from the liquid layer (hybridization step) to an array of nanodroplets (enzymatic accumulation and detection steps) was performed through the filling of the hybridization chamber with a solution containing the enzymatic substrates, the drawing of this solution, and the simultaneous creation of droplets thanks to retention areas based on circular rims or hydrophilic rings. Using this approach, hybridization is achieved in a liquid layer as usual, followed by the enzymatic accumulation in nanodroplets to avoid the cross-talk between neighboring sites. Moreover, working in droplets enables a fast increase in the concentration of the product generated by the enzymatic reaction and thus an improvement of the detection limit of the system.     

Embedded DNA-polypyrrole biosensor for rapid detection of Escherichia Coli

The principal objective of this paper was to present the design and fabrication of a single-strand (ss) DNA biosensor for the detection of Escherichia coli (E. coli) DNA synthetic oligonucleotides as a model of rapid detection of bacterial select bioterrorism agents. Molecular biology and chemical electrodeposition techniques, such as cyclic voltammetry (CV), were combined to develop and test a model DNA-based biosensor on a platinum (Pt) electrode electropolimerized with polypyrrole (PPY). The hybridization on embedded DNA into PPY with complementary DNA samples was determined. The recognition element was a 25 base pair (bp) oligonucleotide specific for E. coli derived from the uidA gene that codes for the enzyme /spl beta/-D glucuronidase. CV scans between 0.0 and +0.70 V at a 50-mV/s scanning rate generated current versus potential graphs. A standard DNA concentration of 1 /spl mu/g//spl mu/L was used to determine the hybridization signal of the biosensor. The model biosensor generated distinctive CV signals between complementary and noncomplementary DNA oligonucleotides. The biosensor proved to be effective in the detection of complementary uidA 25-bp oligonucleotide for E. coli K-12.     

Antimicrobial peptides for detection of bacteria in biosensor assays

Bacteria, plants, and higher and lower animals have evolved an innate immune system as a first line of defense against microbial invasion. Some of these organisms produce antimicrobial peptides (AMPs) as a part of this chemical immune system. AMPs exert their antimicrobial activity by binding to components of the microbe's surface and disrupting the membrane. The overall goal of this study was to apply the AMP magainin I as a recognition element for Escherichia coli O157:H7 and Salmonella typhimurium detection on an array-based biosensor. We immobilized magainin I on silanized glass slides using biotin-avidin chemistry, as well as through direct covalent attachment. Cy5-labeled, heat-killed cells were used to demonstrate that the immobilized magainin I can bind Salmonella with detection limits similar to analogous antibody-based assays. Detection limits for E. coli were higher than in analogous antibody-based assays, but it is expected that other AMPs may possess higher affinities for this target. The results showed that both specific and nonspecific binding strongly depend on the method used for peptide immobilization. Direct attachment of magainin to the substrate surface not only decreased nonspecific cell binding but also resulted in improved detection limits for both Salmonella and E. coli.     

Application of nanostructured ZnO films for electrochemical DNA biosensor

Nanostructured zinc oxide (nsZnO) films have been fabricated onto conducting indium–tin–oxide (ITO) coated glass plate, by cathodic electro-deposition to immobilize probe DNA specific to M. tuberculosis via physisorption based on strong electrostatic interactions between positively charged ZnO (isoelectric point = 9.5) and negatively charged DNA to detect its complementary target. Electrochemical studies reveal that the presence of nano-structured ZnO results in increased electro-active surface area for loading of DNA molecules. The DNA–nsZnO/ITO bioelectrode exhibits interesting characteristics such as detection range of 1 × 10^?6 ? 1 × 10^?12 M, detection limit of 1 × 10^?12 M (complementary target) and 1 × 10^?13 M (genomic DNA), reusability of about 10 times, response time of 60s and stability of up to 4 months when kept at 4°C.