Detection Of Single-stranded DNA Research Articles

Surface regeneration and reusability of label-free DNA biosensors based on weak polyelectrolyte-modified capacitive field-effect structures

The reusability of capacitive field-effect electrolyte-insulator-semiconductor (EIS) sensors modified with a cationic weak polyelectrolyte (poly(allylamine hydrochloride) (PAH)) for the label-free electrical detection of single-stranded DNA (ssDNA), in-solution- and on-chip-hybridized double-stranded DNA (dsDNA) has been studied. It has been demonstrated that via simply regeneration of the gate surface of the EIS sensor by means of an electrostatic adsorption of a new PAH layer, the same biosensor can be reused for at least five DNA-detection measurements. Because of the reversal of the charge sign of the outermost layer after each surface modification with the cationic PAH or negatively charged DNA molecules, the EIS-biosensor signal exhibits a zigzag-like behavior. The amplitude of the signal changes has a tendency to decrease with increasing number of macromolecular layers. The direction of the EIS-signal shifts can serve as an indicator for a successful DNA-immobilization or -hybridization process. In addition, we observed that the EIS-signal changes induced by each surface-modification step (PAH adsorption, immobilization of ssDNA or dsDNA molecules and on-chip hybridization of complementary target cDNA) is decreased with increasing the ionic strength of the measurement solution, due to the more efficient macromolecular charge-screening by counter ions. The results of field-effect experiments were supported by fluorescence-intensity measurements of the PAH- or DNA-modified EIS surface using various fluorescence dyes.

A DNA electrochemical biosensor based on homogeneous hybridization for the determination of Cryptococcus neoformans

The sensitive analysis of DNA is of extreme importance in the field of clinical diagnosis, targeted therapeutics, gene therapy, and a variety of biomedical studies. Even though significant achievements have been made in the detection of single-stranded DNA (ssDNA), facile strategy for the detection of double-stranded DNA (dsDNA) is still lacking. In this study, we have constructed an electrochemical DNA sensor based on homogeneous hybridization. Target dsDNA is thermal denatured and hybridized with thiolated capture probe and biotin-labeled reporter probe in solution phase. Excessive amount of the probes and precise control of hybridization temperature ensure the predominant formation of sandwich SH-dsDNA-biotin rather than reannealing product of the target dsDNA. A bovine serum albumin (BSA)-modified gold surface is designed to improve self-assembly capability of the sandwich SH-dsDNA-biotin structure in the presence of excessive SH-ssDNA probe. Thus, the target dsDNA can be successfully detected by using enzyme-linked amperometric amplification. By employing this strategy, dsDNA can be detected in a linear range from 5 pM to 1 nM with a detection limit down to 800 fM (S/N = 3). Cryptococcus neoformans in clinical real samples from cryptococcal meningitis patients can be discriminated successfully by the proposed method. Our research would make the electrochemical biosensor be an excellent candidate for pathogens detection in clinical diagnosis and prognosis.

Single stranded-DNA detection: the role of Wip1 in ATR-dependent pathway

Single-stranded DNA (ssDNA) areas arise in cells as a result of exposure to stress agents - like UVC - or during repair of DNA double-strand breaks. ATR(ataxia telangiectasia mutated and Rad3-related) is responsible for detecting ssDNA. Recently, it has been shown that one of the most important components of cellular response to the damage is Wip1 phosphatase, which inactivates main elements of DNA damage response (DDR) pathways. We developed a mathematical model of ATR detector system, connected to p53 tumor suppressor responsible for activation of genes involved in cellular response to the damage (DNA repair/apoptosis). Moreover, we added Wip1 phosphatase, as a main agent responsible for turning o DDR. Our results show that the apoptotic threshold, where more than half of cells die, is equal to 20 J/m2. The threshold shifts when activity of the specied proteins involved in the pathway is blocked or reduced. Moreover with accurate dose of UVC and silenced or blocked Wip1, it may be possible to drive cancer cells to apoptotic pathway.

Sulforaphane and myricetin act synergistically to induce apoptosis in 3T3‑L1 adipocytes.

The aim of the present study was to investigate whether sulforaphane (SFN) and myricetin (Myr) synergistically induce apoptosis in adipocytes. The viability of mature 3T3-L1 adipocytes treated with 40 µM SFN and/or 100 µM Myr was assessed using an MTT assay. Apoptosis was assessed by Hoechst 33258 nuclear staining, and by detection of single-stranded DNA using an enzyme-linked immunosorbent assay. Compared with the effects of each compound alone, the combination of SFN and Myr synergistically reduced cell viability, induced apoptosis, increased pro-apoptotic Bcl-2 associated X protein expression, decreased anti-apoptotic B-cell lymphoma-2 expression, enhanced Bcl-2-associated death promoter (Bad) translocation from the cytoplasm to the mitochondria, and reduced Bad phosphorylation at Ser112. These effects were accompanied by increased cleavage of caspase 3 and poly-ADP-ribose-polymerase. In addition, combined SFN and Myr treatment significantly decreased the protein expression levels of phosphorylated AKT serine/threonine kinase 1 (Akt) at Ser473, as well as the phosphorylation of the downstream protein ribosomal protein, S6 kinase β-1. Therefore, SFN plus Myr was a more potent inducer of apoptosis in 3T3-L1 adipocytes than either compound alone. The results of the present study suggest that the mechanism of SNF/Myr-induced apoptosis involved activation of the Akt-mediated mitochondrial apoptotic pathway. This may aid treatment of animal models of obesity and preclinical testing.

Single-stranded DNA detection by solvent-induced assemblies of a metallo-peptide-based complex.

DNA detection is highly important for the sensitive sensing of different pathogenic bacteria and viruses. The major challenge is to create a sensor that can selectively detect very small concentrations of DNA without the need for amplification or complicated equipment. Different technologies such as optical, electrochemical and microgravimetric approaches can detect DNA fragments. Here we show, for the first time, the use of self-assembled nanostructures generated by a metallo-peptide as an optical sensing platform for DNA detection. The system can selectively detect single stranded DNA fragments by fluorescence measurements as it can discriminate even one base mismatch and can perform in the presence of other interfering proteins. This system may be useful in lab-on-a-chip applications.

A universal design for a DNA probe providing ratiometric fluorescence detection by generation of silver nanoclusters

DNA-stabilized silver nanoclusters (AgNCs), the fluorescence emission of which can rival that of typical organic fluorophores, have made possible a new class of label-free molecular beacons for the detection of single-stranded DNA. Like fluorophore-quencher molecular beacons (FQ-MBs) AgNC-based molecular beacons (AgNC-MBs) are based on a single-stranded DNA that undergoes a conformational change upon binding a target sequence. The new conformation exposes a stretch of single-stranded DNA capable of hosting a fluorescent AgNC upon reduction in the presence of Ag(+) ions. The utility of AgNC-MBs has been limited, however, because changing the target binding sequence unpredictably alters cluster fluorescence. Here we show that the original AgNC-MB design depends on bases in the target-binding (loop) domain to stabilize its AgNC. We then rationally alter the design to overcome this limitation. By separating and lengthening the AgNC-stabilizing domain, we create an AgNC-hairpin probe with consistent performance for arbitrary target sequence. This new design supports ratiometric fluorescence measurements of DNA target concentration, thereby providing a more sensitive, responsive and stable signal compared to turn-on AgNC probes. Using the new design, we demonstrate AgNC-MBs with nanomolar sensitivity and singe-nucleotide specificity, expanding the breadth of applicability of these cost-effective probes for biomolecular detection.

Tetraphenylethene-based Zn complexes for the highly sensitive detection of single-stranded DNA

Metal–ligand coordination interactions were utilized to develop tetraphenylethene-based DNA probes, which exhibited a higher fluorescent on/off ratio than ethidium bromide.

Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation.

We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).

Direct detection of DNA below ppb level based on thionin-functionalized layered MoS2 electrochemical sensors.

A layered MoS2-thionin composite was prepared by sonicating their mixture in an ionic liquid and gradient centrifugation. Because DNA is rarely present in single-stranded form, either naturally or after PCR amplification, the composite was used for fabrication of a double-stranded DNA (dsDNA) electrochemical biosensor due to stable electrochemical response, intercalation, and electrostatic interaction of thionin with DNA. The linear range over dsDNA concentration from 0.09 ng mL(-1) to 1.9 ng mL(-1) is obtained, and moreover, it is suitable for the detection of single-stranded DNA (ssDNA). The biosensor has been applied to the detection of circulating DNA from healthy human serum, and satisfactory results have been obtained. The constructed DNA electrochemical biosensor shows potential application in the fields of bioanalysis and clinic diagnosis. Furthermore, this work proposes a new method to construct electrochemical biosensors based on MoS2 sheets.

Rolling cycle amplification based single-color quantum dots–ruthenium complex assembling dyads for homogeneous and highly selective detection of DNA

In this work, a new, label-free, homogeneous, highly sensitive, and selective fluorescent biosensor for DNA detection is developed by using rolling-circle amplification (RCA) based single-color quantum dots–ruthenium complex (QDs–Ru) assembling dyads. This strategy includes three steps: (1) the target DNA initiates RCA reaction and generates linear RCA products; (2) the complementary DNA hybridizes with the RCA products to form long double-strand DNA (dsDNA); (3) [Ru(phen)2(dppx)]2+ (dppx=7,8-dimethyldipyrido [3,2-a:2′,3′-c] phenanthroline) intercalates into the long dsDNA with strong fluorescence emission. Due to its strong binding propensity with the long dsDNA, [Ru(phen)2(dppx)]2+ is removed from the surface of the QDs, resulting in restoring the fluorescence of the QDs, which has been quenched by [Ru(phen)2(dppx)]2+ through a photoinduced electron transfer process and is overlaid with the fluorescence of dsDNA bonded Ru(II) polypyridyl complex (Ru-dsDNA). Thus, high fluorescence intensity is observed, and is related to the concentration of target. This sensor exhibits not only high sensitivity for hepatitis B virus (HBV) ssDNA with a low detection limit (0.5pM), but also excellent selectivity in the complex matrix. Moreover, this strategy applies QDs–Ru assembling dyads to the detection of single-strand DNA (ssDNA) without any functionalization and separation techniques.

Surface modification of solid-state nanopores for sticky-free translocation of single-stranded DNA.

Nanopore technology is one of the most promising approaches for fast and low-cost DNA sequencing application. Single-stranded DNA detection is primary objective in such device, while solid-state nanopores remain less explored than their biological counterparts due to bio-molecule clogging issue caused by surface interaction between DNA and nanopore wall. By surface coating a layer of polyethylene glycol (PEG), solid-state nanopore can achieve long lifetime for single-stranded DNA sticky-free translocation at pH 11.5. Associated with elimination of non-specific binding of molecule, PEG coated nanopore presents new surface characteristic as less hydrophility, lower 1/f noise, and passivated surface charge responsiveness on pH. Meanwhile, conductance blockage of single-stranded DNA is found to be deeper than double-stranded DNA, which can be well described by a string of blobs model for a quasi-equilibrium state polymer in constraint space.

Surface plasmon resonance technique for directly probing the interaction of DNA and graphene oxide and ultra-sensitive biosensing

The binding of DNA with graphene oxide (GO) is important for applications in disease diagnosis, genetic screening, and drug discovery. The standard assay methods are mainly limited to indirect observation via fluorescence labeling. Here we report the use of surface plasmon resonance for direct sensing of DNA/GO binding. We show that this can be used for ultra-sensitive detection of single-stranded DNA (ssDNA). Furthermore, the results provide a more direct probe of DNA/GO binding abilities and confirm that hydrogen bonding plays a key role in the interaction between GO and ssDNA. This enables to a novel biosensor for highly sensitive and selective detection of ssDNA based on indirect competitive inhibition assay (ICIA). We report development of such a sensor with a linear dynamic range of 10−14–10−6M, a detection limit of 10fM and a high level of stability during repeated regeneration.

Characterization of the cryptic plasmid pWCZ from Lactobacillus paracasei WCZ isolated from silage

A cryptic plasmid from Lactobacillus paracasei WCZ, designated as pWCZ, was sequenced and analyzed. It consisted of 3,078 bp with a G+C content of 42.6 %. The plasmid was predicted to encode three putative coding sequences. Based on homology, the three coding sequences were identified as genes encoding transcriptional repressor (CopG), replication initiation (Rep) and mobilization (Mob) protein, respectively. Various regulatory regions like promoters and ribosome binding site (RBS) were then deduced from the sequences of copG and mob. A double-strand origin (dso), which contained the conserved nick sequence of the rolling-circle replication (RCR) pMV158 family was identified. A putative single-strand origin (sso) consisting of successive inverted repeats was also detected. Detection of single-stranded DNA (ssDNA) intermediates by Southern hybridization and S1 nuclease treatment confirmed that pWCZ replicated via the RCR mechanism. Furthermore, the relative copy number of pWCZ was estimated by real-time PCR to be about 99 copies in each cell.

Liposome–Quantum Dot Complexes Enable Multiplexed Detection of Attomolar DNAs without Target Amplification

Sensitive detection of DNA usually relies on target amplification approaches such as polymerase chain reaction and rolling circle amplification. Here we describe a new approach for sensitive detection of low-abundance DNA using liposome-quantum dot (QD) complexes and single-particle detection techniques. This assay allows for detection of single-stranded DNA at attomolar concentrations without the involvement of target amplification. Importantly, this strategy can be employed for simultaneous detection of multiple DNA targets.

Construction of a microfluidic chip, using dried-down reagents, for LATE-PCR amplification and detection of single-stranded DNA

LATE-PCR is an advanced form of non-symmetric PCR that efficiently generates single-stranded DNA which can readily be characterized at the end of amplification by hybridization to low-temperature fluorescent probes. We demonstrate here for the first time that monoplex and duplex LATE-PCR amplification and probe target hybridization can be carried out in double layered PDMS microfluidics chips containing dried reagents. Addition of a set of reagents during dry down overcomes the common problem of single-stranded oligonucleotide binding to PDMS. These proof-of-principle results open the way to construction of inexpensive point-of-care devices that take full advantage of the analytical power of assays built using LATE-PCR and low-temperature probes.

A New Trace Analytic Method for the Determination of Sequence-Specific DNA with Fluorescent Probes

A new method of fluorescence spectrometry detection of single-strand DNA (ssDNA) was established by hybridizing the ssDNA with its complementary ssDNA to form double-stranded DNA (dsDNA). Our results show that the fluorescence intensity increased significantly when the nucleic acid molecular “light switch"(Ru(phen)2dppx2+) or Hoechst 33258 dye interacted with dsDNA, and the fluorescence intensity also increased as the DNA concentration increased. The changing law was also studied about how the fluorescence intensity changed when the two kinds of fluorescent probes interacted with oligonucleotide of different lengths and different sequences, as well as DNA-DNA′ hybridization products. Then, the effect of the bases mismatch, varying length of DNA chain, and different DNA sequences on the fluorescence intensity were explored at the same time, by detecting the specific DNA sequence of avian influenza H1N1 virus, cauliflower mosaic virus, and hepatitis C virus. Additionally, the selectivity, linear range, and sensitivity of the two probes were compared.

Investigation and Development of Quantum Dot-Encoded Microsphere Bioconjugates for DNA Detection by Flow Cytometry

The development of screening assays continues to be an active area of research in molecular diagnostics. Fluorescent microspheres conjugated to biomarkers (nucleic acids, proteins, lipids, carbohydrates) and analyzed on flow cytometer instruments offered a new approach for multiplexed detection platform in a suspension format. Quantum dots encoded into synthetic microspheres have the potentials to improve current screening bioassays and specifically suspension array technology. In this paper, commercialized quantum dot-encoded microsphere were evaluated and optimized as fluorescent probes to address some of the limitations of suspension array technologies. A comprehensive study was undertaken to adapt the bioconjugation procedure to the quantum dot-encoded microsphere structural and optical properties. Both the leaching-out of quantum dots and microspheres degradation under bioconjugation experimental conditions were minimized. A rapid, efficient and reproducible conjugation method was developed for the detection of single-stranded DNA with the commercialized quantum dot-encoded microsphere. Approximately ten thousand microspheres were conjugated to short amino-modified DNA sequences in one hour with high efficiency. The bioconjugated microspheres acting as fluorescent probes successfully detected a DNA target in suspension with high specificity. Quantum dot-encoded microsphere commercial products are limited which strongly prevents reproducible and comparative studies between laboratories. The method developed here contributes to the understanding of quantum dot-encoded microsphere reactivity, and to the optimization of adapted experimental procedure. This step is essential in the development of this new fluorescent probe technology for multiplex genotyping assay and molecular diagnostic applications.

Electrochemical DNA Biosensor for the Detection of Short DNA Species by Using Compound Co(phen)<sub>3</sub><sup>2+</sup>

The application of electrochemical techniques for DNA detection is motivated by their potential to detect hybridization events in a more rapid, simplistic and cost-effective manner compared to conventional methods. Here, we present an electrochemical DNA biosensor for the specific and quantitative detection of single-stranded DNA (ssDNA). Probe oligonucleotides were immobilized onto gold electrodes by a 5′ end thiol-group linker. Following hybridization with the complementary DNA, the cobalt complex was electrochemically accumulated on the double-stranded DNA layer and the differential pulse voltammogram (DPV) for this electrode gave an electrochemical signal due to the redox reaction of [Co(phen)3]2+/3+ that was bound to the double-stranded DNA on the electrode, and it can sense single base-pair mismatche within the sequence of the hybridized double-stranded DNA (dsDNA).

Single-strand DNA detection using a planar photonic-crystal-waveguide-based sensor

We report an experimental demonstration of single-strand DNA (ssDNA) detection at room temperature using a photonic-crystal-waveguide-based optical sensor. The sensor surface was previously biofunctionalized with ssDNA probes to be used as specific target receptors. Our experiments showed that it is possible to detect these hybridization events using planar photonic-crystal structures, reaching an estimated detection limit as low as 19.8 nM for the detection of the complementary DNA strand.

Visual detection of single-stranded target DNA using pyrroloquinoline-quinone-loaded liposomes as a tracer

The preparation of DNA-tagged liposomes containing an encapsulated prosthetic group tracer, pyrroloquinoline quinone (PQQ), and their application to the development of a sandwich-type hybridization assay for the visual detection of single-stranded DNA are described. Capture DNA is conjugated to the surface of microtiter plate wells through a biotin–streptavidin interaction. Target DNA is incubated with the plate in high salt concentrations. The reporter DNA-tagged liposomes encapsulating PQQ, the prosthetic group of the apo-enzyme glucose dehydrogenase (GDH), are used as the label to probe for bound target DNA. After washing away unbound liposomes and subsequent lysis of the bound fraction by surfactant, PQQ is released and available to activate the apo-enzyme. In the presence of glucose and a redox dye, 2,6-dichlorophenol indophenol (DCPIP), the dye is reduced to yield an optical color change from blue to colorless. This transition is observed visually or spectrophotometrically. The degree of optical change is proportional to the amount of PQQ present, which directly relates to the number of liposomes and, thus, the total amount of target DNA. An arbitrary target DNA sequence is used as a model system, and a limit of detection of 62fmol is achieved.