Capture of DNA in microfluidic channel using magnetic beads: Increasing capture efficiency with integrated microfluidic mixer

We have studied the hybridization of target DNA in solution with probe DNA on magnetic beads immobilized on the channel sidewalls in a magnetic bead separator. The hybridization is carried out under a liquid flow and is diffusion limited. Two systems are compared: one with a straight microfluidic channel and one with an integrated staggered herringbone mixer. Fluorescence microscopy studies show that the hybridization is much more efficient in the system with the integrated mixer. The results, which are discussed in terms of a simple model, are relevant for any diffusion-limited reaction taking place on the surface in a microfluidic system.     

Low cost optical detection of DNA hybridization on biochips

The detection of DNA hybridization can be either complicated or require expensive devices. Some methods use a fluorescence signal to investigate hybridization. Here, we present an optical probe based on optical fibers both for illumination and for fluorescence collection. The detection is made with a microspectrophotometer and the signal is then treated with a PC. We also developed the DNA biochips (glass plate with a gold layer functionalized with target DNA) as well as a dedicated microtank which maintains a constant flow of probe DNA over the target one. Finally, the detection of hybridization with this simple and versatile system is presented.     

基于无标记荧光共振能量转移的microRNA检测方法研究

利用以阳离子共轭聚合物为能量供体的荧光共振能量转移(FRET)策略和滚环扩增放大技术,建立了一种新型的microRNA(miRNA)检测方法。阳离子共轭聚合物采用聚[(9,9-双(6’-N,N,N-三乙基铵)己基)亚芴基亚苯基二溴化物](PFP)。PFP是一种由大量吸光单元共轭而成的阳离子聚合物,具有独特的光捕获和荧光增强性能,可以和带有负电荷的DNA通过静电作用相互结合。SG是一种能够结合于所有双链DNA双螺旋小沟区域的染料,其在游离状态下,荧光微弱,但一旦与双链DNA结合后,荧光会大大的增强。首先,设计了一条可与目标分子特异性杂交的锁式探针和与RCA产物序列互补的DNA链。当体系中存在miRNA时,在T4 DNA连接酶作用下,锁式探针连接成环;随后,在phi29 DNA聚合酶和dNTPs共同作用下,在miRNA的3’端滚环扩增出一条与锁式探针序列互补的长单链DNA,所得产物与互补DNA链杂交形成双链DNA(dsDNA)。此时SG作为FRET受体掺入其中,形成SG-dsDNA共同体。随后, SG-dsDNA与PFP因静电相互作用而紧密接近,由于PFP的发射光谱与SG的激发光谱有重叠,因此二者之间可以发生FRET现象。反之,当体系中不存在miRNA时,挂锁探针则无法连接成环,阻止了扩增反应的进行及其产物与互补DNA链的杂交反应。加入SG后,由于SG与单链DNA的结合能力很弱, SG则游离于溶液中,不会与PFP发生有效的FRET。因此目标分子的浓度与体系的FRET效率直接相关。以let 7a作为待测miRNA分子,在0.05~5 nmol·L-1的范围内, let 7a的浓度与从反应体系测得的FRET效率(I520/I423)成正比。同时以无PFP参加的检测方案作为对比实验,证明了PFP确实具有提高灵敏度的作用。另外,以四种同族miRNA分子及两种其他miRNA分子作为干扰物质对方法的特异性进行了考察,发现除了两种与目标分子序列高度相似的物质存在干扰外,其他物质几乎不产生信号。利用该方法对细胞总RNA提取液中let 7a的含量及其加标含量进行了检测,测量所得回收率基本令人满意。所建立的方案不需要荧光标记探针,有效降低了检测成本,简化了操作步骤,在与miRNA相关的疾病诊断领域具有一定的应用前景。     

Homogeneous Detection of Specific DNA Sequences by Fluorescence Quenching and Energy Transfer

The use of fluorescence quenching and energy transfer in DNA hybridization assays is reviewed. Placement of DNA probe labels within interacting distances by hybridization of DNA probes to target DNA or to one another allows rapid homogeneous analysis of specific DNA sequences. Due to the inherently lower sensitivity relative to heterogeneous assays, the fluorescence assays have been coupled with DNA amplification methods such as PCR to provide highly sensitive, clinically relevant homogeneous assays which can be performed in closed systems.     

DNA hybridization and phosphinothricin acetyltransferase gene sequence detection based on zirconia/nanogold film modified electrode

This study reports a novel electrochemical DNA biosensor based on zirconia (ZrO₂) and gold nanoparticles (NG) film modified glassy carbon electrode (GCE). NG was electrodeposited onto the glassy carbon electrode at 1.5 V, and then zirconia thin film on the NG/GCE was fabricated by cyclic voltammetric method (CV) in an aqueous electrolyte of ZrOCl₂ and KCl at a scan rate of 20 mV/s. DNA probes were attached onto the ZrO₂/NG/GCE due to the strong binding of the phosphate group of DNA with the zirconia film and the excellent biocompatibility of nanogold with DNA. CV and electrochemical impedance spectroscopy (EIS) were used to characterize the modification of the electrode and the probe DNA immobilization. The electrochemical response of the DNA hybridization was measured by differential pulse voltammetry (DPV) using methylene blue (MB) as the electroactive indicator. After the hybridization of DNA probe (ssDNA) with the complementary DNA (cDNA), the cathodic peak current of MB decreased obviously. The difference of the cathodic peak currents of MB between before and after the hybridization of the probe DNA was used as the signal for the detection of the target DNA. The sequence-specific DNA of phosphinothricin acetyltransferase (PAT) gene in the transgenic plants was detected with a detection range from 1.0 × 10⁻¹⁰ to 1.0 × 10⁻⁶ mol/L, and a detection limit of 3.1 × 10⁻¹¹ mol/L.     

Detection of <Emphasis Type="Italic">Staphylococcus aureus</Emphasis> Carrying the Gene for Toxic Shock Syndrome Toxin 1 by Quantum-Dot-Probe Complexes

In this study, a high-sensitive and high-specific method to detect the toxic shock syndrome toxin-1 (TSST-1)-producing Staphylococcus aureus was developed based on quantum dot (QD) and oligonucleotide probe complexes. S. aureus carrying tst gene which is responsible for the production of TSST-1 were detected based on fluorescence resonance energy transfer (FRET) occurring between CdSe/ZnS QD donors and black hole quencher (BHQ) acceptors. QD-DNA probe was prepared by conjugating the carboxyl-modified QD and the amino-modified DNA with the EDC. Photoluminescence (PL) quenching was achieved through FRET after the addition of BHQ-DNA which was attached to tst gene probe by match sequence hybridization. The PL recovery was detected in the presence of target DNA by BHQ-DNA detached from QD-DNA probe because of the different affinities. In contrast, mismatch oligonucleotides and DNAs of other bacteria did not contribute to fluorescence intensity recovery, which exhibits the higher selectivity of the biosensor. The experimental results showed clearly that the intensity of recovered QD PL is linear to the concentration of target DNA within the range of 0.2–1.2 μM and the detection limit was 0.2 μM.     

Electrochemical DNA biosensor based on avidin-biotin conjugation for influenza virus (type A) detection

An electrochemical DNA biosensor (E-DNA biosensor) was fabricated by avidin-biotin conjugation of a biotinylated probe DNA, 5′-biotin-ATG AGT CTT CTA ACC GAG GTC GAA-3′, and an avidin-modified glassy carbon electrode (GCE) to detect the influenza virus (type A). An avidin-modified GCE was prepared by the reaction of avidin and a carboxylic acid-modified GCE, which was synthesized by the electrochemical reduction of 4-carboxyphenyl diazonium salt. The current value of the E-DNA biosensor was evaluated after hybridization of the probe DNA and target DNA using cyclic voltammetry (CV). The current value decreased after the hybridization of the probe DNA and target DNA. The DNA that was used follows: complementary target DNA, 5′-TTC GAC CTC GGT TAG AAG ACT CAT-3′ and two-base mismatched DNA, 5′-TTC GAC AGC GGT TAT AAG ACT CAT-3′.     

Characterization of DNA chips on the molecular scale before and after hybridization with an atomic force microscope

Using two different 25-mer oligonucleotide probes covalently grafted on a silicon substrate, we demonstrate how efficient atomic force microscopy (AFM) can be for monitoring each step of DNA chip preparation: from probe immobilization to hybridization on the molecular scale. We observed the probe-molecule organization on the chip after immobilization, and the target molecules, which hybridized with probes could be individually identified. This article presents a method of straightforwardly identifying not only single and double DNA strands, but also, and more significantly, the hybridized part on them.     

Immobilization/hybridization of amino-modified DNA on plasma-polymerized allyl chloride

The present work describes the fabrication and characterization of chloride-derivatized polymer coatings prepared by continuous wave (cw) plasma polymerization as adhesion layers in DNA immobilization/hybridization. The stability of plasma-polymerized allyl chloride (ppAC) in H₂O was characterized by variation of the thickness of polymer films and its wettability was examined by water contact angle technique. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) were used to study polymer matrix properties and oligonucleotide/DNA binding interaction. With the same carrier gas rate and process pressure, plasma polymers deposited at different input powers show various comparable immobilization properties; nevertheless, low input power plasma-polymerized films gives a lower sensitivity toward DNA binding than that from high input power plasma-deposited films. The following DNA immobilization on chloride-functionalized surfaces was found dependence on the macromolecular architecture of the plasma films. The hybridization between probe DNA and total mismatch target DNA shows no non-specific adsorption between target and ppAC.     

Colorimetric DNA detection of transgenic plants using gold nanoparticles functionalized with L-shaped DNA probes

In this study, a DNA colorimetric detection system based on gold nanoparticles functionalized with L-shaped DNA probes was prepared and evaluated. We investigated the hybridization efficiency of the L-shaped probes and studied the effect of nanoparticle size and the L-shaped DNA probe length on the performance of the as-prepared system. Probes were attached to the surface of gold nanoparticles using an adenine sequence. An optimal sequence of 35S rRNA gene promoter from the cauliflower mosaic virus, which is frequently used in the development of transgenic plants, and the two complementary ends of this gene were employed as model target strands and probe molecules, respectively. The spectrophotometric properties of the as-prepared systems indicated that the large NPs show better changes in the absorption spectrum and consequently present a better performance. The results of this study revealed that the probe/Au-NPs prepared using a vertical spacer containing 5 thymine oligonucleotides exhibited a stronger spectrophotometric response in comparison to that of larger probes. These results in general indicate the suitable performance of the L-shaped DNA probe-functionalized Au-NPs, and in particular emphasize the important role of the gold nanoparticle size and length of the DNA probes in enhancing the performance of such a system.     

Studies on the Fluorescence Fiber-Optic DNA Biosensor Using <Emphasis Type="Italic">p</Emphasis>-Hydroxyphenylimidazo[f]1,10-phenanthroline Ferrum(III) as Indicator

A complex Fe(phen)₂·PHPIP·3ClO₄·2H₂O, where phen = 1,10-phenanthroline and PHPIP = p-hydroxyphenylimidazo[f]1,10-phenanthroline, was synthesized and acted as a good fluorescence indicator based on its interaction with double-duplex DNA. Then a fiber-optic DNA biosensor of fluorimetric detection was developed based on the recognition of target DNA in DNA hybridization assays. A probe ssDNA was covalently immobilized onto the surface of quartz optical fibers and then the probe ssDNA hybridized with complementary ssDNA introduced into the local environment of the sensor. The hybridization with complementary strands was monitored in real time by fluorimetric detection. Several factors affecting the probe immobilization, target DNA hybridization, and indicator binding reactions were optimized to maximize the sensitivity and shorten the assay time. Using this method, a sequence of the 16-mer oligonucleotides could be quantified over the range from 4.98 × 10⁻⁷ to 4.88 × 10⁻⁶ M and a detection limit of 1.08 × 10⁻⁷ M. And the designed optic-fiber biosensor could be conveniently regenerated by thermal denature. The utility of the novel hybridization indicator could provide a simple, rapid, low toxicity and reusable detection.     

Fluorescence Turn-On Analysis of Trace Protein Based on Carbon Nanodots and Hybridization Chain Reaction

In this work, an ultrasensitive method for trace protein detection based on fluorescent carbon nanodots and hybridization chain reaction (HCR) is designed. Generally, the synthesized bright carbon nanodots are conjugated with two hairpin-structured DNA probes, respectively, which act as subsequent HCR fuel strands. Since single-stranded parts of DNA probes could be easily absorbed on graphene oxide (GO) nanosheets, fluorescence emission of carbon nanodots is effectively quenched via fluorescence resonance energy transfer. However, in the presence of target protein, the aptamer sequence in another hairpin-structured DNA probe specially interacts with target and the hairpin is opened. A single-stranded region is thus exposed, which initiates HCR by coupling with the DNA fuel strands on carbon nanodots. The formed HCR product displays a rigid, long double-stranded structure, which facilitates the release of carbon nanodots from GO surface. As a result, fluorescence of carbon nanodots is recovered and initial concentration of target protein can be estimated. This protein detection method shows a favorable linear response with a low limit of detection (2.3 fg mL⁻¹). Furthermore, it is highly selective and capable of detecting target in biological fluids like serum samples, which demonstrates the promising applications of this method.     

Interference swapping in scattering from a nonlocal quantum target

We describe a new and distinctive interferometry in which a probe particle scatters off a superposition of locations of a single free target particle. Probe particles scattering off a single free "mirror" (in one dimension) or a single free "slit" (in two dimensions) can "swap" interference with the superposed target states. The condition for interference is loss of orthogonality of the target states and reduces, in simple examples, to transfer of orthogonality from target to probe states. We analyze experimental parameters and conditions necessary for interference to be observed.     

A Simple QD–FRET Bioprobe for Sensitive and Specific Detection of Hepatitis B Virus DNA

We report here a simple quantum dot-FRET (QD-FRET) bioprobe based on fluorescence resonance energy transfer (FRET) for the sensitive and specific detection of hepatitis B virus DNA (HBV DNA). The proposed one-pot HBV DNA detection method is very simple, rapid and convenient due to the elimination of the washing and separation steps. In this study, the water-soluble CdSe/ZnS QDs were prepared by replacing the trioctylphosphine oxide on the surface of QDs with mercaptoacetic acid (MAA). Subsequently, DNA was attached to QDs surface to form the functional QD-DNA bioconjugates by simple surface ligand exchange. After adding 6-carboxy-X-rhodamine (ROX)-modified HBV DNA (ROX-DNA) into the QD-DNA bioconjugates solution, DNA hybridization between QD-DNA bioconjugates and ROX-DNA was formed. The resulting hybridization brought the ROX fluorophore, the acceptor, and the QDs, the donor, into proximity, leading to energy transfer from QDs to ROX. When ROX-DNA was displaced by the unlabeled HBV DNA, the efficiency of FRET was dramatically decreased. Based on the changes of both fluorescence intensities of QDs and ROX, HBV DNA could be detected with high sensitivity and specificity. Under the optimized conditions, the linear range of HBV DNA determination was 2.5 – 30 nmol L^?1, with a correlation coefficient (R) of 0.9929 and a limit of detection (3σ black) of 1.5 nmol L^?1. The relative standard deviation (R.S.D.) for 12 nmol L^?1 HBV DNA was 0.9 % (n?=?5). There was no interference to non-complementary DNA. Time-resolved fluorescence spectra and fluorescence images were performed to verify the validity of this method and the results were satisfying.     

The frequency characteristics analysis of series photodetector frequency circuit system based on circuit parameters of quartz crystal and its application for bacterial DNA identification

The circuit parameters of quartz crystal were employed for frequency sensitivity analysis of series photodetector frequency circuit system. The influence of circuit parameters of quartz crystal on the oscillation frequency and response sensitivity were theoretically derived and experimentally verified. On the basis of optimal circuit parameters, the DNA probe detection limit 2 pmol/L can be measured by 49.4 MHz sensor system. In comparison with the conventional fluorescence technique, the frequency method showed that the detection limits of DNA probe AH642 with Cy5 fluorescence dye and DNA probe VA180 with Cy5 fluorescence dye were lower than the conventional fluorescence technique by 2–3 orders; meanwhile, through the feature of probe uniqueness, Aeromonas hydrophila DNA and fluorescence probe AH642-Cy5 can be successfully judged for hybridization reaction. Moreover, Vibro alginolyticus DNA and fluorescence probe VA180-Cy5 can be successfully judged for hybridization reaction.     

Brownian ratchet mechanism of translocation in T7 RNA polymerase facilitated by a post-translocation energy bias arising from the conformational change of the enzyme

T7 RNA polymerase can transcribe DNA to RNA by translocating along the DNA. Structural studies suggest that the pivoting rotation of the O helix in the fingers domain may drive the movement of the O helix C-terminal Tyr639 from pre- to post-translocation positions. In a series of all-atom molecular dynamics simulations, we show that the movement of Tyr639 is not tightly coupled to the rotation of the O helix, and that the two processes are only weakly dependent on each other. We also show that the internal potential of the enzyme itself generates a small difference in free energy (ΔE) between the post- and pre-translocation positions of Tyr639. The calculated value of ΔE is consistent with that obtained from single-molecule experimental data. These findings lend support to a model in which the translocation takes place via a Brownian ratchet mechanism, with the small free energy bias ΔE arising from the conformational change of the enzyme itself.     

Silicon nanowires for sequence-specific DNA sensing: device fabrication and simulation

Highly sensitive, sequence-specific and label-free DNA sensors were demonstrated by monitoring the electronic conductance of silicon nanowires (SiNWs) with chemically bonded single-stranded (ss) DNA or peptide nucleic acid (PNA) probe molecules. For a 12-mer oligonucleotide, tens of pM of target ss-DNA in solution was recognized when the complementary DNA oligonucleotide probe was attached to the SiNW surfaces. In contrast, ss-DNA samples of ×1000 concentration with a single-base mismatch produce only a weak signal due to nonspecific binding. In order to gain a physical understanding of the change in conductance of the SiNWs with the attachment of the DNA targets and the probes, process and device simulations of the two-dimensional cross sections of the SiNWs were performed. The simulations explained the width dependence of the SiNW conductance and provided understanding to improve the sensor performance. PACS 85.35.-p; 87.83.+a; 07.07.Df     

Direct immobilization and hybridization of DNA on group III nitride semiconductors

A key concern for group III-nitride high electron mobility transistor (HEMT) biosensors is the anchoring of specific capture molecules onto the gate surface. To this end, a direct immobilization strategy was developed to attach single-stranded DNA (ssDNA) to AlGaN surfaces using simple printing techniques without the need for cross-linking agents or complex surface pre-functionalization procedures. Immobilized DNA molecules were stably attached to the AlGaN surfaces and were able to withstand a range of pH and ionic strength conditions. The biological activity of surface-immobilized probe DNA was also retained, as demonstrated by sequence-specific hybridization experiments. Probe hybridization with target ssDNA could be detected by PicoGreen fluorescent dye labeling with a minimum detection limit of 2 nM. These experiments demonstrate a simple and effective immobilization approach for attaching nucleic acids to AlGaN surfaces which can further be used for the development of HEMT-based DNA biosensors.     

Nonperturbative scaling theory of free magnetic moment phases in disordered metals

The crossover between a free magnetic moment phase and a Kondo phase in low-dimensional disordered metals with dilute magnetic impurities is studied. We perform a finite-size scaling analysis of the distribution of the Kondo temperature obtained from a numerical renormalization group calculation of the local magnetic susceptibility for a fixed disorder realization and from the solution of the self-consistent Nagaoka-Suhl equation. We find a sizable fraction of free (unscreened) magnetic moments when the exchange coupling falls below a critical value Jc. Between the free moment phase due to Anderson localization and the Kondo-screened phase we find a phase where free moments occur due to the appearance of random local pseudogaps at the Fermi energy whose width and power scale with the elastic scattering rate 1/tau.