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.     

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.     

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.     

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.     

Low-cost fibered fluorescence spectroscopic probe designed for biomolecular film characterization

We present a new combination of a fluorescent film deposited onto a chip and a new kind of low-cost optical fluorescence probe. The probe consists of an optical fiber which guides the excitation beam to the chip and a second one which collects the fluorescence light toward a spectrometer slotted into a PC. The resulting data are then processed to extract the pertinent information. This system is designed for the detection of DNA but, at present, we have achieved the detection of functionalized lipidic vesicles and studied the photobleaching process of such films.     

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.     

基于酶剪切量子点荧光放大技术的双元miRNA定量检测

将量子点荧光特性与双链特异性核酸酶的DNA剪切特性相结合,提出一种高灵敏度、高特异性的双元miRNA定量检测方案.首先,将量子点和四氧化三铁磁性纳米粒子分别与捕获DNA链接形成捕获探针,再与待测miRNA互补配对形成异源双链杂合结构,随后双链特异性核酸酶对杂合结构中的捕获DNA进行特异性剪切,实现量子点和待测miRNA从捕获探针分离,且分离的待测miRNA与捕获探针上未配对的DNA开始新一轮杂交和再剪切.经过上述循环过程,量子点从捕获探针大量释放,荧光信号不断增强,实现肿瘤标志物miRNA的高灵敏检测.实验结果表明,基于酶剪切量子点荧光放大技术,在1fmol/L至100pmol/L的浓度范围内,同时实现了肿瘤标志物miRNA-141及循环miRNA内参miRNA-1228的特异性定量检测,其检出限分别达到0.69fmol/L和0.21fmol/L.与实时荧光定量多聚核苷酸链式反应方法相比,该方案获得了相同的检测结果,且具有更高灵敏度.     

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.     

Goldview标记的DNA荧光毛细生物传感器的研究

对Goldview(GV)作为荧光标记物的DNA荧光毛细生物传感器进行了研究。以荧光毛细分析法(fluorescence capillary analysis, FCA)为基础, 在毛细管内壁通过Poly-l-lysine将20-mer-ssDNA探针固定, 制成DNA荧光毛细生物传感器(DNA fluorescence capillary biosensor, DNA-FCB),DNA-FCB与互补靶DNA杂交,通过GV染色后,检测杂交产物的荧光强度,实现对靶DNA的定性和定量分析。样品用量12 μL, 靶DNA的浓度在0.4～4 μmol·L-1(2.4～24 mg·L-1)范围内和荧光强度有良好的线性关系(y=65.911x+3.994 4,r=0.998 9);RSD<3.5%,检出限0.39 μmol·L-1(2.2 mg·L-1),能达到定量检测靶DNA的目的。用DNA-FCB测定靶DNA操作简便, 试样、试剂用量少,测定成本极低, 能大大减少环境污染。     

Two-Photon Excited Fluorescence Energy Transfer: A Study Based on Oligonucleotide Rulers

The use of two-photon excitation of fluorescence for detection of fluorescence resonance energy transfer (FRET) was studied for a selected fluorescent donor–acceptor pair. A method based on labeled DNA was developed for controlling the distance between the donor and the acceptor molecules. The method consists of hybridization of fluorescent oligonucleotides to a complementary single-stranded target DNA. As the efficiency of FRET is strongly distance dependent, energy transfer does not occur unless the fluorescent oligonucleotides and the target DNA are hybridized. A high degree of DNA hybridization and an excellent FRET efficiency were verified with one-photon excited fluorescence studies. Excitation spectra of fluorophores are usually wider in case of two-photon excitation than in the case of one-photon excitation [1]. This makes the selective excitation of donor difficult and might cause errors in detection of FRET with two-photon excited fluorescence. Different techniques to analyze the FRET efficiency from two-photon excited fluorescence data are discussed. The quenching of the donor fluorescence intensity turned to be the most consistent way to detect the FRET efficiency. The two-photon excited FRET is shown to give a good response to the distance between the donor and the acceptor molecules.     

Study on the Interaction of the CpG Alternating DNA with CdTe Quantum Dots

A novel sensitive method for detection of DNA methylation was developed with thioglycollic acid (TGA)-capped CdTe quantum dots (QDs) as fluorescence probes. Recognition of methylated DNA sites would be useful strategy due to the important roles of methylation in disease occurrence and developmental processes. DNA methylation occurs most often at cytosine-guanine sites (CpG dinucleotides) of gene promoters. The QDs significantly interacted with hybridized unmethylated and methylated DNA. The interaction of CpG rich methylated and unmethylated DNA hybrid with quantum dots as an optical probe has been investigated by fluorescence spectroscopy and electrophoresis assay. The fluorescence intensity of QDs was highly dependent to unmethylated and methylated DNA. Specific site of CpG islands of Adenomatous polyposis coli (APC), a well-studied tumor suppressor gene, was used as the detection target. Under optimum conditions, upon the addition of unmethylated dsDNA, the fluorescence intensity increased in linear range from 1.0?×?10^??10 to 1.0?×?10^??6M with detection limit of 6.2?×?10^??11 M and on the other hand, the intensity of QDs showed no changes with addition of methylated dsDNA. We also demonstrated that the unmethylated and methylated DNA and QDs complexes showed different mobility in electrophoresis assay. This easy and reliable method could distinguish between methylated and unmethylated DNA sequences.     

快速简便的杂交检测DNA

Southern杂交作为黄金标准,已广泛运用于DNA的检测上。但是,经典的southern杂交和近年来一些DNA检测方法存在放射性污染,操作繁琐,耗时,对实验仪器设备要求高等问题。本文利用异硫氰酸荧光素(FITC)标记的dUTP合成DNA探针建立了快速检测DNA的液相杂交方法。该方法包括探针制备、液相杂交、电泳分离和信号检测四个步骤,并在此基础上对FITC-双链和FITC-单链探针的杂交效果作了比较。结果显示,使用FITC标记的两种探针都能取得良好的实验结果,但单链探针较双链的检测灵敏度高;双链DNA探针可以检测出0.8 μg(3.64×10-13 mol)的质粒,而单链DNA探针可以检测出0.38 μg(1.82×10-13 mol)的质粒DNA,在检出效率上是前者的2.1倍。整个检测过程操作简便,可在3 h内完成,可较好地解决了其他DNA检测方法存在的费时费力的问题。     

Investigation of a Fluorescence Signal Amplification Mechanism Used for the Direct Molecular Detection of Nucleic Acids

A fluorescence signal amplification mechanism allowing detection limits for DNA in the zeptomolar range was investigated. Photophysical properties of the molecular system were studied in order to better explain the signal amplification that is observed. We show that the confinement of a fluorescent DNA hybridization transducer in aggregates improves its quantum yield and photostability. Furthermore, we show that the combination of the resonance energy transfer occurring within the aggregates with the use of a conjugated polymer as the hybridization transducer and donor allows ultrafast and efficient energy coupling to the aggregates and can lead to the excitation of a large number of acceptors by only one donor.     

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.     

Thermodynamics of RNA/DNA hybridization in high-density oligonucleotide microarrays

We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high-density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity vs. the hybridization free energy of RNA/DNA duplexes in solution, for perfect matching and mismatching probes. Both values tend to align on a single master curve in good agreement with Langmuir adsorption theory, provided one takes into account the decrease of the effective target concentration due to target–target hybridization in solution. We give an example of a deviation from the expected thermodynamical behavior for the probe set 1091_at due to annotation problems, i.e., the surface-bound probe is not the exact complement of the target RNA sequence, because of errors present in public databases at the time when the array was designed. We show that the parametrization of the experimental data with RNA/DNA free energy improves the quality of the fits and enhances the stability of the fitting parameters compared to previous studies.     

Detection of <Emphasis Type="Italic">Bifidobacterium</Emphasis> Species-specific 16S rDNA Based on QD FRET Bioprobe

Fluorescence resonance energy transfer (FRET) that consists of quantum dot as donors and organic fluorophore dyes as acceptors has been a very important method to detect biomolecules such as nucleic acids. In this work, we established a new FRET detection system of Bifidobacterium species-specific 16S rDNA using QD—ROX FRET bioprobe, in which 525 nm QD-DNA conjugation consisted of the carboxyl-modified QD and the amino-modified DNA in the presence of EDC. Both ROX-DNA and the conjugation above could hybridize with the target DNA after forming the QD—ROX bioprobe. When the hybridization made the distance between the QD and ROX to meet FRET effect needed, 525 nm QD fluorescence intensity decreased and ROX fluorescence intensity increased. In the control, there was no notable change of fluorescence intensities without target DNA. It is very clear that the change of the QD and ROX fluorescence intensities provide the good base and guaranty for this rapid and simple detection system.     

基于荧光分析的氨基甲酸酯类农药残留检测系统

通过对氨基甲酸酯类农药在紫外光照射下能够产生荧光的机理研究,设计了一种用于检测氨基甲酸酯类农药残留的荧光系统。该系统采用单光源、双光路结构,能够对测量信号和参考信号同时进行处理。采用所设计的筒式光纤探头激发并探测荧光,设计了相应的信号处理电路,实现了计算机管理。利用该系统和稳态光谱仪对西维因进行了对比实验。结果表明:在激发波长为319nm、荧光波长为654nm时,最小检测浓度为5×10-7μg/L。当西维因浓度范围在0.0～120.0μg/L之间时,系统具有较好的线性关系,线性相关系数r=0.9996(信噪比S/N=5)。该系统达到了荧光检测的指标。     

Real-time detection of DNA interactions with long-period fiber-grating-based biosensor

Using an optical biosensor based on a dual-peak long-period fiber grating, we have demonstrated the detection of interactions between biomolecules in real time. Silanization of the grating surface was successfully realized for the covalent immobilization of probe DNA, which was subsequently hybridized with the complementary target DNA sequence. It is interesting to note that the DNA biosensor was reusable after being stripped off the hybridized target DNA from the grating surface, demonstrating a function of multiple usability.     

Design optimization of fiber optic probes for remote fluorescence spectroscopy

Fiber optic probes are designed, developed and fabricated in the laboratories for remote fluorescence spectroscopic studies in various fields such as investigation of tissues, environmental monitoring, and analysis of samples in hostile environment. Optimized probe design is very much important for efficient transport and collection of photons, which ultimately helps in quantifying resultant emission and understanding light-matter interaction. Instead of the conventional ray optics, Monte Carlo technique has been used to optimize the design of fiber optic probes, comprising only of flat tipped fibers with and without focusing lenses, for remote fluorescence measurement in three different types of target media having different optical properties. Typical probe geometry consists of one excitation fiber surrounded by a ring of collection fibers. The effects of fiber parameters like fiber diameter, numerical aperture, core-clad ratio, arrangement of collection fibers around the excitation fiber and dead space between them, and optical properties of the medium on the performance of probes have been analysed and compared with the results of previous observations, wherever the data are available. The results show a significant difference between the collected emission with and without consideration of dead space, which plays a very significant role in probe design and is dependent on the number of collection fibers in the geometry, relative dimension of collection and excitation fibers and separation between the two. Introduction of a convex lens in the probe increases the amount of fluorescence signal for a given probe arrangement.