Real-time fluorescent quantitative immuno-PCR method for determination of fluoranthene in water samples with a molecular beacon

A reliable and sensitive competitive real-time fluorescent quantitative immuno-PCR （RTFQ-IPCR） assay using a molecular beacon was developed for the determination of trace fluoranthene （FL） in the environment.Under optimized assay conditions,FL can be determined in the concentration range from 1 fg/mL to 100 ng/mL,with y=0.194x ＋ 7.859,and a correlation coefficient of 0.967 was identified,with a detection limit of 0.6 fg/mL.Environmental water samples were successfully analyzed,recovery was between 90% and 116%,with intra-day relative standard deviation （RSD） of 6.7%-12.8% and inter-day RSD of 8.4%-15.2%.The results obtained from RTFQ-IPCR were confirmed by ELISA,showing good accuracy and suitability to analyze FL in field samples.As a highly sensitive method,the molecular beacon-based RTFQ-IPCR is acceptable and promising for providing reliable test results to make environmental decisions.

REAL-TIME DETECTION OF SURVIVIN mRNA EXPRESSION IN CERVICAL CANCER CELL LINES USING MOLECULAR BEACON IMAGING

Objective To detect the expression of survivin mRNA in cervical cancer cell lines using molecular beacon imaging technology. Methods Human cervical cancer cells (HeLa and SiHa) and human fetal lung fibroblast HFL-I were cultured in vitro. After adding 100nmol/L survivin mRNA molecular beacon, the fluorescent signals were observed under fluorescent microscope. The expressions of survivin in cervical cancer cells and HFL-I cell were examined by immunocytochemical streptravidin-biothin peroxidase (SP) assay at the same time. Results Two kinds of survivin mRNA molecular beacon, with different color fluorescence, had strong fluorescent signal in cervical cancer cell lines, and the signal in SiHa cell line was stronger, but these signals were not found in HFL-I ; Immunocytochemical staining of positive survivin was located in the cytoplasm of cervical cancer cell lines HeLa and SiHa, whereas, no expression of survivin was detected in HFL-I cell line. Conclusion The technology of molecular beacon imaging can be used to detect the expression of survivin mRNA in viable cells successfully, and may provide a new approach to the diagnosis of early stage cervical cancer and the following-up in the clinic.

Real-time Monitoring of Nucleotide Excision of Molecular Beacon Catalyzed by Klenow Fragment

Klenow fragment（KF） uses the activity of a separate exonuclease to excise nucleotide, which is a crucial step in DNA replication and repair. Here is a novel sensitive and convenient method introduced for real-time monitoring nucleotide excision by KF with a molecular beacon as a detecting probe in a homogeneous solution. This method, which overcomes the drawbacks of traditional methods such as discontinuity, time consuming and low sensitivity, was used to assay KF activity and the detection limit reached up to 0.4 U/mL. In addition, the method was applied to investigating the effects of metal ions and chemical drugs on the reaction. The results demonstrate that it is a potential high-throughput assay for screening inhibitors and activity analysis of KF in vitro.

Use of siRNA molecular beacons to detect and attenuate mycobacterial infection in macrophages

Tuberculosis is one of the leading infectious diseases plaguing mankind and is mediated by the facultative pathogen, Mycobacterium tuberculosis(MTB). Once the pathogen enters the body, it subverts the host immune defenses and thrives for extended periods of time within the host macrophages in the lung granulomas, a condition called latent tuberculosis(LTB). Persons with LTB are prone to reactivation of the disease when the body's immunity is compromised. Currently there are no reliable and effective diagnosis and treatment options for LTB, which necessitates new research in this area. The mycobacterial proteins and genes mediating the adaptive responses inside the macrophage is largely yet to be determined. Recently, it has been shown that the mce operon genes are critical for host cell invasion by the mycobacterium and for establishing a persistent infection in both in vitro and in mouse models of tuberculosis. The Yrb E and Mce proteins which are encoded by the MTB mce operons display high degrees of homology to the permeases and the surface binding protein of the ABC transports, respectively. Similarities in structure and cell surface location impute a role in cell invasion at cholesterol rich regions and immunomodulation. The mce4 operon is also thought to encode a cholesterol transport system that enables the mycobacterium to derive both energy and carbon from the host membrane lipids and possibly generating virulence mediating metabolites, thus enabling the bacteria in its long term survival within the granuloma. Various deletion mutation studies involving individual or whole mce operon genes have shown to be conferring varying degrees of attenuation of infectivity or at times hypervirulence to the host MTB, with the deletion of mce4 A operon gene conferring the greatest degree of attenuation of virulence. Antisense technology using synthetic si RNAs has been used in knocking down genes in bacteria and over the years this has evolvedinto a powerful tool for elucidating the roles of various genes mediating infectivity and survival in mycobacteria. Molecular beacons are a newer class of antisense RNA tagged with a fluorophore/quencher pair and their use for in vivo detection and knockdown of mR NA is rapidly gaining popularity.

Graphene oxide and molecular beacons-based multiplexed DNA detection by synchronous fluorescence analysis

We have developed a multiplexed DNA detection method based on graphene oxide （GO） and molecular beacons （MBs） by synchronous fluorescence analysis, demonstrated it by an oligonucleotide sequence of wild-type HBV （T1） and a re- verse-transcription oligonucleotide sequence of the RNA fragment of HIV （T2） as a model system. In the absence of targets DNA, FAM-tagged free MB probes （PHBv） and ROX-tagged free MB probes （PHIv） are adsorbed on GO via π-π interactions between DNA nucleobases and nucleosides, and the π-rich GO brings the fluorophores of MB and GO into close proximity. And then, the fluorescence of fluorophores is quenched by GO. But in the presence of targets DNA, PHBV and PHW hybridize with their targets DNA resulting in the formation of double-stranded DNA （dsDNA）, causing the separation of PHBV and PHW from the surface of GO and the recovery of the fluorescence of fluorophores （FAM and ROX） simultaneously. The simultane- ous detection of T1 and T2 can be realized by measuring fluorescence signals of FAM and ROX, respectively. Under the op- timum conditions, the fluorescence intensities of two dyes all exhibit good linear dependence on their target DNA concentra- tion in the range of 5×10-11-5×10 9 M. The detection limit of T1 is 3×10-11 M （3σ）, and that of T2 is 2×10-11 M. Compared with other methods for DNA detection based on GO, the proposed method has some advantages including higher selectivity and shorter analytical time.

Engineering Novel Molecular Beacon Constructs to Study Intracellular RNA Dynamics and Localization

With numerous advancements in novel biochemical techniques, our knowledge of the role of RNAs in the regulation of cellular physiology and pathology has grown significantly over the past several decades. Nevertheless, detailed information regarding RNA processing, trafficking, and localization in living cells has been lacking due to technical limitations in imaging single RNA transcripts in living cells with high spatial and temporal resolution. In this review, we discuss tech- niques that have shown great promise for single RNA imaging, followed by highlights in our recent work in the development of molecular beacons （MBs）, a class of nanoscale oligonucleotide-probes, for detecting individual RNA transcripts in living cells. With further refinement of MB design and development of more sophisticated fluorescence microscopy techniques, we envision that MB-based approaches could promote new discoveries of RNA functions and activities.

Inhibited aptazyme-based catalytic molecular beacon for amplified detection of adenosine

Combining the inhibited aptazyme and molecular beacon （MB）, we developed a versatile sensing strategy for amplified detection of adenosine. In this strategy, the adenosine aptamer links to the 8-17 DNAzyme to form an aptazyme. A short sequence, denoted as inhibitor, is designed to form a duplex spanning the aptamer-DNAzyme junction, which blocks the catalytic function of the DNAzyme. Only in the presence of target adenosine, the aptamer binds to adenosine, thus the inhibitor dissociates from the aptamer portion of the aptazyme and can no longer form the stable duplex required to inhibit the catalytic activity of the aptazyme. The released DNAzyme domain will hybridize to the MB and catalyze the cleavage in the presence of Zn2＋, making the fluorophore separate from the quencher and resulting in fluorescence signal. The results showed that the detection method has a dynamic range from 10 nmol/L to 1nmol/L, with a detection limit of 10 nmol/L.

Ligase-based ultrasensitive detection of DNAzyme cleavage product using molecular beacon

Detection for deoxyribozyme （DNAzyme） cleavage usually needs complex and time-consuming radial labeling, gel electro- phoresis and autoradiography. A new approach was reported for detection DNAzyme cleavage product based on molecular beacon （MB）. Part of the loop of MB was designed to complementary to DNAzyme cleavage product. MB was employed to monitor ligation process of RNA/DNA complex and to convert directly cleavage product information into fluorescence signal. Detection limit of the assay is 0.02 nmol/L. The cleavage product of 8-17 DNAzyme against HCV-RNA was detected perfectly based on this assay. The method is fast, simple and ultrasensitive, which might hold great promise in DNAzyme reaction and DNAzyme gene therapy.

Mechanics of molecular beacons for mRNA detecting

Decoding genetic information is crucial for gene therapy and cancer diagnosis,which has attracted growing interest in the field of clinical medicine and life science.In this study,we conducted a comprehensive exploration to obtain the detection mechanism of molecular beacons from a mechanics point of view.The potential energy function of molecular beacon/target system is established firstly,based on which the profile of molecular beacons is solved by genetic algorithm optimization.The length of stem and the total energy are further calculated when the target is hybridized with loop and stem.The results show that the hybridization between target and stem is energetically favorable compared with that between target and loop,indicating a new detection strategy.These analyses may cast light on understanding the mechanism of molecular beacons detection,and further help to design novel molecular beacons with high resolution and quantification.

The exploration of quantum dot-molecular beacon based MoS_(2) fluorescence probing for myeloma-related Mirnas detection

Highly sensitive and reliable detection of multiple myeloma remains a major challenge in liquid biopsy. Herein, for the first time, quantum dot-molecular beacon (QD-MB) functionalized MoS_(2) (QD-MB @MoS_(2)) fluorescent probes were designed for the dual detection of multiple myeloma (MM)-related miRNA-155 and miRNA-150. The results indicate that the two probes can effectively detect miRNA-155 and miRNA-150 simultaneously with satisfactory recovery rates, and the limit of detections (LODs) of miRNA-155 and miRNA-150 in human serum are low to 7.19 fM and 5.84 fM, respectively. These results indicate that our method is the most sensitive detection so far reported and that the designed fluorescent probes with signal amplification strategies can achieve highly sensitive detection of MM-related miRNAs for MM diagnosis.

A simple aptamer molecular beacon assay for rapid detection of aflatoxin B1

Aflatoxin B1(AFB1)is a highly toxic mycotoxin,and rapid and sensitive detection of AFB1 is in demand for food safety and environmental analysis.Here we described a simple aptamer molecular beacon assay for rapid detection of aflatoxin B1(AFB1)by using an aptamer with a fluorescein(FAM)label at the 50 end and a fluorescence quencher(black hole quencher 1,BHQ1)at the 30 end.In the presence of AFB1,the aptamer probe bound with AFB1 and induced a hairpin structure,drawing FAM and BHQ1 into close proximity and leading to fluorescence quenching.This assay allowed for a detection limit of 3.9 nmol/L and a dynamic range from 3.9 nmol/L to 4 mmol/L.Specificity test showed other mycotoxins including ochratoxin A,ochratoxin B,fumonisin B1,fumonisin B2,and zearalenone had negligible influence on detection of AFB1.AFB1 spiked in diluted liquor wine,methanol,or corn flour samples was successfully detected by using this aptamer probe,and the assay showed potential for real sample analysis.

Ribozyme probe based on molecular beacon for real time monitoring of enzymatic cleavage process

Ribozyme probe based on molecular beacon (MBR) for monitoring enzymatic cleavage process in real time is designed and studied. The approach relies on ri-bozyme substrates modified at the two arms, with a fluores-cent moiety attached to the end of one arm and a non-fluorescent quenching moiety attached to the end of the other arm. MBR is employed to directly convert the cleavage information into fluorescence signal in real time. Compared with traditional approach, this method provides a no-radiolabeling, sensitive and effective way to research on the ribozyme activity, enzymatic dynamic process and ri-bozyme function during gene therapy. The activity of the ribozyme against hepatitis C virus RNA (HCV-RNA) is stud-ied based on this assay.

Quantitative detection of ING1 mRNA under different gene regulation based on molecular beacon

The effects of drug treatment, gene transfection, and p53 RNA interference (RNAi) on level of ING1 mRNA in tumor cells were quantitatively detected with the help of ING1 molecular beacon (MB)/cRNA standard curve based on MB detection technology. Results showed that the level of ING1 mRNA could be upregulated by 5-FU treatment or ING1 transfection in low expression cell line of MCF-7 and be inhibited by silencing p53 with RNAi technology in normal expression cell line of CNE2. The level of ING1 varied from 7.7×10?16 to 53.4× 10?16 mol/μg total RNA of tumor cells. The results not only provided evidence for the regulation effects of gene expression but also were applied to investigat- ing the interaction of multigenes on signal transduc- tion pathway.

Protein analysis based on molecular beacon probes and biofunctionalized nanoparticles

With the completion of the human genome-sequencing project, there has been a resulting change in the focus of studies from genomics to proteomics. By utilizing the inherent advantages of molecular beacon probes and biofunctionalized nanoparticles, a series of novel principles, methods and techniques have been exploited for bioanalytical and biomedical studies. This review mainly discusses the applications of molecular beacon probes and biofunctionalized nanoparticles-based technologies for realtime, in-situ, highly sensitive and highly selective protein analysis, including the nonspecific or specific protein detection and separation, protein/DNA interaction studies, cell surface protein recognition, and antigen-antibody binding process-based bacteria assays. The introduction of molecular beacon probes and biofunctionalized nanoparticles into the protein analysis area would necessarily advance the proteomics research.

Monitoring p21 mRNA expression in living cell based on molecular beacon fluorescence increasing rate

Studying the expression level of mRNA in living cells will offer tremendous opportunities for ad-vancement in cell biology research,disease diagnostics,and drug discovery.In this paper,a molecular beacon(MB)specific for the important tumor suppressor gene p21 has been designed and synthesized.The fluorescence signal was detected in real-time after the MB entered the cytoplasm of nasopharyn-geal carcinoma cells.After injecting the p21MB into nasopharyngeal carcinoma cell and p33-trans-fected nasopharyngeal carcinoma cell,the consistent increase of fluorescent signal intensity was de-tected in both cell lines,and maximum fluorescence intensity achieved in about 15 min.In about 4 min following microinjection,the fluorescence increasing rate was significantly different between these two cell lines,which indicate the different p21 mRNA expression levels.The results obtained in the real-time detection were also validated by RT-PCR.Analysis of the initial fluorescence increasing rate can effi-ciently reduce the side effect of enzyme and improve the accuracy in living cell mRNA detection.

mRNA detection in living cell using phosphorothioate-modified molecular beacon

In this study, GFP mRNA in COS-7 cell and GFP-transfected COS-7 cell was detected in real time using phosphorothioate-modified molecular beacon based on living cell imaging method. Results showed that phosphorothioate-modified molecular beacon still kept the advantages of molecular beacon, such as, excellent selectivity, high sensitivity, and no separation detection. In addition, this modification could significantly increase the nuclease resistance of molecular beacon. Phosphorothioate-modified molecular beacon can efficiently reduce the false positive signal and improve the accuracy of living cell mRNA detection.

Real time monitoring of nucleic acids ligation based on molecular beacon

A novel method has been developed to monitor the nucleic acids ligation process. Molecular beacon was employed here to convert the ligation information into fluo-rescence signal quickly and quantitatively. This method pro-vides effective and original approach to researching the dy-namic ligation process and the interactions between nucleic acids and ligase. An analytical method for T4 DNA ligase based on this way has been built up with a linear detection range from 2.3×10-4 U/mL to 0.23 U/mL. It is rapid and sensitive to detect 2.8×10-5 U T4 DNA ligase in 10 min.

Development and Application of Detection Methods for Capture and Transcription Elongation Rate of Bacterial Nascent RNA

Objective Detection and quantification of RNA synthesis in cells is a widely used technique for monitoring cell viability,health,and metabolic rate.After exposure to environmental stimuli,both the internal reference gene and target gene would be degraded.As a result,it is imperative to consider the accurate capture of nascent RNA and the detection of transcriptional levels of RNA following environmental stimulation.This study aims to create a Click Chemistry method that utilizes its property to capture nascent RNA from total RNA that was stimulated by the environment.Methods The new RNA was labeled with 5-ethyluridine(5-EU)instead of uracil,and the azido-biotin medium ligand was connected to the magnetic sphere using a combination of“Click Chemistry”and magnetic bead screening.Then the new RNA was captured and the transcription rate of 16S rRNA was detected by fluorescence molecular beacon(M.B.)and quantitative reverse transcription PCR(qRT-PCR).Results The bacterial nascent RNA captured by“Click Chemistry”screening can be used as a reverse transcription template to form cDNA.Combined with the fluorescent molecular beacon M.B.1,the synthesis rate of rRNA at 37℃is 1.2 times higher than that at 15℃.The 16S rRNA gene and cspI gene can be detected by fluorescent quantitative PCR,it was found that the measured relative gene expression changes were significantly enhanced at 25℃and 16℃when analyzed with nascent RNA rather than total RNA,enabling accurate detection of RNA transcription rates.Conclusion Compared to other article reported experimental methods that utilize screening magnetic columns,the technical scheme employed in this study is more suitable for bacteria,and the operation steps are simple and easy to implement,making it an effective RNA capture method for researchers.

奥曲肽修饰的壳聚糖纳米递送分子信标成像肺癌研究

目的 探究通过奥曲肽(OCT)修饰的壳聚糖(CS)miR-155分子信标(miR-155-MB)纳米(CS-miR-155-MB-OCT)识别miR-155并成像肺癌细胞用于肺癌早期诊断。方法 通过尾静脉注射A549肺癌细胞建立肺移植瘤裸鼠模型;通过鼻腔滴入Cre腺病毒,分别在滴入腺病毒后的4、6、8、12周处死小鼠建立LSL K-ras G12D转基因小鼠肺部的非典型增生、腺瘤、原位癌、肺腺癌的不同病变时期肺腺癌模型;取肺组织行HE染色观察。免疫组化染色检测肺移植瘤组织及不同病变时期转基因小鼠肺组织生长抑素受体2(SSTR2)的表达;实时荧光定量PCR检测不同病变时期转基因小鼠肺组织miR-155的表达。在肺移植瘤裸鼠模型中,尾静脉注射CS-miR-155-MB或CS-miR-155-MB-OCT;转基因小鼠模型中,尾静脉注射CS-miR-155-MB-OCT;活体成像仪检测肺移植瘤裸鼠及转基因小鼠不同病变时期肺部荧光信号;制作肺组织冰冻切片,激光共聚焦扫描显微镜(CLSM)检测荧光信号来源。结果 HE染色显示成功构建了肺移植瘤裸鼠模型及转基因小鼠肺部的非典型增生、腺瘤、原位癌、肺腺癌的不同病变时期肺癌模型。肺移植瘤及不同病变时期病变组织均表达SSTR2。转基因小鼠模型中,随着疾病进展,miR-155表达逐渐升高(P<0.05)。在肺移植瘤裸鼠模型中,CS-miR-155-MB-OCT组肺部荧光信号强于CS-miR-155-MB组(P<0.05);转基因小鼠模型中,随着肺癌的进展,荧光信号逐渐增强(P<0.05);将肺组织再次成像后发现荧光信号来自肺部,CLSM发现荧光信号来自肿瘤细胞及部分正常肺泡上皮细胞。结论 CS-miR-155-MB-OCT能够根据产生的荧光强度变化动态反映肺癌的发生发展,从而为肺癌的早期诊断提供新技术。

基于DNAzyme的荧光生物传感器快速检测金黄色葡萄球菌研究

【目的】为解决传统方法检测金黄色葡萄球菌耗时长、操作复杂等问题,研发一种基于脱氧核酶(DNAzyme)的荧光生物传感器,实现金黄色葡萄球菌的快速检测。【方法】将特异性DNAzyme和互补链Subatrate相结合制成荧光生物传感器,并对荧光生物传感器进行生物材料浓度和溶液pH优化,并对金黄色葡萄球菌、大肠埃希菌、芽孢杆菌、无乳链球菌、变形杆菌等进行特异性检测;最后对牛奶样品进行基于DNAzyme的荧光生物传感器的试验验证。【结果】基于DNAzyme的荧光生物传感器在pH为6.8时,3 min内可以实现对金黄色葡萄球菌的检测,线性范围为1~1×10^(7) cfu·mL^(−1),最低检测限为1 cfu·mL^(−1)。【结论】基于DNAzyme的荧光生物传感器解决了传统检测方法耗时长、操作复杂等问题,实现了对金黄色葡萄球菌的快速检测,具有重要的应用价值。