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Molecular beacon

Atefeh Javani, Fatemeh Javadi-Zarnaghi, Mohammad Javad Rasaee
Lateral flow assays (LFAs) have promising potentials for point-of-care applications. Recently, many LFAs have been reported that are based on hybridization of oligonucleotide strands. Mostly, biotinylated capture DNAs are immobilized on the surface of a nitrocellulose membrane via streptavidin interactions. During the assay, stable colorful complexes get formed that are visible by naked eyes. Here, we present an inexpensive and unique design of LFA that applies unmodified oligonucleotides at capture lines. The presented LFA do not utilize streptavidin or any other affinity protein...
September 11, 2017: Analytical Biochemistry
Lanbo Wang, Hongyan Zhou, Bin Liu, Chuan Zhao, Jialong Fan, Wei Wang, Chunyi Tong
As a highly conserved damage repair protein, RNase H can specifically hydrolyze RNA in DNA-RNA chimeric strands. DNAzyme, a synthetic single-stranded DNA consisting of binding and catalytic sites, can cleave RNA in the presence of cofactors. In this study, we establish a highly sensitive RNase H assay assisted with DNAzyme's cleavage property. A DNA-RNA chimeric strand, which contains DNAzyme sequences, is used as the hydrolysis substrate of RNase H. The RNase H hydrolysis of the chimeric substrate results in the release of DNAzyme...
September 15, 2017: Analytical Chemistry
Fan Yang, Tingting Zhang, Shan-Shan Li, Pei Song, Kai Zhang, Qi-Yuan Guan, Bin Kang, Jing-Juan Xu, Hong-Yuan Chen
It is a great challenge to design a drug delivery system with controlled manner, especially, triggered by an exclusive endogenous disease marker and with an easily-tracked release process. Herein, we developed a drug delivery platform of carbon dots which connected to stem-loop molecular beacon loaded with doxorubicin and polyethylene glycol modified folic acid. Such platform enables to release drugs on demand under the stimuli of endogenous microRNA-21, and turn on the fluorescence of carbon dots and doxorubicin, which allows to monitor the drug release process...
September 8, 2017: Analytical Chemistry
Benjamin Luby, Gang Zheng
MicroRNA detection is a valuable method for determining cell identity. Molecular beacons are elegant sensors that can transform intracellular microRNA concentration into a fluorescence intensity. While target binding enhances beacon fluorescence, the degree of enhancement is insufficient for demanding applications. Addition of specialty nucleases can allow target recycling and amplify the signal, but this process complicates the assay. We develop and characterize a novel class of beacons susceptible to the endogenous nuclease Argonaute-2 (Ago2)...
September 4, 2017: Angewandte Chemie
Ilya Aparin, Gleb V Proskurin, Andrey V Golovin, Alexey V Ustinov, Andrey A Formanovsky, Timofei S Zatsepin, Vladimir A Korshun
Oligonucleotide probes labeled with pyrene pairs that form excimers have a number of applications in hybridization analysis of nucleic acids. A long excited state lifetime, large Stokes shift and chemical stability make pyrene excimer an attractive fluorescent label. Here we report synthesis of a chiral phosphoramidite building blocks based on (R)-4-amino-2,2-dimethylbutane-1,3-diol, easily available from an inexpensive D-(-)-pantolactone. 1-Pyreneacetamide, 1-pyrenecarboxamide and Dabcyl derivatives have been used in preparation of molecular beacon (MB) probes labeled with one or two pyrenes/quenchers...
August 31, 2017: Journal of Organic Chemistry
Won Jong Rhee, Seunga Jeong
Many studies have recently focused on extracellular vesicles. Extracellular vesicles including exosomes are nanosized vesicles that are produced and secreted by cells. Extracellular vesicles contain various types of nucleic acid biomarkers, including microRNAs (miRNAs ) from their parent cells. As high concentrations of extracellular vesicles are found in most body fluids, miRNA detection of exosomes in body fluids, including blood and urine, enables early and easy disease diagnosis. In this context, the in situ detection method of extracellular vesicles miRNA using molecular beacons is described here...
2017: Methods in Molecular Biology
Ji Won Lee, Ye-Seul Son, Jun Yeon Hwang, Yoojin Park, Gil Tae Hwang
Three fluorescent nucleosides-U(FL), U(AF), and U(DAF), containing fluorene, 2-aminofluorene, and 2-dimethylaminofluorene units, respectively, covalently attached to 2'-deoxyuridine-have been incorporated into the central positions of oligodeoxynucleotides (ODNs) to examine the effects of their flanking bases (FBs) and pH on the emission properties upon hybridization with fully matched and single-base-mismatched targets. The ODN containing U(FL) and cytosine-FBs in the pH range from 5.5 to 8.0 and the ODN containing U(DAF) and cytosine-FBs under slightly acidic conditions (pH 6...
August 30, 2017: Organic & Biomolecular Chemistry
Laura Rindi, Greta Alì, Barbara Fabiani, Gabriella Fontanini, Carlo Garzelli
GeneXpert MTB/RIF (Xpert) assay, a rapid and automated system based on real-time PCR and molecular beacon technology, proved to be a sensitive and specific tool capable of detecting Mycobacterium tuberculosis and rifampin resistance in clinical specimens. In this study we provide a Xpert-dedicated successful protocol for processing paraffin-embedded tissue and assess the feasibility of the Xpert assay-based tuberculosis (TB) diagnosis on these specimens, thus proving the Xpert assay as a valuable TB diagnostic tool in supporting conventional histopathological methods...
September 2017: Tuberculosis
Wei Ma, Pan Fu, Maozhong Sun, Liguang Xu, Hua Kuang, Chuanlai Xu
The development of a unique and universal strategy for the simultaneous quantification of different types of biomolecules (i.e., nucleic acids and proteins) in living cells is extremely challenging. Herein, a two-signal platform, based upon surface-enhanced Raman scattering and upconversion, for the ultrasensitive and quantitative in situ detection of microRNA (miR)-21 and telomerase in living cells is reported. In the presence of miR-21 and telomerase, the hybridization of miR-21 with a molecular beacon leads to the separation of 3,3'-diethylthiocarbamyl cyanine iodide-modified Au NR dimers, resulting in a decrease in Raman signal...
August 18, 2017: Journal of the American Chemical Society
Chan Liu, Sifang Lv, Hang Gong, Chunyan Chen, Xiaoming Chen, Changqun Cai
A quencher-free and enzyme-free fluorescent sensor was proposed to simply and sensitively detect miRNA via the target catalyzed hairpin assembly (CHA) signal amplification in combination with 2-aminopurine (2-AP) molecular beacon (MBs). This sensor contains two DNA hairpins termed as H1 and H2. H1 labeled by 2-AP needs no quenchers because 2-AP can be quenched through its stacking interaction with the adjacent bases. H2 is partially complementary to H1. In the presence of the target microRNA (miRNA), H1 is unfolded and produces the DNA/RNA complexes, enhancing the fluorescent signal...
November 1, 2017: Talanta
Dongshan Xiang, Fengquan Li, Chenyi Wu, Boan Shi, Kun Zhai
We designed two double quenching molecular beacons (MBs) with simple structure based on guanine (G base) and Black Hole Quencher (BHQ), and developed a new analytical method for sensitive simultaneous detection of two DNAs by synchronous fluorescence analysis. In this analytical method, carboxyl fluorescein (FAM) and tetramethyl-6-carboxyrhodamine (TAMRA) were respectively selected as fluorophore of two MBs, Black Hole Quencher 1 (BHQ-1) and Black Hole Quencher 2 (BHQ-2) were respectively selected as organic quencher, and three continuous nucleotides with G base were connected to organic quencher (BHQ-1 and BHQ-2)...
November 1, 2017: Talanta
Stephanie T Young, Joshua R Moore, Clifton P Bishop
We have developed a technique that allows investigators to confirm the presence of blood, semen, and/or saliva in a crime scene sample. It is a confirmatory test where multiple samples can be processed in less than an hour, and it is potentially portable, permitting samples to be processed at the crime scene. Samples at a scene giving a positive result can be further processed while those failing to do so may be ignored. There is a large and growing backlog of DNA evidence in the USA, slowing down the criminal justice system...
July 18, 2017: Journal of Forensic Sciences
Nitesh Sule, Sasi Pasupuleti, Nandita Kohli, Rani Menon, Lawrence J Dangott, Michael D Manson, Arul Jayaraman
Enterohemorrhagic E. coli (EHEC) is a commonly occuring foodborne pathogen responsible for numerous multistate outbreaks in the US. It is known to infect the host gastrointestinal tract, specifically in locations associated with lymphoid tissue. These niches serve as sources of enteric neurotransmitters such as epinephrine and norepinephrine that are known to increase virulence in several pathogens, including enterohemorrhagic E. coli The mechanisms that allow pathogens to target these niches are poorly understood...
July 17, 2017: Infection and Immunity
Zhan-Ming Ying, Zhan Wu, Bin Tu, Weihong Tan, Jian-Hui Jiang
Light-up RNA aptamers are valuable tools for fluorescence imaging of RNA in living cells and thus for elucidating RNA functions and dynamics. However, no light-up RNA sensor has been reported for imaging of microRNAs (miRs) in mammalian cells. We report a novel genetically encoded RNA sensor for fluorescent imaging of miRs in living tumor cells using a light-up RNA aptamer that binds to sulforhodamine and separates it from a conjugated contact quencher. On the basis of the structural switching mechanism for molecular beacon, we show that the RNA sensor activates high-contrast fluorescence from the sulforhodamine-quencher conjugate when its stem-loop responsive motif hybridizes with target miR...
July 18, 2017: Journal of the American Chemical Society
Arash Darbandi, Debopam Datta, Krunal Patel, Gary Lin, Michael A Stroscio, Mitra Dutta
In this article, we report a graphene oxide-based nanosensor incorporating semiconductor quantum dots linked to DNA-aptamers that functions as a 'turn-off' fluorescent nanosensor for detection of low concentrations of analytes. A specific demonstration of this turn-off aptasensor is presented for the case of the detection of mercury (II) ions. In this system, ensembles of aptamer-based quantum-dot sensors are anchored onto graphene oxide (GO) flakes which provide a platform for analyte detection in the vicinity of GO...
July 11, 2017: Nanotechnology
Xiaojuan Liu, Mengmeng Song, Feng Li
Melamine detection has attracted much attention since the discovery of the damage of melamine to human health. Herein, we have developed a sensitive homogeneous electroanalytical platform for melamine detection, which is relied on the formation of triplex molecular beacon integrated with exonuclease III (Exo III)-mediated signal amplification. The formation of triplex molecular beacon was triggered by the recognition and incorporation of melamine to the abasic (AP) site contained in the triplex stem. The stem of the triplex molecular beacon was designed to have a protruding double-strand DNA, which can be recognized and hydrolyzed by Exo III for releasing methylene blue (MB)-labeled mononucleotide...
July 3, 2017: Scientific Reports
Bingzhi Li, Lei Xu, Yue Chen, Wanying Zhu, Xin Shen, Chunhong Zhu, Jieping Luo, Xiaoxu Li, Junli Hong, Xuemin Zhou
Transcription factors (TFs) regulate gene expression by binding to regulatory regions, and their dysregulation is involved in numerous diseases. Thus, they are therapeutic targets and potential diagnostic markers. However, widely used methods for TFs detection are either cumbersome or costly. Herein, we first applied DNA-Ag nanoclusters molecular beacons (AgMBs) in TFs analysis and designed an assay based on the switchable fluorescence of AgMBs. In the absence of TFs, a single-stranded DNA functioned as a reporter is released from a double-stranded DNA probe (referred as dsTFs probe) under exonuclease III (Exo III) digestion...
June 28, 2017: Analytical Chemistry
Ruixue Duan, Zhenyu Zhang, Fuxin Zheng, Longwang Wang, Ju Guo, Tianchi Zhang, Xiaomeng Dai, Shengwei Zhang, Dong Yang, Renrui Kuang, Gongxian Wang, Chaohong He, Abdul Hakeem, Chang Shu, Ping Yin, Xiaoding Lou, Fuqing Zeng, Huageng Liang, Fan Xia
We combine the telomerase extension reaction and microRNA (miRNA)-induced rolling circle amplification, followed by graphene oxide (GO) and nicking enzyme-assisted signal amplification as a method to analyze telomerase and miRNA-21 in urine samples with the following merits. First, it is a binary assay and can simultaneously output double signals that correspond to the quantities of telomerase and miRNA, respectively. Second, telomerase activity is enhanced by using a DNA molecular beacon probe to inhibit the formation of G-quadruplex...
July 19, 2017: ACS Applied Materials & Interfaces
Manali Datta, Dignya Desai, Ashok Kumar
Gene specific DNA based sensors have potential applications for rapid and real time monitoring of hybridization signal with the target nucleic acid of pathogens. Different types of DNA based sensors and their applications have been studied for rapid and accurate detection of pathogens causing human diseases. These sensors are based on surface plasmon resonance, quantum-dots, molecular beacons, piezoelectric and electrochemical etc. Curbing epidemics at an early stage is one of the massive challenges in healthcare systems...
June 2017: Indian Journal of Microbiology
Camilo Molina-Romero, Claudia Rangel-Escareño, Alette Ortega-Gómez, Gerardo J Alanis-Funes, Alejandro Aviles-Salas, Federico Avila-Moreno, Gabriela E Mercado, Andres F Cardona, Alfredo Hidalgo-Miranda, Oscar Arrieta
The current lung cancer classification from the Association for the Study of Lung Cancer (IASLC) / the American Thoracic Society (ATS)/ the European Respiratory Society (ERS) has considerably changed the pathologic diagnosis of lung invasive adenocarcinoma, identifying disease subtypes with substantial implications for medical practice, such as clinical, radiological, molecular and prognostic differences. We analyzed the differences in the genetic expression of adenocarcinoma subtypes according to the new classification...
June 8, 2017: Human Pathology
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