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Molecular beacon

Aurélie Stallivieri, Ludovic Colombeau, Jérôme Devy, Nicolas Etique, Carine Chaintreuil, Bauyrzhan Myrzakhmetov, Mathilde Achard, Francis Baros, Philippe Arnoux, Régis Vanderesse, Céline Frochot
Further improvements in Photodynamic therapy (PDT) necessitate that the dye targets more selectively tumour tissues or neovascularization than healthy cells. Different enzymes such as matrix metalloproteinases (MMPs) are overexpressed in tumour areas. Among these MMPs, gelatinases (MMP-2 and MMP-9) and its activator MMP-14 are known to play a key role in tumour angiogenesis and the growth of many cancers such as glioblastoma multiforme (GBM), an aggressive malignant tumour of the brain. These last years, the concept of photodynamic molecular beacons (PMB) became interesting for controlling the photosensitizer's ability to generate singlet oxygen (1O2) close to target biomolecules as MMPs...
December 24, 2017: Bioorganic & Medicinal Chemistry
Gil Tae Hwang
Sequence-specific detection of nucleic acids has been intensively studied in the field of molecular diagnostics. In particular, the detection and analysis of single-nucleotide polymorphisms (SNPs) is crucial for the identification of disease-causing genes and diagnosis of diseases. Sequence-specific hybridization probes, such as molecular beacons bearing the fluorophore and quencher at both ends of the stem, have been developed to enable DNA mutation detection. Interestingly, DNA mutations can be detected using fluorescently labeled oligonucleotide probes with only one fluorophore...
January 8, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Wancun Zhang, Fang Hu, Qi Zhang, Jiaqi Zhang, Yibo Mao, Peng Wang, Yueqing Gu
In this study, a rapid, sensitive, and specific assay for detecting miRNAs was developed based on a two-stage amplification reaction (TSAR) using molecular beacons (MBs) as turn-on probes. In the TSAR, different miRNAs can be converted to the same reporter oligonucleotides (Y), which can hybridize with the same MB. Therefore, in combination with specific templates, this method can be applied to multiplex miRNA detection by simply using the same MB. The loop region of the MB was screened by computer simulation methods...
March 1, 2018: Talanta
Qian Zhao, Jiafang Piao, Weipan Peng, Yang Wang, Bo Zhang, Xiaoqun Gong, Jin Chang
Identifying the microRNA (miRNA) expression level can provide critical information for early diagnosis of cancers or monitoring the cancer therapeutic efficacy. This paper focused on a kind of gold nanoparticles coated polystyrene microbeads (PS@Au microspheres)-based DNA probe as miRNA capture and duplex specific nuclease (DSN) signal amplification platform based on RGB value read-out for miRNAs detection. In virtue of the outstanding selectivity and simple experimental operation, 5'- fluorochrome -labeled molecular beacons (MBs) were immobilized on PS@Au microspheres via their 3'-thiol, in the wake of the fluorescence quenching by nanoparticle surface energy transfer (NSET)...
January 4, 2018: ACS Applied Materials & Interfaces
Mariia Andrianova, Natalia Komarova, Vitaliy Grudtsov, Evgeniy Kuznetsov, Alexander Kuznetsov
The electrochemical detection of interactions between aptamers and low-molecular-weight targets often lacks sensitivity. Signal amplification improves the detection of the aptamer-analyte complex; Bsm DNA polymerase was used to amplify the signal from the interaction of vanillin and its aptamer named Van_74 on an ion-sensitive field-effect transistor (ISFET)-based biosensor. The aptamer was immobilized on the ISFET sensitive surface. A short DNA probe was hybridized with the aptamer and dissociated from it upon vanillin addition...
December 26, 2017: Sensors
Megan E Dempsey, Hetal D Marble, Tunli Shen, Nicolas L Fawzi, Eric M Darling
Gene expression is used extensively to describe cellular characteristics and behaviors; however, most methods of assessing gene expression are unsuitable for living samples, requiring destructive processes such as fixation or lysis. Recently, molecular beacons have become a viable tool for live-cell imaging of mRNA molecules in situ. Historically, beacon-mediated imaging has been limited to fluorescence-based approaches. We propose the design and synthesis of a novel molecular beacon for magnetic resonance detection of any desired target nucleotide sequence...
December 22, 2017: Bioconjugate Chemistry
Yoojin Park, Duangrat Nim-Anussornkul, Tirayut Vilaivan, Takashi Morii, Byeang Hyean Kim
We have developed RNA-based quencher-free molecular aptamer beacons (RNA-based QF-MABs) for the detection of ATP, taking advantage of the conformational changes associated with ATP binding to the ATP-binding RNA aptamer. The RNA aptamer, with its well-defined structure, was readily converted to the fluorescence sensors by incorporating a fluorophore into the loop region of the hairpin structure. These RNA-based QF-MABs exhibited fluorescence signals in the presence of ATP relative to their low background signals in the absence of ATP...
December 6, 2017: Bioorganic & Medicinal Chemistry Letters
Kensuke Sawamura, Masahiko Hashimoto
A fluorescence quenching assay based on a ligase detection reaction was developed for facile and rapid detection of point mutations present in a mixed population of non-variant DNA. If the test DNA carried a targeted mutation, then the two allele-specific primers were ligated to form a molecular beacon resulting in the expected fluorescence quenching signatures. Using this method, we successfully detected as low as 5% mutant DNA in a mixture of wild-type DNA (t test at 99% confidence level).
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
Jiao Li, Yalan Liu, Xiaoqian Zhu, Gang Chang, Hanping He, Xiuhua Zhang, Shengfu Wang
Electrochemical sensors now play an important role in analysis and detection of nucleic acids. In this work, we present a novel double-signal technique for electrochemically measuring the sequence and length of the d(CAG)n repeat. The double-signal technique used an electrochemical molecular beacon (a hairpin DNA labeled with ferrocene), which was directly modified on the surface of a gold electrode. While a reporter probe (a DNA sequence labeled with horseradish peroxidase) was hybridized to the target DNA...
November 20, 2017: ACS Applied Materials & Interfaces
Cheng Jin, Ting Fu, Ruowen Wang, Hui Liu, Jianmei Zou, Zilong Zhao, Mao Ye, Xiaobing Zhang, Weihong Tan
Molecular beacons (MBs) are simple, but practical, fluorescent nanoprobes widely used to detect small molecules, nucleic acids and proteins. However, some challenges still remain when MBs are employed in complex biological environments, such as instability and non-target interference. To meet such challenges, we have designed and synthesized fluorinated molecular beacons (FMBs) as functional DNA nanomolecules for cellular imaging, in which the stem sequence is simply composed of artificial nucleotides with 3,5-bis(trifluoromethyl)benzene (F) as the surrogate base of natural A, T, C and G bases...
October 1, 2017: Chemical Science
Sarah Elisabeth Ochmann, Carolin Vietz, Kateryna Trofymchuk, Guillermo P Acuna, Birka Lalkens, Philip Tinnefeld
Due to the limited signal-to-background ratio, molecular diagnostics requires molecular amplification of the target molecules or molecular signal amplification after target recognition. For direct molecular detection, we demonstrate a purely physical fluorescence enhancement process which can elevate the fluorescence signal of single fluorescent dyes by several orders of magnitude. To this end, DNA origami-based optical antennas with a height of around 125 nm are used, which utilize metallic nanoparticles to create a hotspot where fluorescence signals are enhanced by plasmonic effects...
November 16, 2017: Analytical Chemistry
Akbar Esmaeili, Meissam Khodaei
Rifampin (RIF) is a bactericidal antibiotic drug and potent inducer of hepatic and intestinal cytochrome P-450 (CYP-450) enzyme systems. Given by mouth or intravenously, it can cause numerous clinical drug interactions; thus, alternative systems of drug delivery that bypass some or all of its toxic effects are well worth investigating. In this study, a controlled layer-by-layer (LBL) process of encapsulating RIF in biocompatible alginate and chitosan polymers loaded onto Fe3 O4 nanoparticles was developed. Fe3 O4 nanoparticles were synthesized from FeCl3 ·6H2 O using a hydrothermal procedure...
November 16, 2017: Journal of Biomedical Materials Research. Part A
Mingming Chen, Yantao Yang, Christopher J Krueger, Antony K Chen
Conventional molecular beacons (MBs) have been used extensively for imaging specific endogenous RNAs in living cells, but their tendency to generate false-positive signals as a result of nuclease degradation and/or nonspecific binding limits sensitive and accurate imaging of intracellular RNAs. In an attempt to overcome this limitation, MBs have been synthesized with various chemically modified oligonucleotide backbones to confer greater biostability. We have recently developed a new MB architecture composed of 2'-O-methyl RNA (2Me), a fully phosphorothioate (PS) modified loop domain and a phosphodiester stem (2Me/PSLOOP MB)...
2018: Methods in Molecular Biology
Yantao Yang, Mingming Chen, Christopher J Krueger, Andrew Tsourkas, Antony K Chen
Molecular beacons (MBs), a class of oligonucleotide-based probes, have enabled researchers to study various RNA molecules in their native live-cell contexts. However, it is also increasingly recognized that, when delivered into cells, MBs have the tendency to be sequestered into the nucleus where they may generate false positive signals. In an attempt to overcome this issue, MBs have been synthesized with chemically modified oligonucleotide backbones to confer greater biostability. Alternatively, strategies have been developed to minimize nuclear entry...
2018: Methods in Molecular Biology
Liang Wan, Tianlan Chen, Jie Gao, Cheng Dong, Ada Hang-Heng Wong, Yanwei Jia, Pui-In Mak, Chu-Xia Deng, Rui P Martins
A digital microfluidic (DMF) system has been developed for loop-mediated isothermal amplification (LAMP)-based pathogen nucleic acid detection using specific low melting temperature (Tm) Molecular Beacon DNA probes. A positive-temperature-coefficient heater with a temperature sensor for real-time thermal regulation was integrated into the control unit, which generated actuation signals for droplet manipulation. To enhance the specificity of the LAMP reaction, low-Tm Molecular Beacon probes were designed within the single-stranded loop structures on the LAMP reaction products...
November 6, 2017: Scientific Reports
Li Min Tay, Christian Wiraja, Yingnan Wu, Zheng Yang, Eng Hin Lee, Chenjie Xu
Proliferative chondrocytes are critical to realize regeneration of damaged epiphyseal growth plate. However, acquiring autologous replacement cells involves highly-invasive procedures and often results in limited cell quantity. Mesenchymal stem cells (MSCs) are a potential source of chondrogenic cells for the treatment of cartilage disorders and injuries. The temporal effect of transforming growth factor beta 3 (TGFβ3) and fibroblast growth factor 2 (FGF2) on the derivation of proliferative chondrocytes from MSCs in 3D agarose was investigated by manipulating the duration of TGFβ3 and FGF2 treatment...
November 6, 2017: Journal of Biomedical Materials Research. Part A
Ivan Petushkov, Daria Esyunina, Vladimir Mekler, Konstantin Severinov, Danil Pupov, Andrey Kulbachinsky
In bacterial RNA polymerase (RNAP), conserved region 3.2 of the σ subunit was proposed to contribute to promoter escape by interacting with the 5'-end of nascent RNA, thus facilitating σ dissociation. RNAP activity during transcription initiation can also be modulated by protein factors that bind within the secondary channel and reach the enzyme active site. To monitor the kinetics of promoter escape in real time, we used a molecular beacon assay with fluorescently labeled σ(70) subunit of Escherichia coli RNAP...
November 3, 2017: Biochemical Journal
Vladimir S Airapetian, Charles H Jackman, Martin Mlynczak, William Danchi, Linda Hunt
The current explosion in detection and characterization of thousands of extrasolar planets from the Kepler mission, the Hubble Space Telescope, and large ground-based telescopes opens a new era in searches for Earth-analog exoplanets with conditions suitable for sustaining life. As more Earth-sized exoplanets are detected in the near future, we will soon have an opportunity to identify habitale worlds. Which atmospheric biosignature gases from habitable planets can be detected with our current capabilities? The detection of the common biosignatures from nitrogen-oxygen rich terrestrial-type exoplanets including molecular oxygen (O2), ozone (O3), water vapor (H2O), carbon dioxide (CO2), nitrous oxide (N2O), and methane (CH4) requires days of integration time with largest space telescopes, and thus are very challenging for current instruments...
November 2, 2017: Scientific Reports
Weijun Zhou, Shaojun Dong
Herein, we report a new fluorescence regulation mechanism of DNA-templated AgNCs caused by coiled DNA. Based on these phenomena, a novel dual fluorescent AgNC-MB with exponential signal enhancement and remarkably low background was developed. The AgNC-MB could effectively facilitate template design and avoid the disturbance caused by undesirable hybridization.
November 2, 2017: Chemical Communications: Chem Comm
Jianguo Xu, Tingting Zheng, Jingqing Le, Lee Jia
Occurrence and application of oligonucleotide probes have promoted great progress in the biochemical analysis field due to their unique biological and chemical properties. In this work, a long-stem shaped multifunctional molecular beacon (LS-MMB) that is responsive to a cancer-related gene, p53, is well-prepared. By designing the probe with long-paired bases at its two ends and short-paired bases between the middle region and the 3' end, the LS-MMB is intelligently endowed with the ability to recognize the target analyte, serve as the polymerization primer/template, and signal the hybridization event synchronously, which is distinctly advantageous over the traditional molecular beacons (MBs)...
October 30, 2017: Analyst
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