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Molecular beacon

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
Nuli Xie, Jin Huang, Xiaohai Yang, Xiaoxiao He, Jianbo Liu, Jiaqi Huang, Hongmei Fang, Kemin Wang
Accurate measurement of intracellular temperature is of great significance in biology and medicine. With use of DNA nanotechnology and inspiration by nature's examples of "protective and reversible responses" exoskeletons, a scallop-inspired DNA nanomachine (SDN) is desgined as a ratiometric nanothermometer for intracellular temperature sensing. The SDN is composed of a rigid DNA tetrahedron, where a thermal-sensitive molecular beacon (MB) is embedded in one edge of the DNA tetrahedron. Relying on the thermal-sensitive MB and fluorescence resonance energy transfer (FRET) signaling mechanism, the "On" to "Off" signal is reversibly responding to "below" and "over" the melting temperature...
November 3, 2017: Analytical Chemistry
Ruili Zhang, Shi Gao, Zhongliang Wang, Da Han, Lin Liu, Qingjie Ma, Weihong Tan, Jie Tian, Xiaoyuan Chen
Multidrug resistance (MDR) resulting from overexpression of P-glycoprotein (Pgp) transporters increases the drug efflux and thereby limits the chemotherapeutic efficacy. It is desirable to administer both an MDR1 gene silencer and a chemotherapeutic agent in a sequential way to generate a synergistic therapeutic effect in multidrug-resistant cancer cells. Herein, we rationally designed an anti-MDR1 molecular beacon (MB)-based micelle (a-MBM) nanosystem, which is composed of a diacyllipid core densely packed with an MB corona...
August 18, 2017: Advanced Functional Materials
Fenglei Gao, Fuyi Zhou, Songjie Chen, Yao Yao, Jing Wu, Dengyang Yin, Deqin Geng, Po Wang
A new homogeneous electrochemical immunoassay strategy was developed for ultrasensitive detection of carcinoembryonic antigen (CEA) based on target-induced proximity hybridization coupled with rolling circle amplification (RCA). The immobilization-free detection of CEA was realized by the use of an uncharged peptide nucleic acid (PNA) probe labeled with ferrocene (Fc) as the electroactive indicator on a negatively charged indium tin oxide (ITO) electrode. In the presence of a target protein and two DNA-labeled antibodies, the proximate complex formed in homogeneous solution could unfold the molecular beacon, and a part of the unfolded molecular beacon as a primer hybridized with the RCA template to initiate the RCA process...
October 20, 2017: Analyst
Seung Won Shin, Byoung Sang Lee, Kisuk Yang, Lunjakorn Amornkitbamrung, Min Su Jang, Bo Mi Ku, Seung-Woo Cho, Jung Heon Lee, Hojae Bae, Byung-Keun Oh, Myung-Ju Ahn, Yong Taik Lim, Soong Ho Um
Since the delivery kinetics of different cell types are different, the signal from the target cell is greatly affected by the noise signal of the diagnostic system. This is a major obstacle hindering the practical application of intracellular diagnostic systems, such as tumor heterogeneity. To address these issues, here we present a microRNA detection platform using fluorescence-encoded nanostructured DNA-based probes. The nanostructured DNA was designed to include molecular beacons for detecting cytosolic microRNA as well as additional fluorophores...
October 18, 2017: Scientific Reports
Anna Dembska, Elzbieta Kierzek, Bernard Juskowiak
Intracellular sensing using fluorescent molecular beacons is a potentially useful strategy for real-time, in vivo monitoring of important cellular events. This work is focused on evaluation of pyrene excimer signaling molecular beacons (MBs) for the monitoring of pH changes in vitro as well as inside living cells. The recognition element in our MB called pHSO (pH-sensitive oligonucleotide) is the loop enclosing cytosine-rich fragment that is able to form i-motif structure in a specific pH range. However, alteration of a sequence of the 6 base pairs containing stem of MB allowed the design of pHSO probes that exhibited different dynamic pH range and possessed slightly different transition midpoint between i-motif and open loop configuration...
October 16, 2017: Analytica Chimica Acta
Lina S Franco, Susan A Holechek, Michael R Caplan, Joseph N Blattman
BACKGROUND: Virus infections often result in quasispecies of viral strains that can have dramatic impacts on disease outcomes. However, sequencing of viruses to determine strain composition is time consuming and often cost-prohibitive. Rapid, cost-effective methods are needed for accurate measurement of virus diversity to understand virus evolution and can be useful for experimental systems. METHODS: We have developed a novel molecular method for sequence-specific detection of RNA virus genetic variants called Tentacle Probes...
October 13, 2017: Virology Journal
Yi-Zhen Lin, Da-Liang Ou, Hsin-Yuan Chang, Wei-Yu Lin, Chiun Hsu, Po-Ling Chang
The family of microRNAs (miRNAs) not only plays an important role in gene regulation but is also useful for the diagnosis of diseases. A reliable method with high sensitivity may allow researchers to detect slight fluctuations in ultra-trace amounts of miRNA. In this study, we propose a sensitive imaging method for the direct probing of miR-10b (miR-10b-3p, also called miR-10b*) and its target (HOXD10 mRNA) in fixed cells based on the specific recognition of molecular beacons combined with highly inclined and laminated optical sheet (HILO) fluorescence microscopy...
September 1, 2017: Chemical Science
Bindu Salim, M V Athira, A Kandaswamy, Madhulika Vijayakumar, T Saravanan, Thiagarajan Sairam
Breast cancer is identified as the highest cause of death in women suffering from cancer. Early diagnosis is the key to increase the survival of breast cancer victims. Molecular diagnosis using biomarkers have advanced much in the recent years. The cost involved in such diagnosis is not affordable for most of the population. The concept being investigated here is to realize a simple diagnosis system for screening cancer by way of a blood test utilizing a miRNA based biomarker with a complementary molecular beacon probe...
September 30, 2017: Biomedical Microdevices
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