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Molecular beacon

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https://www.readbyqxmd.com/read/28302966/highly-sensitive-fluorescence-quantitative-detection-of-mercury-in-soil-based-on-non-labeled-molecular-beacon-and-fluorescent-dye-hoechst-33258
#1
Dongshan Xiang, Kun Zhai, Qiuzhang Sang, Boan Shi, Xiaohong Yang
A highly sensitive and selective fluorescence method of quantitative detection for mercury in soil was developed using non-labeled molecular beacon (MB), single-stranded nucleic acid (ssDNA) and fluorescent dye Hoechst 33258. In this analytical method, the loop of MB was designed to be a sequence that was complementary to the ssDNA with multiple T-T mismatches, the stem of MB was completely designed as C-G base pairs, and both ends of the MB are not modified by any fluorophore and quencher. In the absence of Hg(2+), the interaction between Hoechst 33258 and the MB was very weak, and the fluorescence signal of Hoechst 33258 was very low...
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28255356/microrna-detection-using-a-double-molecular-beacon-approach-distinguishing-between-mirna-and-pre-mirna
#2
Amanda Marie James, Meredith B Baker, Gang Bao, Charles D Searles
MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally regulate gene expression and are recognized for their roles both as modulators of disease progression and as biomarkers of disease activity, including neurological diseases, cancer, and cardiovascular disease (CVD). Commonly, miRNA abundance is assessed using quantitative real-time PCR (qRT-PCR), however, qRT-PCR for miRNA can be labor intensive, time consuming, and may lack specificity for detection of mature versus precursor forms of miRNA...
2017: Theranostics
https://www.readbyqxmd.com/read/28220155/specificity-of-snp-detection-with-molecular-beacons-is-improved-by-stem-and-loop-separation-with-spacers
#3
Valentina M Farzan, Mikhail L Markelov, Alexander Yu Skoblov, German A Shipulin, Timofei S Zatsepin
Molecular beacons (MBs) are valuable tools in molecular biology, clinical diagnostics and analytical chemistry. Here we describe a novel approach for the design of MBs with nucleotide or non-nucleotide linkers between the stem and loop regions. Such modified MBs have significantly improved specificity and performance for single nucleotide polymorphism (SNP) detection. These advantages are especially distinct, when compared to the classic MBs, in the case of possible interactions between the stem and loop regions...
March 13, 2017: Analyst
https://www.readbyqxmd.com/read/28217801/nucleic-acid-detection-using-bret-beacons-based-on-bioluminescent-protein-dna-hybrids
#4
Wouter Engelen, Kayleigh M van de Wiel, Lenny H H Meijer, Bedabrata Saha, Maarten Merkx
Bioluminescent molecular beacons have been developed using a modular design approach that relies on BRET between the bright luciferase NanoLuc and a Cy3 acceptor. While classical molecular beacons are hampered by background fluorescence and scattering, these BRET-beacons allow detection of low pM concentrations of nucleic acids directly in complex media.
February 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28213328/an-integrated-dual-functional-recognition-amplification-bio-label-for-the-one-step-impedimetric-detection-of-micro-rna-21
#5
Sawsen Azzouzi, Wing Cheung Mak, Kamalodin Kor, Anthony P F Turner, Mounir Ben Ali, Valerio Beni
Alteration in expression of miRNAs has been correlated with different cancer types, tumour stage and response to treatments. In this context, a structurally responsive oligonucleotide-based electrochemical impedimetric biosensor has been developed for the simple and sensitive detection of miRNA-21. A highly specific biotinylated DNA/LNA molecular beacon (MB) probe was conjugated with gold nanoparticles (AuNPs) to create an integrated, dual function bio-label (biotin-MB-AuNPs) for both biorecognition and signal generation...
June 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28194461/a-3d-microblade-structure-for-precise-and-parallel-droplet-splitting-on-digital-microfluidic-chips
#6
Cheng Dong, Yanwei Jia, Jie Gao, Tianlan Chen, Pui-In Mak, Mang-I Vai, Rui P Martins
Existing digital microfluidic (DMF) chips exploit the electrowetting on dielectric (EWOD) force to perform droplet splitting. However, the current splitting methods are not flexible and the volume of the droplets suffers from a large variation. Herein, we propose a DMF chip featuring a 3D microblade structure to enhance the droplet-splitting performance. By exploiting the EWOD force for shaping and manipulating the mother droplet, we obtain an average dividing error of <2% in the volume of the daughter droplets for a number of fluids such as deionized water, DNA solutions and DNA-protein mixtures...
February 14, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28139463/microfluidic-chip-based-micro-rna-detection-through-the-combination-of-fluorescence-and-surface-enhanced-raman-scattering-techniques
#7
Zhile Wang, Shenfei Zong, Zhuyuan Wang, Lei Wu, Peng Chen, Binfeng Yun, Yiping Cui
We present a novel microfluidic chip based method for the detection of micro RNA (miRNA) via the combination of fluorescence and surface enhanced Raman scattering (SERS) spectroscopies. First, silver nanoparticles (Ag NPs) are immobilized onto a glass slide, forming a SERS enhancing substrate. Then a specificially designed molecular beacon (MB) is attached to the SERS substrate. The 3' end of the MB is decorated with a thiol group to facilitate the attachment of the MB, while the 5' end of the MB is labeled with an organic dye 6-FAM, which is used both as the fluorophore and SERS reporter...
March 10, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28119518/molecular-beacons-to-identify-gifted-microbes-for-genome-mining
#8
Richard H Baltz
Microbial genome mining is a promising technology that is revitalizing natural product discovery. It is now well documented that many bacteria with large genomes, particularly actinomycetes, encode many more secondary metabolites (SMs) than was previously known from their expressed secondary metabolomes. There are effective bioinformatics tools for counting the numbers and nature of SMs, and determining the total coding capacity from finished microbial genomes. However, these methods do not translate well to draft genomes, particularly for large SM gene clusters that contain nonribosomal peptide synthetase (NRPS) or type I polyketide synthase (PKS-I) mega-genes which are prone to fragmentation and misassembly...
January 25, 2017: Journal of Antibiotics
https://www.readbyqxmd.com/read/28119250/single-palindromic-molecular-beacon-based-amplification-for-genetic-analysis-of-cancers
#9
Feng Li, Hui Zhao, Zheng-Yong Wang, Zai-Sheng Wu, Zhe Yang, Cong-Cong Li, Huo Xu, Jian-Xin Lyu, Zhi-Fa Shen
The detection of biomarkers is of crucial importance in reducing the morbidity and mortality of complex diseases. Thus, there is a great desire to develop highly efficient and simple sensing methods to fulfill the different diagnostic and therapeutic purposes. Herein, using tumor suppressor p53 gene as model target DNA, we developed a novel palindromic fragment-incorporated molecular beacon (P-MB) that can perform multiple functions, including recognition element, signal reporter, polymerization template and primer...
May 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28117861/dynamic-imaging-of-myc-and-cdkn1a-mrnas-as-an-indicator-of-cell-g1-phase-arrest
#10
Linglu Yi, Xuexia Lin, Haifang Li, Yuan Ma, Jin-Ming Lin
The identification of G1-phase arrest requires a dynamic capturing method. In this work, we reported an indicator based on MYC and CDKN1A mRNA imaging to visualize G1-phase cycle arrest. A typical G1-phase arrest imaging is shown as a green-to-red conversion by fluorescence molecular beacons indicating the change as down-regulating of MYC and up-regulating of CDKN1A mRNA. We performed G1-phase arrest imaging on proliferated cancer cells inhibited by TMPyP4 and explore the role of HIF-1α in the proliferation inhibition effect...
January 24, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28110250/detection-and-discrimination-of-maintenance-and-de-novo-cpg-methylation-events-using-methylbreak
#11
William Hsu, Augustus T Mercado, George Hsiao, Jui-Ming Yeh, Chung-Yung Chen
Understanding the principles governing the establishment and maintenance activities of DNA methyltransferases (DNMTs) can help in the development of predictive biomarkers associated with genetic disorders and diseases. A detection system was developed that distinguishes and quantifies methylation events using methylation-sensitive endonucleases and molecular beacon technology. MethylBreak (MB) is a 22-mer oligonucleotide with one hemimethylated and two unmethylated CpG sites, which are also recognition sites for Sau96I and SacII, and is attached to a fluorophore and a quencher...
May 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28107965/loopback-rolling-circle-amplification-for-ultrasensitive-detection-of-kras-gene
#12
Huo Xu, Dong Wu, Yifan Jiang, Rongbo Zhang, Qingzheng Wu, Yiyun Liu, Feng Li, Zai-Sheng Wu
Mutations in Kras gene may be used as a diagnostic marker and a target for treatment of the broad spectrum of human cancers. In this study, we developed a new class of amplification assay, double-hairpin molecular beacon (DHMB)-based cascade rolling circle amplification (RCA), for ultrasensitive and selective detection of Kras gene in a homogenous solution. Specifically, target DNA can hybridize with DHMB and activate cyclical target strand-displacement polymerization (CTDP) and nicking-mediated strand-displacement polymerization (NMDP)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107834/a-label-free-colorimetric-isothermal-cascade-amplification-for-the-detection-of-disease-related-nucleic-acids-based-on-double-hairpin-molecular-beacon
#13
Dong Wu, Huo Xu, Haimei Shi, Weihong Li, Mengze Sun, Zai-Sheng Wu
K-Ras mutations at codon 12 play an important role in an early step of carcinogenesis. Here, a label-free colorimetric isothermal cascade amplification for ultrasensitive and specific detection of K-Ras point mutation is developed based on a double-hairpin molecular beacon (DHMB). The biosensor consists of DHMB probe and a primer-incorporated polymerization template (PPT) designed partly complementary to DHMB. In the presence of polymerase, target DNA is designed to trigger strand displacement amplification (SDA) via promote the hybridization of PPT with DHMB and subsequently initiates cascade amplification process with the help of the nicking endonuclease...
March 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28105835/silver-nanoclusters-beacon-as-stimuli-responsive-versatile-platform-for-multiplex-dnas-detection-and-aptamer-substrate-complexes-sensing
#14
Guoliang Liu, Jingjing Li, Da-Qian Feng, Jun-Jie Zhu, Wei Wang
An activatable silver nanoclusters beacon (ASNCB) was synthesized through a facile one-pot approach and applied for multiplex DNAs, small molecule, and protein sensing. Multifunctional single-stranded DNA sequences are rationally designed and used for ASNCB in situ synthesis. Via target-responsive structure transformation of ASNCB, target recognition induced ASNCB conformational transition and lit up the fluorescent signal of silver nanoclusters. By further implementing two different color ASNCBs (520 and 600 nm), the parallel multiplexed analysis of two target genes (Influenza A virus genes H1N1 and H5N1) is achieved...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28100783/dual-functional-roles-of-molecular-beacon-a-microrna-detector-and-inhibitor
#15
Wai Ming Li, Ching-Man Chan, Andrew L Miller, Chow H Lee
MicroRNAs are essential in many cellular processes. The ability to detect microRNAs is important for understanding its function and biogenesis. This study is aimed at using a molecular beacon to detect miR-430 in developing zebrafish embryos as a proof of principle. miR-430 is crucial for the clearance of maternal mRNA during maternal zygotic transition (MZT) in embryonic development. Despite its known function, the temporal and spatial expression of miR-430 remains unclear. We used various imaging techniques, including laser scanning confocal microscopy, spinning disk and lightsheet microscopy, to study the localization of miR-430 and any developmental defects possibly caused by the molecular beacon...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28088177/a-novel-quantitative-pcr-detects-babesia-infection-in-patients-not-identified-by-currently-available-non-nucleic-acid-amplification-tests
#16
Lavoisier Akoolo, Samantha Schlachter, Rasel Khan, Laura Alter, Albert D Rojtman, Kristine Gedroic, Purnima Bhanot, Nikhat Parveen
BACKGROUND: Ticks transmit Babesia microti, the causative agents of babesiosis in North America and Europe. Babesiosis is now endemic in Northeastern USA and affects people of all ages. Babesia species infect erythrocytes and can be transmitted through blood transfusion. Whole blood and blood products, which are not tested for Babesia, can cause transfusion-transmitted babesiosis (TTB) resulting in severe consequences in the immuno-compromised patients. The purpose of this study was epidemiological evaluation of babesiosis in a tick-infested state...
January 14, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28067855/detection-of-naja-atra-cardiotoxin-using-adenosine-based-molecular-beacon
#17
Yi-Jun Shi, Ying-Jung Chen, Wan-Ping Hu, Long-Sen Chang
This study presents an adenosine (A)-based molecular beacon (MB) for selective detection of Naja atra cardiotoxin (CTX) that functions by utilizing the competitive binding between CTX and the poly(A) stem of MB to coralyne. The 5'- and 3'-end of MB were labeled with a reporter fluorophore and a non-fluorescent quencher, respectively. Coralyne induced formation of the stem-loop MB structure through A₂-coralyne-A₂ coordination, causing fluorescence signal turn-off due to fluorescence resonance energy transfer between the fluorophore and quencher...
January 7, 2017: Toxins
https://www.readbyqxmd.com/read/28059137/establishment-of-an-accurate-and-fast-detection-method-using-molecular-beacons-in-loop-mediated-isothermal-amplification-assay
#18
Wei Liu, Simo Huang, Ningwei Liu, Derong Dong, Zhan Yang, Yue Tang, Wen Ma, Xiaoming He, Da Ao, Yaqing Xu, Dayang Zou, Liuyu Huang
This study established a constant-temperature fluorescence quantitative detection method, combining loop-mediated isothermal amplification (LAMP) with molecular beacons. The advantages of LAMP are its convenience and efficiency, as it does not require a thermocycler and results are easily visualized by the naked eye. However, a major disadvantage of current LAMP techniques is the use of indirect evaluation methods (e.g., electrophoresis, SYBR Green I dye, precipitation, hydroxynaphthol blue dye, the turbidimetric method, calcein/Mn(2+) dye, and the composite probe method), which cannot distinguish between the desired products and products of nonspecific amplification, thereby leading to false positives...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043515/evaluation-of-rifampicin-resistance-and-81-bp-rifampicin-resistant-determinant-region-of-rpob-gene-mutations-of-mycobacterium-tuberculosis-detected-with-xpertmtb-rif-in-cross-river-state-nigeria
#19
Ernest A Ochang, Ubong A Udoh, Ubleni E Emanghe, Gerald O Tiku, Jonah B Offor, Micheal Odo, Emmanuel Nkombe, Oju E Owuna, Sunday M Obeten, Martin M Meremikwu
OBJECTIVE/BACKGROUND: World Health Organization tuberculosis (TB) indices from 2014 to 2016 showed that Nigeria had the 6th highest prevalence, 4th highest incidence, and the highest mortality rate globally. In efforts to improve TB care, the XpertMTB/Rif (GeneXpert) technology, Cepheid, Sunnyvale, California, USA, which has revolutionized TB detection with concomitant rifampicin-resistance molecular detection, was introduced in Cross River State, South-South Nigeria, in 2014. The GeneXpert uses molecular beacons to detect five overlapping 81-bp regions in the rpoB gene known as the Rifampicin Resistant Determinant Region (RRDR)...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28018742/multiplexed-fluorescence-readout-using-time-responses-of-color-coded-signals-for-biomolecular-detection
#20
Takahiro Nishimura, Yusuke Ogura, Jun Tanida
Fluorescence readout is an important technique for detecting biomolecules. In this paper, we present a multiplexed fluorescence readout method using time varied fluorescence signals. To generate the fluorescence signals, coded strands and a set of universal molecular beacons are introduced. Each coded strand represents the existence of an assigned target molecule. The coded strands have coded sequences to generate temporary fluorescence signals through binding to the molecular beacons. The signal generating processes are modeled based on the reaction kinetics between the coded strands and molecular beacons...
December 1, 2016: Biomedical Optics Express
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