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https://www.readbyqxmd.com/read/28738589/2-aminopurine-probe-in-combination-with-catalyzed-hairpin-assembly-signal-amplification-for-simple-and-sensitive-detection-of-microrna
#1
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
https://www.readbyqxmd.com/read/28738581/the-g-bhq-synergistic-effect-improved-double-quenching-molecular-beacons-based-on-guanine-and-black-hole-quencher-for-sensitive-simultaneous-detection-of-two-dnas
#2
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
https://www.readbyqxmd.com/read/28718918/a-rapid-confirmatory-test-for-body-fluid-identification
#3
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
https://www.readbyqxmd.com/read/28717028/the-norepinephrine-metabolite-3-4-dihydroxymandelic-acid-is-produced-by-the-commensal-microbiota-and-promotes-chemotaxis-and-virulence-gene-expression-in-enterohemorrhagic-escherichia-coli
#4
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
https://www.readbyqxmd.com/read/28714696/genetically-encoded-fluorescent-rna-sensor-for-ratiometric-imaging-of-microrna-in-living-tumor-cells
#5
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
https://www.readbyqxmd.com/read/28696331/molecular-beacon-anchored-onto-a-graphene-oxide-substrate
#6
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 (QD) sensors are anchored on graphene oxide (GO) flakes which provide a platform for analyte detection in the vicinity of GO operating in the "turn-off" mode...
July 11, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28674450/triplex-dna-based-bioanalytical-platform-for-highly-sensitive-homogeneous-electrochemical-detection-of-melamine
#7
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
https://www.readbyqxmd.com/read/28657304/sensitive-and-label-free-fluorescent-detection-of-transcription-factors-based-on-dna-ag-nanoclusters-molecular-beacons-and-exonuclease-iii-assisted-signal-amplification
#8
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
https://www.readbyqxmd.com/read/28636312/combining-protein-and-mirna-quantification-for-bladder-cancer-analysis
#9
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
https://www.readbyqxmd.com/read/28611490/gene-specific-dna-sensors-for-diagnosis-of-pathogenic-infections
#10
REVIEW
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
https://www.readbyqxmd.com/read/28603066/differential-gene-expression-profiles-according-to-the-iaslc-ats-ers-histopathological-classification-in-lung-adenocarcinoma-subtypes
#11
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
https://www.readbyqxmd.com/read/28602196/sequence-specific-recognition-of-hiv-1-dsdna-in-the-large-amount-of-normal-dsdna-based-upon-nicking-enzyme-signal-amplification-and-triplex-dna
#12
Houya Zhu, Manjun Zhang, Li Zou, Ruimin Li, Liansheng Ling
A sensitive fluorescent strategy for sequence specific recognition of HIV dsDNA was established based upon Nicking Enzyme Signal Amplification (NESA) and triplex formation. dsDNA sequence from the site 7960 to site 7991 of the HIV1 dsDNA gene was designed as target dsDNA, which was composed of two complementary strands Oligonucleotide 1 with the sequence of 3'-CTT CCT TAT CTT CTT CTT CCA CCT CTC TCT CT-5' (Oligo-1) and Oligonucleotide 2 with the sequence of 5'-GAA GGA ATA GAA GAA GAA GGT GGA GAG AGA GA-3' (Oligo-2)...
October 1, 2017: Talanta
https://www.readbyqxmd.com/read/28600768/detection-and-differentiation-of-lyme-spirochetes-and-other-tick-borne-pathogens-from-blood-using-real-time-pcr-with-molecular-beacons
#13
Samantha Schlachter, Kamfai Chan, Salvatore A E Marras, Nikhat Parveen
Real-time PCR assays have recently been implemented in diagnostics for many bacterial pathogens, allowing rapid and accurate detection, which ultimately results in improved clinical intervention. Here, we describe a sensitive method of detection for three common tick-borne pathogens Borrelia burgdorferi, Anaplasma phagocytophilum, and Babesia microti since coinfections with these pathogens have started occurring with increasing frequency over the last several years in both North America and Europe. A shared geographic region, the same tick vectors, and similar transmission cycle all favor simultaneous transmission of these three tick-borne pathogens...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28594266/simple-fluorescence-based-detection-of-protein-kinase-a-activity-using-a-molecular-beacon-probe
#14
Changbei Ma, Xiaoyuan Lv, Kemin Wang, Shunxin Jin, Haisheng Liu, Kefeng Wu, Weimin Zeng
Protein kinase A was detected by quantifying the amount of ATP utilized after a protein kinase reaction. The ATP assay was performed using the T4 DNA ligase and a molecular beacon (MB). In the presence of ATP, DNA ligase catalyzed the ligation of short DNA. The ligation product then hybridized to MB, resulting in a fluorescence enhancement of the MB. This assay was capable of determining protein kinase A in the range of 12.5∼150 nM, with a detection limit of 1.25 nM. Furthermore, this assay could also be used to investigate the effect of genistein on protein kinase A...
June 8, 2017: Bioengineered
https://www.readbyqxmd.com/read/28593769/structure-and-dynamics-of-a-n-methylfulleropyrrolidine-mediated-gold-nanocomposite-a-spectroscopic-ruler
#15
Sanjeeb Sutradhar, Archita Patnaik
A mechanistic understanding of the structure and dynamics of a chemically tunable N-methylfulleropyrrolidine (8-NMFP)-assisted gold nanocomposite and its aggregation via a controllable interparticle interaction is reported as a function of the molar ratio and pH of the medium. Electronic structure calculations adopting density functional theory methods implied electrostatic interactions to play a dominant role between 8-NMFP and citrate-capped gold nanoparticles. MM(+) molecular mechanics force field computations revealed intermolecular gold-gold interactions, contributing toward the formation of spherical composite aggregates...
June 20, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28549267/the-construction-of-a-novel-nucleic-acids-detection-microplatform-based-on-the-nset-for-one-step-detecting-tk1-dna-and-microrna-21
#16
Jian Zhang, Qian Zhao, Yudong Wu, Bo Zhang, Weipan Peng, Jiafang Piao, Yurui Zhou, Weichen Gao, Xiaoqun Gong, Jin Chang
Microbeads-based microchip technology has become the potential for a new generation of nucleic acids detection in a high-throughput and sensitive manner. However the specificity and operational complexity limit the microchip applied in nucleic acids detection. Herein, in this work, we designed a kind of gold-nanoparticles coated polystyrene microbeads as microplatform conjugating with the molecular beacons as probes. Due to the nanoparticle surface energy transfer of gold-nanoparticles, the fluorescence of dye on one end of molecular beacons was effectively quenched...
May 23, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28535205/a-transcriptional-serenaid-the-role-of-noncoding-rnas-in-class-switch-recombination
#17
William T Yewdell, Jayanta Chaudhuri
During an immune response, activated B cells may undergo class switch recombination (CSR), a molecular rearrangement that allows B cells to switch from expressing IgM and IgD to a secondary antibody heavy chain isotype such as IgG, IgA, or IgE. Secondary antibody isotypes provide the adaptive immune system with distinct effector functions to optimally combat various pathogens. CSR occurs between repetitive DNA elements within the immunoglobulin heavy chain (Igh) locus, termed switch (S) regions, and requires the DNA modifying enzyme activation-induced cytidine deaminase (AID)...
May 23, 2017: International Immunology
https://www.readbyqxmd.com/read/28524648/instantaneous-ph-boosted-functionalization-of-stellate-gold-nanoparticles-for-intracellular-imaging-of-mirna
#18
Jisun Ki, Eunji Jang, Seungmin Han, Moo-Kwang Shin, Byunghoon Kang, Yong-Min Huh, Seungjoo Haam
Various types of nanoprobes have recently been utilized to monitor living organisms by detecting and imaging intracellular biomarkers, such as microRNAs (miRs). We here present a simple one-pot method to prepare stellate gold nanoparticles functionalized with miR-detecting molecular beacons (SGNP-MBs); low pH conditions permitted the rapid-high loading of MBs on the surface of SGNPs. Compared to the conventional gold nanoparticle-based MBs, SGNPs carried a 4.5-fold higher load of MBs and exhibited a 6.4-fold higher cellular uptake...
May 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28485713/super-resolution-imaging-of-a-2-5-kb-non-repetitive-dna-in-situ-in-the-nuclear-genome-using-molecular-beacon-probes
#19
Yanxiang Ni, Bo Cao, Tszshan Ma, Gang Niu, Yingdong Huo, Jiandong Huang, Danni Chen, Yi Liu, Bin Yu, Michael Q Zhang, Hanben Niu
High-resolution visualization of short non-repetitive DNA in situ in the nuclear genome is essential for studying looping interactions and chromatin organization in single cells. Recent advances in fluorescence in situ hybridization (FISH) using Oligopaint probes have enabled super-resolution imaging of genomic domains with a resolution limit of 4.9 kb. To target shorter elements, we developed a simple FISH method that uses molecular beacon (MB) probes to facilitate the probe-target binding, while minimizing non-specific fluorescence...
May 9, 2017: ELife
https://www.readbyqxmd.com/read/28484218/a-molecular-beacon-based-approach-for-live-cell-imaging-of-rna-transcripts-with-minimal-target-engineering-at-the-single-molecule-level
#20
Mingming Chen, Zhao Ma, Xiaotian Wu, Shiqi Mao, Yantao Yang, Jie Tan, Christopher J Krueger, Antony K Chen
Analysis of RNA dynamics and localization at the single-molecule level in living cells has been predominantly achieved by engineering target RNAs with large insertions of tandem repeat sequences that are bound by protein-based or oligonucleotide-based fluorescent probes. Thus, individual RNAs are tagged by multiple fluorescent probes, making them detectable by fluorescence microscopy. Since large insertions may affect RNA processes including trafficking and localization, here we present a strategy to visualize single RNA transcripts in living cells using molecular beacons (MBs) - fluorogenic oligonucleotide probes - with minimal target engineering...
May 8, 2017: Scientific Reports
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