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Molecular beacon

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https://www.readbyqxmd.com/read/28636312/combining-protein-and-mirna-quantification-for-bladder-cancer-analysis
#1
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, to analyze telomerase and miRNA 21 in urine samples with following merits. Firstly, it is a binary assay and can simultaneously output double signals which corresponds to the quantities of telomerase and miRNA, respectively. Secondly, telomerase activity is firstly enhanced by using DNA molecular beacon probe to inhibit the formation of G-quadruplex...
June 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28611490/gene-specific-dna-sensors-for-diagnosis-of-pathogenic-infections
#2
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
#3
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
#4
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
#5
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
#6
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-n-methylfulleropyrrolidine-mediated-gold-nanocomposite-a-spectroscopic-ruler
#7
Sanjeeb Sutradhar, Archita Patnaik
A mechanistic understanding of the structure and dynamics in a chemically tunable N-methylfulleropyrrolidine (8-NMFP) assisted gold nanocomposite and its aggregation via controllable interparticle interaction is reported as a function of molar ratio and pH of the medium. Electronic structure calculations adopting DFT methods implied electrostatics to play a dominant role between 8-NMFP and the citrate capped gold nanoparticles (Ct@AuNPs). MM+ Molecular Mechanics force field computations revealed intermolecular gold-gold interaction contributing towards the formation of spherical composite aggregates...
June 8, 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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28475957/double-loop-hairpin-probe-and-doxorubicin-loaded-gold-nanoparticles-for-the-ultrasensitive-electrochemical-sensing-of-microrna
#13
Yiyi Tao, Dan Yin, Mingchao Jin, Jie Fang, Tao Dai, Yi Li, Yuxia Li, Qinli Pu, Guoming Xie
An electrochemical microRNA (miRNA) analysis platform by combining double-loop hairpin probe (DHP) and doxorubicin-loaded gold nanoparticles (AuNPs@Dox) for ultrasensitive miRNA detection is proposed. Firstly, we here report a DHP that is simultaneously engineered to incorporate a miRNA recognition sequence, an output segment and output's complementary fragment. The important aspect of this hairpin probe is that it would not be degraded by duplex specific nuclease (DSN) and circumvents elaborately chemical modification disadvantages encountered by classic molecular beacon...
May 2, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28451274/a-metal-mediated-base-pair-that-discriminates-between-the-canonical-pyrimidine-nucleobases
#14
Biswarup Jash, Philipp Scharf, Nikolas Sandmann, Célia Fonseca Guerra, Dominik A Megger, Jens Müller
A nucleoside analogue comprising the ligand 1H-imidazo[4,5-f][1,10]phenanthroline (P) was applied to develop a molecular beacon capable of discriminating the canonical nucleobases cytosine and thymine. The beacon is based on the formation of a stable Ag(+)-mediated base pair between P and cytosine, whereas the presence of Ag(+) strongly destabilizes nucleic acids comprising an artificial base pair between P and thymine. Metal-mediated base pair formation was investigated by temperature-dependent UV spectroscopy and CD spectroscopy and complemented by extensive DFT calculations...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28451240/ultra-specific-discrimination-of-single-nucleotide-mutations-using-sequestration-assisted-molecular-beacons
#15
Shichao Hu, Wei Tang, Yan Zhao, Na Li, Feng Liu
Reliably distinguishing single-nucleotide mutations (SNMs) at low abundance is of great significance in clinical diagnosis. However, the specificity of most current SNM discrimination methods based on the Watson-Crick hybridization is seriously limited by the cross-reactivity of the probe with closely related unintended sequences. Herein, we propose a sequestration-assisted molecular beacon (MB) strategy for highly specific SNM discrimination. The new SNM discrimination system consists of a target-specific MB and a series of hairpin sequestering agents (SEQs)...
February 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28445812/portable-aptamer-biosensor-of-platelet-derived-growth-factor-bb-using-a-personal-glucose-meter-with-triply-amplified
#16
Lu Hong, Fu Zhou, Dongmin Shi, Xiaojun Zhang, Guangfeng Wang
Sensitive and rapid detection of platelet-derived growth factor BB (PDGF-BB), a cancer-related protein, could help early diagnosis, treatment, and prognosis of cancers. Although some methods have been developed to detect PDGF-BB, few can provide quantitative results using an affordable and portable device that is suitable for home use or field application. In this work, we report the first use of a portable kind of personal glucose meter (PGM) combining a catalytic and molecular beacon (CAMB) system with a cation exchange reaction (CX reaction) for ultrasensitive PDGF-BB assay...
September 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28441712/virus-based-devices-prospects-for-allopoiesis
#17
Bogdan Dragnea
The assembly line is a commonly invoked example of allopoiesis, the process whereby a system produces a different system than itself. In this sense, virus production in plants is an instance of bio-enabled bottom-up allopoiesis because the plant host can be regarded as a programmable assembly line for the virus. Reprogramming this assembly line and integrating it into a larger lineup of chemical manipulations has seen a flurry of activity recently, with more sophisticated systems emerging every year. The field of virus nanomaterials now has several subdisciplines that focus on virus shells as assemblers, scaffolds for molecular circuitry, chemical reactors, magnetic and photonic beacons, and therapeutic carriers...
April 25, 2017: ACS Nano
https://www.readbyqxmd.com/read/28424856/homogenous-assay-for-protein-detection-based-on-proximity-dna-hybridization-and-isothermal-circular-strand-displacement-amplification-reaction
#18
Manjun Zhang, Ruimin Li, Liansheng Ling
This work proposed a homogenous fluorescence assay for proteins, based on the target-triggered proximity DNA hybridization in combination with strand displacement amplification (SDA). It benefited from target-triggered proximity DNA hybridization to specifically recognize the target and SDA making recycling signal amplification. The system included a molecular beacon (MB), an extended probe (EP), and an assistant probe (AP), which were not self-assembly in the absence of target proteins, due to the short length of the designed complementary sequence among MB, EP, and AP...
April 19, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28418641/classics-in-chemical-neuroscience-ketamine
#19
Marshall W Tyler, Harmony B Yourish, Dawn F Ionescu, Stephen J Haggarty
Ketamine, a molecule of many faces, has contributed immeasurably to numerous realms of clinical practice and scientific inquiry. From anesthesia and analgesia to depression and schizophrenia, it continues to shed light on the molecular underpinnings of pain, consciousness, and the pathophysiology of neuropsychiatric disorders. In particular, research on ketamine's mechanism of action is providing new hope in the search for therapies for treatment-resistant depression and affords insights into disorders of glutamatergic dysfunction...
June 21, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28379274/a-sensitive-ratiometric-electrochemical-biosensor-based-on-dna-four-way-junction-formation-and-enzyme-assisted-recycling-amplification
#20
Lin Cui, Mengfei Lu, Xiao-Yun Yang, Bo Tang, Chun-Yang Zhang
A simple ratiometric electrochemical biosensor is developed for sensitive detection of target DNA based on DNA four-way junction (DNA-4WJ) formation and enzyme-assisted recycling amplification. This biosensor can be easily fabricated by a one-step assembly of ratiometric probes and simply performed by a one-step incubation procedure. In the presence of target DNA, two unmodified DNA oligonucleotides may cooperatively hybridize with a hairpin probe in the triple-helix molecular beacon (THMB) to form a DNA-4WJ, which may cause conformational transduction and induce the change in the distance between two redox labeling probes and the electrode surface...
May 2, 2017: Analyst
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