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Molecular beacon

Y Ma, X Dai, T Hong, G B Munk, M Libera
Despite their many advantages and successes, molecular beacon (MB) hybridization probes have not been extensively used in microarray formats because of the complicating probe-substrate interactions that increase the background intensity. We have previously shown that tethering to surface-patterned microgels is an effective means for localizing MB probes to specific surface locations in a microarray format while simultaneously maintaining them in as water-like an environment as possible and minimizing probe-surface interactions...
December 7, 2016: Analyst
Miguel Ángel Pavón, Inés María López-Calleja, Isabel González, Rosario Martín, Teresa García
Real-time polymerase chain reaction (PCR) is a molecular biology technique based on the detection of the fluorescence produced by a reporter molecule, which increases as the reaction proceeds proportionally to the accumulation of the PCR product within each amplification cycle. The fluorescent reporter molecules include dyes that bind to the double-stranded DNA (i.e., SYBR(®) Green) or sequence-specific probes (i.e., Molecular Beacons or TaqMan(®) Probes). Real-time PCR provides a tool for accurate and sensitive quantification of target fungal DNA...
2017: Methods in Molecular Biology
Mingxuan Gao, Lin Yang, Yi Zheng, Xiaoxi Yang, Hongyan Zou, Jing Han, Zexi Liu, Yuanfang Li, Cheng Zhi Huang
Surface functionalization is an essential prerequisite for wide and specific applications of nanoparticles such as photoluminescent (PL) carbon quantum dots (CQDs), but still remains as a major challenge. In this report, alkynylated CQDs, which were prepared at first from carboxyl-rich CQDs through amidation with propargylamine in the presence of 1,1'-carbonyldiimidazole, were efficiently modified with azido molecular beacon DNA through copper(I)-catalyzed alkyne-azide cycloaddition reaction (CuAAC). As the proof of concept, the DNA-modified CQDs was then bonded with 5-nm gold nanoparticles (AuNPs) through gold-sulfur bond...
December 3, 2016: Chemistry: a European Journal
Zerrin Fidan, Andy Wende, Ute Resch-Genger
Quality control requirements imposed on assays used in clinical diagnostics and point-of-care-diagnostic testing (POCT), utilizing amplification reactions performed at elevated temperatures of 35 to 95 °C are very stringent. As the temperature of a reaction vessel has a large impact on the specificity and sensitivity of the amplification reaction, simple tools for local in situ temperature sensing and monitoring are required for reaction and assay control. We describe here a platform of stem-and-loop structured DNA hairpins (molecular beacons, MBs), absorbing and emitting in the visible and red spectral region, rationally designed for precise temperature measurements in microfluidic assays for POCT, and their application for temperature measurements in a common DNA-based molecular biological assay utilizing thermophilic helicase-dependent amplification (tHDA)...
November 29, 2016: Analytical and Bioanalytical Chemistry
Oluwasesan Adegoke, Enoch Y Park
In biosensor design, localized surface plasmon resonance (LSPR)-induced signal from gold nanoparticle (AuNP)-conjugated reporter can produce highly sensitive nanohybrid systems. In order to retain the physicochemical properties of AuNPs upon conjugation, high colloidal stability in aqueous solution is needed. In this work, the colloidal stability with respect to the zeta potential (ZP) of four negatively charged thiol-functionalized AuNPs, thioglycolic (TGA)-AuNPs, 3-mercaptopropionic acid (MPA)-AuNPs, L-cysteine-AuNPs and L-glutathione (GSH)-AuNPs, and a cationic cyteamine-capped AuNPs was studied at various pHs, ionic strength, and NP concentration...
December 2016: Nanoscale Research Letters
Li Min Tay, Christian Wiraja, David Yeo, Yingnan Wu, Zheng Yang, Yon Jin Chuah, Eng Hin Lee, Yuejun Kang, Chenjie Xu
Chondrogenic differentiation of human mesenchymal stem cells (MSCs) in 3D hydrogel holds promise as a method for repairing injured articular cartilage. Given MSC plasticity (its potential to mature into alternative lineages), non-destructive monitoring is critical for the optimization of chondrogenic differentiation conditions and the evaluation of the final product. However, conventional validation/assessment of the differentiation process (i.e. quantitative reverse transcription polymerase chain (qRT-PCR) and histology) are end-point assays requiring disruption of the sample...
November 21, 2016: Tissue Engineering. Part C, Methods
Asger Givskov, Emil L Kristoffersen, Kamilla Vandsø, Yi-Ping Ho, Magnus Stougaard, Birgitta R Knudsen
The so-called Rolling Circle Amplification allows for amplification of circular DNA structures in a manner that can be detected in real-time using nucleotide-based molecular beacons that unfold upon recognition of the DNA product, which is being produced during the amplification process. The unfolding of the molecular beacons results in a fluorescence increase as the Rolling Circle Amplification proceeds. This can be measured in a fluorometer. In the current study, we have investigated the possibility of using two different molecular beacons to detect two distinct Rolling Circle Amplification reactions proceeding simultaneously and in the same reaction tube by measurement of fluorescence over time...
November 15, 2016: Sensors
Fengping Zhan, Xiaolei Liao, Feng Gao, Weiwei Qiu, Qingxiang Wang
A novel electrochemical DNA biosensor has been facilely constructed by in-situ assembly of electroactive 4'-aminobenzo-18-crown-6-copper(II) complex (AbC-Cu(2+)) on the free terminal of the hairpin-structured molecule beacon. The 3'-SH modified molecule beacon probe was first immobilized on the gold electrode (AuE) surface through self-assembly chemistry of Au-S bond. Then the crow ester of AbC was covalently coupled with 5'-COOH on the molecule beacon, and served as a platform to attach the Cu(2+) by coordination with ether bond (-O-) of the crown cycle...
October 21, 2016: Biosensors & Bioelectronics
Yanchun Wei, Cuixia Lu, Qun Chen, Da Xing
Purposes: Retinoblastoma (RB) is the most common primary intraocular malignancy of infancy. An alternative RB treatment protocol is proposed and tested. It is based on a photodynamic therapy (PDT) with a designed molecular beacon that specifically targets the murine double minute x (MDMX) high-expressed RB cells. Methods: A MDMX mRNA triggered photodynamic molecular beacon is designed by binding a photosensitizer molecule (pyropheophorbide-a, or PPa) and a black hole quencher-3 (BHQ3) through a complementary oligonucleotide sequence...
November 1, 2016: Investigative Ophthalmology & Visual Science
Wentao Xu, Jingjing Tian, Xiangli Shao, Longjiao Zhu, Kunlun Huang, Yunbo Luo
For previously reported aptasensor, the sensitivity and selectivity of aptamers to targets were often suppressed due to the reporter label of single-stranded molecular beacon or hindrance of the duplex DNA strand displacement. To solve the affinity declining of aptamers showed in traditional way and realize on-site rapid detection of Lipopolysaccharides (LPS), we developed an ingenious structure-switching aptasensor based on the bulb-like triplex turn-on switch (BTTS) as the effective molecular recognition and signal transduction element and streptavidin-horseradish peroxidase modified hybridization chain reaction (HCR-HRP) nanocomposites as the signal amplifier and signal report element...
October 5, 2016: Biosensors & Bioelectronics
Yacui Liu, Jiangyan Zhang, Jingxiao Tian, Xiaofei Fan, Hao Geng, Yongqiang Cheng
A simple, highly sensitive, and specific assay was developed for the homogeneous and multiplex detection of microRNAs (miRNAs) by combining molecular beacon (MB) probes and T7 exonuclease-assisted cyclic amplification. An MB probe with five base pairs in the stem region without special modification can effectively prevent the digestion by T7 exonuclease. Only in the presence of target miRNA is the MB probe hybridized with the target miRNA, and then digested by T7 exonuclease in the 5' to 3' direction. At the same time, the target miRNA is released and subsequently initiates the nuclease-assisted cyclic digestion process, generating enhanced fluorescence signal significantly...
November 4, 2016: Analytical and Bioanalytical Chemistry
Soumitesh Chakravorty, Sandy S Roh, Jennifer Glass, Laura E Smith, Ann Marie Simmons, Kevin Lund, Sergey Lokhov, Xin Liu, Peng Xu, Guolong Zhang, Laura E Via, Qingyu Shen, Xianglin Ruan, Xing Yuan, Hong Zhu Zhu, Ekaterina Viazovkina, Shubhada Shenai, Mazhgan Rowneki, Jong Seok Lee, Clifton E Barry, Qian Gao, David Persing, Robert Kwiatkawoski, Martin Jones, Alexander Gall, David Alland
Extensively Drug Resistant (XDR) tuberculosis (TB) cannot be easily or quickly diagnosed. We developed a rapid, automated, point-of-care assay for XDR-TB, plus resistance to the drug Isoniazid. Using a simple filter-based cartridge with an integrated sample processing function, the assay identified a wide selection of wild type and mutant sequences associated with XDR-TB directly from sputum. Four new large Stokes-shift fluorophores were developed, which when combined with six conventional fluorophores, enabled 10-color probe detection in a single PCR tube...
November 2, 2016: Journal of Clinical Microbiology
Scott R Evans, Andrea M Hujer, Hongyu Jiang, Carol B Hill, Kristine M Hujer, Jose R Mediavilla, Claudia Manca, Thuy Tien T Tran, T Nicholas Domitrovic, Paul G Higgins, Harald Seifert, Barry N Kreiswirth, Robin Patel, Michael R Jacobs, Liang Chen, Rangarajan Sampath, Thomas Hall, Christine Marzan, Vance G Fowler, Henry F Chambers, Robert A Bonomo
The widespread dissemination of carbapenem-resistant Acinetobacter spp. has created significant therapeutic challenges. At present, rapid molecular diagnostics (RMDs) that can identify this phenotype are not commercially available. Two RMD platforms, polymerase chain reaction combined with electrospray ionization mass spectrometry (PCR/ESI-MS) and molecular beacons (MB), for detecting genes conferring resistance/susceptibility to carbapenems in Acinetobacter spp. were evaluated. An archived collection of 200 clinical Acinetobacter spp...
October 26, 2016: Journal of Clinical Microbiology
Yue Cao, Tao Xie, Ruo-Can Qian, Yi-Tao Long
Plasmon resonance energy transfer (PRET) from a single metallic nanoparticle to the molecules adsorbed on its surface has attracted more and more attentions in recent years. Here, a molecular beacon (MB)-regulated PRET coupling system composed of gold nanoparticles (GNPs) and chromophore molecules has been designed to study the influence of PRET effect on the scattering spectra of GNPs. In this system, the chromophore molecules are tagged to the 5'-end of MB, which can form a hairpin structure and modified on the surface of GNPs by its thiol-labeled 3'-end...
October 27, 2016: Small
Aleksei Agapov, Daria Esyunina, Danil Pupov, Andrey Kulbachinskiy
The Gre-family transcription factors bind within the secondary channel of bacterial RNA polymerase (RNAP) directly modulating its catalytic activities. Universally conserved Gre factors activate RNA cleavage by RNAP, by chelating catalytic metal ions in the RNAP active site, and facilitate both promoter escape and transcription elongation. Gfh factors are Deinococcus/Thermus -specific homologues of Gre factors whose transcription functions remain poorly understood. Recently, we found that Gfh1 and Gfh2 proteins from Deinococcus radiodurans dramatically stimulate RNAP pausing during transcription elongation in the presence of Mn(2+) but not Mg(2+) ions...
October 17, 2016: Biochemical Journal
Dmitry A Tsybulsky, Maksim V Kvach, Dmitry Y Ryazantsev, Ilya O Aparin, Alexander A Stakheev, Igor A Prokhorenko, Yury V Martynenko, Sergey V Gontarev, Andrey A Formanovsky, Timofei S Zatsepin, Vadim V Shmanai, Vladimir A Korshun, Sergey K Zavriev
Molecular beacons carrying JOE dye (4',5'-dichloro-2',7'-dimethoxy-6-carboxyfluorescein) on a rigid or flexible linker and one or two BHQ1 quenchers have been prepared and tested in real-time PCR using Fusarium avenaceum elongation factor 1α DNA template. The probes were different in their structures (loop size and stem length), linkers for dye attachment (6-aminohexanol or trans-4-aminocyclohexanol), quencher composition (single and double BHQ1) to elucidate the influence of all these features. Fluorogenic properties of the probes were studied and compared to those of FAM (fluorescein)-based probes...
October 6, 2016: Molecular and Cellular Probes
Meltem Göksel, Mahmut Durmuş, Devrim Atilla
A series of phthalocyanine-peptide-quencher conjugates (6-9) were synthesized as photosensitizers for photodynamic therapy in cancer treatment. The photophysical, photochemical and photobiological properties of these activatable molecular beacons were also investigated in this study. For this purpose, the fluorescence, singlet oxygen and photodegradation quantum yields and fluorescence lifetime values of the compounds were determined in DMSO solutions. The phototoxicity and cytotoxicity of the systems were studied against the cervical cancer cell line named HeLa for an evaluation of their suitability for photodynamic therapy...
October 5, 2016: Photochemical & Photobiological Sciences
C Y Song, Y J Yang, B Y Yang, Y Z Sun, Y P Zhao, L H Wang
Simultaneous detection of multiple trace cancer associated serum miRNA biomarkers is considered as a feasible method for early cancer screening and diagnosis. In the present work, an ultrasensitive SERS sensor was prepared based on an Ag nanorod array SERS substrate by assembling special hairpin-shaped molecular beacons (MBs) for the detection of multiple lung cancer-related miRNA biomarkers. The portable SERS sensor exhibits excellent performance for the qualitative and quantitative detection of miRNAs, with advantages of ultra-sensitivity, good specificity, uniformity, reproducibility and stability, as well as remarkable reusability...
October 6, 2016: Nanoscale
Huning Jia, Ying Bu, Bingjie Zou, Jianping Wang, Shalen Kumar, Janet L Pitman, Guohua Zhou, Qinxin Song
Micro ribose nucleic acids (miRNAs) play an important role in biological processes such as cell differentiation, proliferation and apoptosis. Therefore, miRNAs are potentially a powerful marker for monitoring cancer and diagnosis. Here, we present sensitive signal amplification for miRNAs based on modified cycling probe technology with strand displacement amplification. miRNA was captured by the template coupled with beads, and then the first cycle based on SDA was repeatedly extended to the nicking end, which was produced by the extension reaction of miRNA...
September 30, 2016: Analyst
Tairong Kuang, Lingqian Chang, Xiangfang Peng, Xianglong Hu, Daniel Gallego-Perez
Heterogeneities and oncogenesis essentially result from proteomic disorders orchestrated by changes in DNA and/or cytoplasmic mRNA. These genetic fluctuations, however, cannot be decoded through conventional label-free methods (e.g., patch clamps, electrochemical cellular biosensors, etc.) or morphological characterization. Molecular beacons (MBs) have recently emerged as efficient probes for interrogating biomarkers in live cancer cells. MBs hybridize with their intracellular targets (e.g., mRNAs, DNAs, or proteins), emitting a fluorescent signal that can be quantified and correlated with the expression levels of their targets...
September 28, 2016: Trends in Biotechnology
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