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Molecular beacon

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
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
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
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
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
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
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
Zhong Mei, Liang Tang
An innovative gold nanorod (GNR) array biochip was developed to systematically investigate the localized surface plasmon resonance (LSPR)-coupled fluorescence enhancement for signal amplification in molecular beacon detection. An ordered GNR assembly in vertical standing array on a glass surface was fabricated as plasmonic substrates, resulting in dramatically intensified LSPR between adjacent nanoparticles as compared to that from an ensemble of random nanorods. We have shown that the plasmonic response of the nanoarray can be tuned by the proper choice of GNR size to overlap the fluorophore excitation and emission wavelengths greater than 600 nm...
December 19, 2016: Analytical Chemistry
Scott Baldwin, Clayton Deighan, Elga Bandeira, Kwang J Kwak, Mohammad Rahman, Patrick Nana-Sinkam, L James Lee, Michael E Paulaitis
We present a method that takes advantage of the fluorophore loading dependence of fluorescence nanoparticle tracking (fNTA) to determine the content of specific miRNA targets in extracellular vesicles (EVs) and their stoichiometry across the entire EV population. The method is based on an assay for detecting EV miRNA by hybridization to fluorescently labeled, miRNA-specific molecular beacons encapsulated in cationic lipoplex nanoparticles that fuse non-specifically with negatively charged EVs. To demonstrate the method, we carry out a stoichiometric analysis of miR-21 in EVs released from A549 lung cancer cells...
October 28, 2016: Nanomedicine: Nanotechnology, Biology, and Medicine
Yonghua Zhang, Junjie Ai, Qiaorong Gu, Qiang Gao, Honglan Qi, Chengxiao Zhang
Low-abundance mutations in the presence of wild-type DNA can be determined using molecular beacon (MB) as probe. A MB is generally used as DNA probe because it can distinguish single-base mismatched target DNA from fully matched target DNA. However, the probe can not determine low-abundance mutations in the presence of wild-type DNA. In this study, this limitation is addressed by enhancing the stability of unpaired base-containing dsDNA with a hydrogen-bonding ligand, which was added after hybridization of the MB to the target DNA...
December 5, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
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 19, 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 C Yeo, Yingnan Wu, Zheng Yang, Yon Jin Chuah, Eng Hin Lee, Yuejun Kang, Chenjie Xu
Chondrogenic differentiation of human mesenchymal stem cells (MSCs) in three-dimensional hydrogel holds promise as a method for repairing injured articular cartilage. Given MSC plasticity (its potential to mature into alternative lineages), nondestructive monitoring is critical for the optimization of chondrogenic differentiation conditions and the evaluation of the final product. However, conventional validation/assessments of the differentiation process (i.e., quantitative reverse transcription polymerase chain reaction [qRT-PCR] and histology) are end-point assays requiring disruption of the sample...
January 2017: 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...
March 15, 2017: Biosensors & Bioelectronics
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