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https://www.readbyqxmd.com/read/29763288/quantum-dot-fullerene-based-molecular-beacon-nanosensors-for-rapid-highly-sensitive-nucleic-acid-detection
#1
Ye Liu, Akash Kannegulla, Bo Wu, Li-Jing Cheng
Spherical fullerene (C60 ) can quench the fluorescence of a quantum dot (QD) through energy transfer and charge transfer processes, with the quenching efficiency regulated by the number of proximate C60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C60 -labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C60 based MBs carried by magnetic nanoparticles (MNPs)...
May 15, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29718399/a-crispr-molecular-beacon-hybrid-system-for-live-cell-genomic-imaging
#2
Xiaotian Wu, Shiqi Mao, Yantao Yang, Muaz N Rushdi, Christopher J Krueger, Antony K Chen
The clustered regularly interspersed short palindromic repeat (CRISPR) gene-editing system has been repurposed for live-cell genomic imaging, but existing approaches rely on fluorescent protein reporters, making sensitive and continuous imaging difficult. Here, we present a fluorophore-based live-cell genomic imaging system that consists of a nuclease-deactivated mutant of the Cas9 protein (dCas9), a molecular beacon (MB), and an engineered single-guide RNA (sgRNA) harboring a unique MB target sequence (sgRNA-MTS), termed CRISPR/MB...
April 30, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29687994/hairpin-hairpin-molecular-beacon-interactions-for-detection-of-survivin-mrna-in-malignant-sw480-cells
#3
Katarzyna Ratajczak, Bartlomiej E Krazinski, Anna E Kowalczyk, Beata Dworakowska, Slawomir Jakiela, Magdalena Stobiecka
Cancer biomarkers offer unique prospects for the development of cancer diagnostics and therapy. One of such biomarkers, protein survivin (Sur), exhibits strong anti-apoptotic and proliferation-enhancing properties and is heavily expressed in multiple cancers. Thus, it can be utilized to provide new modalities for modulating the cell-growth rate, essential for an effective cancer treatment. Herein, we have focused on the development of a new survivin-based cancer detection platform for colorectal cancer cells SW480 using a turn-on fluorescence oligonucleotide molecular beacon (MB) probe, encoded to recognize Sur mRNA...
April 24, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29687247/novel-and-label-free-colorimetric-detection-of-radon-using-aunps-and-lead-ii-induced-gr5-dnazyme-based-amplification-strategy
#4
Hongwen Liu, Yating Chen, Chunli Song, Gang Tian, Shiya Li, Guiying Yang, Changyin Lv
Radioactive radon decays into a stable daughter product, 210 Pb, which was used as the detection target to determine the radon radiation dose in a new technique. Pb2+ triggers DNAzyme to cleave a molecular beacon (MB), resulting in the stem-loop structure opening and forming two single DNA strands (ssDNA). The ssDNA binds to unmodified gold nanoparticles and effectively prevents their aggregation in a salt solution. The detached enzyme strands continue to complement the remaining MB to amplify the response signal...
April 23, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29676728/detection-of-candida-species-in-pregnant-chinese-women-with-a-molecular-beacon-method
#5
Yanhong Zhai, Jing Liu, Li Zhou, Tongzhen Ji, Lingxin Meng, Yang Gao, Ran Liu, Xiao Wang, Lin Li, Binghuai Lu, Zheng Cao
PURPOSE: Candida pathogens are commonly found in women and can cause vulvovaginal candidiasis (VVC), whose infection rate is further increased during pregnancy. We aimed to study the Candida prevalence and strain distribution in pregnant Chinese women with a molecular beacon assay. METHODOLOGY: From March 2016 to February 2017, a total of 993 pregnant women attending routine antenatal visits at the Beijing Obstetrics and Gynecology Hospital were enrolled. For Candida detection and identification, a unique molecular beacon assay was presented and compared with a traditional phenotypic method...
April 20, 2018: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29675313/high-sensitivity-and-label-free-oligonucleotides-detection-using-photonic-bandgap-sensing-structures-biofunctionalized-with-molecular-beacon-probes
#6
Ángela Ruiz-Tórtola, Francisco Prats-Quílez, Daniel González-Lucas, María-José Bañuls, Ángel Maquieira, Guy Wheeler, Tamas Dalmay, Amadeu Griol, Juan Hurtado, Jaime García-Rupérez
A label-free sensor, based on the combination of silicon photonic bandgap (PBG) structures with immobilized molecular beacon (MB) probes, is experimentally developed. Complementary target oligonucleotides are specifically recognized through hybridization with the MB probes on the surface of the sensing structure. This combination of PBG sensing structures and MB probes demonstrates an extremely high sensitivity without the need for complex PCR-based amplification or labelling methods.
April 1, 2018: Biomedical Optics Express
https://www.readbyqxmd.com/read/29664230/experimental-study-of-the-evanescent-wave-photonic-sensors-response-in-presence-of-molecular-beacon-conformational-changes
#7
Ángela Ruiz-Tórtola, Francisco Prats-Quílez, Daniel Gónzalez-Lucas, María-José Bañuls, Ángel Maquieira, Guy Wheeler, Tamas Dalmay, Amadeu Griol, Juan Hurtado, Helge Bohlmann, Reiner Götzen, Jaime García-Rupérez
An experimental study of the influence of the conformational change suffered by molecular beacon (MB) probes -upon the biorecognition of nucleic acid target oligonucleotides over evanescent wave photonic sensors- is reported. To this end, high sensitivity photonic sensors based on silicon photonic bandgap (PBG) structures were used, where the MB probes were immobilized via their 5' termination. Those MBs incorporate a biotin moiety close to their 3' termination in order to selectively bind a streptavidin molecule to them...
April 17, 2018: Journal of Biophotonics
https://www.readbyqxmd.com/read/29663807/reversing-multidrug-resistance-by-multiplexed-gene-silencing-for-enhanced-breast-cancer-chemotherapy
#8
Yanli Li, Xiaonan Gao, Zhengze Yu, Bo Liu, Wei Pan, Na Li, Bo Tang
Multidrug resistance (MDR), as one of the main problems in clinical breast cancer chemotherapy, is closely related with the overexpression of drug efflux transporter P-glycoprotein (P-gp). In this study, a novel drug-loaded nanosystem was developed for inhibiting the P-gp expression and reversing multidrug resistance by multiplexed gene silencing, which composes of graphene oxide (GO) modified with two molecular beacons (MBs) and Doxorubicin (Dox). When the nanosystem was uptaken by the MDR breast cancer cells, Dox was released in the acidic endosomes and MBs were hybridized with target sequences...
April 17, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29656473/rapid-electron-transfer-of-stacked-heterodimer-of-perylenediimide-derivatives-in-a-dna-duplex
#9
Tadao Takada, Syunya Ishino, Ami Takata, Mitsunobu Nakamura, Mamoru Fujitsuka, Tetsuro Majima, Kazushige Yamana
We have demonstrated the rapid electron transfer in homo- and hetero-complexes composed of the parent perylenediimide (PDI, PH) and pyrrolidine-substituted PDI (PN) in DNA analyzed by steady-state fluorescence and femtosecond transient absorption measurements. The DNA molecules possessing PH and PN were prepared by our recently developed method using the reaction of enzymatically-generated abasic sites, by which the PDI molecules can be incorporated as base surrogates within the DNA base stack. The melting temperature analysis showed that the PH and PN monomer, and their homo- and heterodimers can contribute to the stabilization of the DNA duplex...
April 15, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29655420/dual-enzyme-free-amplification-strategy-for-ultra-sensitive-fluorescent-detection-of-bisphenol-a-in-water
#10
Wen Yun, Hong Wu, Lin Chen, Lizhu Yang
An ultra-sensitive strategy for bisphenol A (BPA) detection based on dual enzyme-free strategies: hybridization chain reaction (HCR) and enzyme-strand recycling reaction has been developed. The BPA aptamer can form hairpins structure by the partly self-complementary sequence. In the presence of BPA, the released BPA aptamer sequence can trigger the HCR between two hairpins to from a long nicked double-helix DNA. The tails of hairpins on the duplex DNA were closely enough to hybridize with molecular beacon (MB) on the gold nanoparticles (AuNPs) to circularly cleave the loop of MB, leading to a "turn-on" fluorescent signal...
August 22, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29653055/solid-phase-nasba-and-length-scale-effects-during-rna-amplification
#11
Youlong Ma, Feiyue Teng, Matthew R Libera
Solid-phase oligonucleotide amplification is of interest because of possible applications to next-generation sequencing, multiplexed microarray-based detection, and cell-free synthetic biology. Its efficiency is, however, less than that of traditional liquid-phase amplification involving unconstrained primers and enzymes, and understanding how to optimize the solid-phase amplification process remains challenging. Here we demonstrate the concept of solid-phase nucleic acid sequence based amplification (SP-NASBA) and use it to study the effect of tethering density on amplification efficiency...
April 13, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29645048/a-2-2-disulfide-bridged-dinucleotide-conformationally-locks-rna-hairpins
#12
Florian Gauthier, Frédéric Beltran, Annabelle Biscans, Françoise Debart, Christelle Dupouy, Jean-Jacques Vasseur
The synthesis and the impact of a disulfide bridge between 2'-O-positions of two adjacent nucleotides in an RNA duplex and in the loop of RNA hairpins are reported. The incorporation of this 2',2'-disulfide (S-S) bridge enabled thermal and enzymatic stabilization of the hairpin depending on its position in the loop. The influence of the disulfide bridge on RNA folding was studied at the HIV Dimerization Initiation Site (DIS) as an RNA sequence model. We have shown that this S-S bridge locked the hairpin form, whereas the extended duplex form was generated after the reduction of the disulfide bond in the presence of tris(2-carboxyethyl)phosphine or glutathione...
April 12, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29629140/simultaneous-sensitive-detection-of-multiple-dna-glycosylases-from-lung-cancer-cells-at-the-single-molecule-level
#13
Juan Hu, Ming-Hao Liu, Ying Li, Bo Tang, Chun-Yang Zhang
DNA glycosylases are involved in the base excision repair pathway, and all mammals express multiple DNA glycosylases to maintain genome stability. However, the simultaneous detection of multiple DNA glycosylase still remains a great challenge. Here, we develop a single-molecule detection method for the simultaneous detection of human 8-oxoguanine DNA glycosylase 1 (hOGG1) and human alkyladenine DNA glycosylase (hAAG) on the basis of DNA glycosylase-mediated cleavage of molecular beacons. We designed a Cy3-labeled molecular beacon modified with 8-oxoguanine (8-oxoG) for a hOGG1 assay and a Cy5-labeled molecular beacon modified with deoxyinosine for a hAAG assay...
January 21, 2018: Chemical Science
https://www.readbyqxmd.com/read/29617556/a-dual-targeting-delivery-system-for-effective-genome-editing-and-in-situ-detecting-related-protein-expression-in-edited-cells
#14
Bo-Ya Liu, Xiao-Yan He, Chang Xu, Lei Xu, Shu-Lun Ai, Si-Xue Cheng, Ren-Xi Zhuo
One of critical steps in genome editing by CRISPR-Cas9 is to deliver the CRISPR-Cas9 system into targeted cells. In this study, we developed a dual-targeting delivery system based on polymer/inorganic hybrid nanoparticles to realize highly efficient genome editing in targeted tumor cells as well as in situ detection on the related protein expression in edited cells. The CRISPR-Cas9 plasmid for CDK11 knockout was encapsulated in the core of the delivery system composed of protamine sulfate, calcium carbonate and calcium phosphate by co-precipitation, and functional derivatives of carboxymethyl chitosan (biotinylated carboxymethyl chitosan with biotin ligands and aptamer incorporated carboxymethyl chitosan with AS1411 ligands) were decorated on the nanovector surface by electrostatic interactions to form the dual-targeting delivery system...
April 4, 2018: Biomacromolecules
https://www.readbyqxmd.com/read/29595962/cross-platform-cancer-cell-identification-using-telomerase-specific-spherical-nucleic-acids
#15
Zhengjie Liu, Jun Zhao, Ruilong Zhang, Guangmei Han, Cheng Zhang, Bianhua Liu, Zhongping Zhang, Ming-Yong Han, Xiaohu Gao
Distinguishing tumor cells from normal cells holds the key to precision diagnosis and effective intervention of cancers. The fundamental difficulties, however, are the heterogeneity of tumor cells and the lack of truly specific and ideally universal cancer biomarkers. Here, we report a concept of tumor cell detection, bypassing the specific genotypic and phenotypic features of different tumor cell types and directly going toward the hallmark of cancer, uncontrollable growth. Combining spherical nucleic acids (SNAs) with exquisitely engineered molecular beacons (SNA beacons, dubbed SNAB technology) is capable of identifying tumor cells from normal cells based on the molecular phenotype of telomerase activity, largely bypassing the heterogeneity problem of cancers...
April 2, 2018: ACS Nano
https://www.readbyqxmd.com/read/29594734/voltammetric-determination-of-attomolar-levels-of-a-sequence-derived-from-the-genom-of-hepatitis-b-virus-by-using-molecular-beacon-mediated-circular-strand-displacement-and-rolling-circle-amplification
#16
Shan Huang, Mengmeng Feng, Jiawen Li, Yi Liu, Qi Xiao
The authors describe an electrochemical method for the determination of the single-stranded DNA (ssDNA) oligonucleotide with a sequence derived from the genom of hepatitis B virus (HBV). It is making use of circular strand displacement (CSD) and rolling circle amplification (RCA) strategies mediated by a molecular beacon (MB). This ssDNA hybridizes with the loop portion of the MB immobilized on the surface of a gold electrode, while primer DNA also hybridizes with the rest of partial DNA sequences of MB. This triggers the MB-mediated CSD...
March 3, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/29594730/fluorometric-determination-of-nucleic-acids-based-on-the-use-of-polydopamine-nanotubes-and-target-induced-strand-displacement-amplification
#17
Jia Ge, Dong-Mei Bai, Xin -Geng, Ya-Lei Hu, Qi-Yong Cai, Ke Xing, Lin Zhang, Zhao-Hui Li
The authors describe a fluorometric method for the quantitation of nucleic acids by combining (a) cycled strand displacement amplification, (b) the unique features of the DNA probe SYBR Green, and (c) polydopamine nanotubes. SYBR Green undergoes strong fluorescence enhancement upon intercalation into double-stranded DNA (dsDNA). The polydopamine nanotubes selectively adsorb single-stranded DNA (ssDNA) and molecular beacons. In the absence of target DNA, the molecular beacon, primer and SYBR Green are adsorbed on the surface of polydopamine nanotubes...
January 10, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/29594715/mos-2-quantum-dots-modified-with-a-labeled-molecular-beacon-as-a-ratiometric-fluorescent-gene-probe-for-fret-based-detection-and-imaging-of-microrna
#18
Xinsheng Yu, Lianzhe Hu, Feng Zhang, Min Wang, Zhining Xia, Weili Wei
A dual-channel ratiometric nanoprobe is described for detection and imaging of microRNA. It was prepared from MoS2 quantum dots (QDs; with blue emission and excitation/emission peaks at 310/398 nm) which acts as both the gene carrier and as a donor in fluorescence resonance energy transfer (FRET). Molecular beacons containing loops for molecular recognition of microRNA and labeled with carboxyfluorescein (FAM) were covalently attached to the MoS2 QDs and serve as the FRET acceptor. In the absence of microRNA, the nanoprobe exhibits low FRET efficiency due to the close distance between the FAM tag and the QDs...
March 27, 2018: Mikrochimica Acta
https://www.readbyqxmd.com/read/29594712/fluorometric-graphene-oxide-based-detection-of-salmonella-enteritis-using-a-truncated-dna-aptamer
#19
Raja Chinnappan, Saleh AlAmer, Shimaa Eissa, Anas Abdel Rahamn, Khalid M Abu Salah, Mohammed Zourob
The work describes a fluorescence-based study for mapping the highest affinity truncated aptamer from the full length sequence and its integration in a graphene oxide platform for the detection of Salmonella enteriditis. To identify the best truncated sequence, molecular beacons and a displacement assay design are applied. In the fluorescence displacement assay, the truncated aptamer was hybridized with fluorescein and quencher-labeled complementary sequences to form a fluorescence/quencher pair. In the presence of S...
December 18, 2017: Mikrochimica Acta
https://www.readbyqxmd.com/read/29594619/colorimetric-detection-of-genetically-modified-organisms-based-on-exonuclease-iii-assisted-target-recycling-and-hemin-g-quadruplex-dnazyme-amplification
#20
Decai Zhang, Weijia Wang, Qian Dong, Yunxiu Huang, Dongmei Wen, Yuejing Mu, Yong Yuan
An isothermal colorimetric method is described for amplified detection of the CaMV 35S promoter sequence in genetically modified organism (GMO). It is based on (a) target DNA-triggered unlabeled molecular beacon (UMB) termini binding, and (b) exonuclease III (Exo III)-assisted target recycling, and (c) hemin/G-quadruplex (DNAzyme) based signal amplification. The specific binding of target to the G-quadruplex sequence-locked UMB triggers the digestion of Exo III. This, in turn, releases an active G-quadruplex segment and target DNA for successive hybridization and cleavage...
December 21, 2017: Mikrochimica Acta
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