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https://www.readbyqxmd.com/read/27911494/determining-functional-aptamer-protein-interaction-by-biolayer-interferometry
#1
Xinhui Lou, Martin Egli, Xianbin Yang
Short single-stranded nucleic acids called aptamers are widely being explored as recognition molecules of high affinity and specificity for binding a wide range of target molecules, particularly protein targets. In biolayer interferometry (BLI), a simple Dip-and-Read approach in which the aptamer-coated biosensors are dipped into microplate wells is used to study the interactions between an aptamer and its target protein. Here we describe the protocol for the analysis of the interaction between a well-characterized anti-thrombin RNA aptamer with thrombin (Basic Protocol)...
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27907160/as1411-induced-growth-inhibition-of-glioma-cells-by-up-regulation-of-p53-and-down-regulation-of-bcl-2-and-akt1-via-nucleolin
#2
Ye Cheng, Gang Zhao, Siwen Zhang, Fares Nigim, Guangtong Zhou, Zhiyun Yu, Yang Song, Yong Chen, Yunqian Li
AS1411 binds nucleolin (NCL) and is the first oligodeoxynucleotide aptamer to reach phase I and II clinical trials for the treatment of several cancers. However, the mechanisms by which AS1411 targets and kills glioma cells and tissues remain unclear. Here we report that AS1411 induces cell apoptosis and cycle arrest, and inhibits cell viability by up-regulation of p53 and down-regulation of Bcl-2 and Akt1 in human glioma cells. NCL was overexpressed in both nucleus and cytoplasm in human glioma U87, U251 and SHG44 cells compared to normal human astrocytes (NHA)...
2016: PloS One
https://www.readbyqxmd.com/read/27906685/targeted-chimera-delivery-to-ovarian-cancer-cells-by-heterogeneous-gold-magnetic-nanoparticle
#3
Yao Chen, Mengjiao Xu, Yi Guo, Keyao Tu, Weimin Wu, Jianjun Wang, Xiaowen Tong, Wenjuan Wu, Lifeng Qi, Donglu Shi
Efficient delivery of small interfering RNAs (siRNAs) to the targeted cells has remained a significant challenge in clinical applications. In the present study, we developed a novel aptamer-siRNA chimera delivery system mediated by cationic Au-Fe3O4 nanoparticles (NPs). The chimera constructed by VEGF RNA aptamer and Notch3 siRNA was bonded with heterogeneous Au-Fe3O4 nanoparticles by electrostatic interaction. The obtained complex exhibited much higher silencing efficiency against Notch3 gene compared with chimera alone and lipofectamine-siRNA complex, and improved the antitumor effects of the loaded chimera...
December 1, 2016: Nanotechnology
https://www.readbyqxmd.com/read/27900665/use-of-capillary-electrophoresis-to-study-the-binding-interaction-of-aptamers-with-wild-type-k103n-and-double-mutant-k103n-y181c-hiv-1-rt-studying-the-binding-interaction-of-wild-type-k103n-and-double-mutant-k103n-y181c-hiv-1-rt-with-aptamers-by-performing
#4
Niran Aeksiri, Chompunuch Warakulwit, Supa Hannongbua, Sasimanas Unajak, Kiattawee Choowongkomon
A number of nucleic acid aptamers with high affinities to human immunodeficiency virus reverse transcriptase (HIV-1 RT) are currently known. They can potentially be developed as broad-spectrum antiviral drugs, but there is little known about their binding interaction with mutant HIV-1 RT. Therefore, we utilized non-equilibrium capillary electrophoresis of equilibrium mixture (NECEEM) to study the interaction of three HIV-1 RTs (wild type, K103N, and double mutant (K103N/Y181C)) with RT1t49 and RT12 aptamers...
November 30, 2016: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/27899589/through-bond-effects-in-the-ternary-complexes-of-thrombin-sandwiched-by-two-dna-aptamers
#5
Andrea Pica, Irene Russo Krauss, Valeria Parente, Hisae Tateishi-Karimata, Satoru Nagatoishi, Kouhei Tsumoto, Naoki Sugimoto, Filomena Sica
Aptamers directed against human thrombin can selectively bind to two different exosites on the protein surface. The simultaneous use of two DNA aptamers, HD1 and HD22, directed to exosite I and exosite II respectively, is a very powerful approach to exploit their combined affinity. Indeed, strategies to link HD1 and HD22 together have been proposed in order to create a single bivalent molecule with an enhanced ability to control thrombin activity. In this work, the crystal structures of two ternary complexes, in which thrombin is sandwiched between two DNA aptamers, are presented and discussed...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899266/dna-aptamers-against-foki-nuclease-domain-for-genome-editing-applications
#6
Maui Nishio, Daisuke Matsumoto, Yoshio Kato, Koichi Abe, Jinhee Lee, Kaori Tsukakoshi, Ayana Yamagishi, Chikashi Nakamura, Kazunori Ikebukuro
Genome editing with site-specific nucleases (SSNs) can modify only the target gene and may be effective for gene therapy. The main limitation of genome editing for clinical use is off-target effects; excess SSNs in the cells and their longevity can contribute to off-target effects. Therefore, a controlled delivery system for SSNs is necessary. FokI nuclease domain (FokI) is a common DNA cleavage domain in zinc finger nuclease (ZFN) and transcription activator-like effector nuclease. Previously, we reported a zinc finger protein delivery system that combined aptamer-fused, double-strand oligonucleotides and nanoneedles...
November 22, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27899264/cyclic-ferrocenylnaphthalene-diimide-derivative-as-a-new-class-of-g-quadruplex-dna-binding-ligand
#7
Md Monirul Islam, Shinobu Sato, Shingo Shinozaki, Shigeori Takenaka
To identify an effective ligand that binds to a G-quadruplex structure but not a double-stranded DNA (dsDNA), a set of biophysical and biochemical experiments were carried out using newly synthesized cyclic ferrocenylnaphthalene diimide (cFNDI, 1) or the non-cyclic derivative (2) with various structures of G-quadruplex DNAs and dsDNA. Compound 1 bound strongly to G-quadruplexes DNAs (10(6)M(-1) order) with diminished binding to dsDNA (10(4)M(-1) order) in 100mM AcOH-AcOK buffer (pH 5.5) containing 100mM KCl...
November 15, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27899028/nano-liposome-based-target-toxicity-machine-an-alternative-complementary-approach-in-atopic-diseases
#8
Behzad Mansoori, Ali Mohammadi, Neda Shajari, Sadaf Davudian, Shima Salehi, Behzad Baradaran
Despite using lots of progression in hypersensitivity, it is not yet a cure. Current treatment for allergy focuses on two approaches, including treats only the symptoms of allergy by utilizing drugs and the other is desensitization therapy (immunotherapy), which involves administration of specific allergens. The main obstacle to hypersensitivity permanent treatment is the IgE producing subclass of B-lymphocytes which is the source of IgE- producing in hypersensitive patients. Removal of these lymphocytes causes noticeable reduction in the levels of IgE and allergic responses significantly...
November 29, 2016: Artificial Cells, Nanomedicine, and Biotechnology
https://www.readbyqxmd.com/read/27898377/upconversion-nanoparticles-grafted-molybdenum-disulfide-nanosheets-platform-for-microcystin-lr-sensing
#9
Jiajia Lv, Sen Zhao, Shijia Wu, Zhouping Wang
Water safety is one of the most pervasive problems afflicting people throughout the world. Microcystin-LR (MC-LR), a representative toxin released by cyanobacteria, poses an increasing and serious threat to water safety. In order to develop facile, specific and sensitive detection methods for MC-LR, we fabricated an ultrasensitive fluorescence aptasensor using the enhanced fluorescence of UCNP and the effective quenching ability, high affinity toward single strand DNA (ssDNA) of MoS2 (termed as FAUM). This assay specifically determined MC-LR in the linear range of 0...
October 4, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27898376/impedimetric-monitoring-of-apoptosis-using-cytochrome-aptamer-bioconjugated-silver-nanocluster
#10
Mojtaba Shamsipur, Afshin Pashabadi, Fatemeh Molaabasi, Saman Hosseinkhani
It is well known that cytochrome c (Cyt c) is a crucial death regulator that triggers programmed cell death, apoptosis. Here, we report on the successful application of an aptamer bioconjugated nanoclusters for the detection of apoptosis based on release of cytochrome c from mitochondria in lysates human embryonic kidney cells HEK293T. The aptamer-conjugated silver nanoclusters (Apt@AgNCs) were synthesized and immobilized on gold electrode for impedimetric detection of Cyt c over the range of 0.15-375nM. It was found that the presence of Ag(I) ions shell at the surface of prepared NCs could increase their affinity to the donor groups (COO(-) and some amine groups in its deprotonated form, NH2) of cysteine attached on the gold electrode surface...
November 23, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27898020/multivalent-aptamers-versatile-tools-for-diagnostic-and-therapeutic-applications
#11
REVIEW
Mariya Vorobyeva, Pavel Vorobjev, Alya Venyaminova
Nucleic acid aptamers generated through an in vitro selection are currently extensively applied as very valuable biomolecular tools thanks to their prominent advantages. Diversity of spatial structures, ease of production through chemical synthesis and a large variety of chemical modifications make aptamers convenient building blocks for the generation of multifunctional constructs. An opportunity to combine different aptamer functionalities with other molecules of interest such as reporter groups, nanoparticles, chemotherapeutic agents, siRNA or antisense oligonucleotides provides a widest range of applications of multivalent aptamers...
November 25, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27897376/photo-tethers-for-the-multi-cyclic-conformational-caging-of-long-oligonucleotides
#12
Patrick Seyfried, Laura Eiden, Nikolai Grebenovsky, Günter Mayer, Alexander Heckel
Intramolecular circularization of DNA oligonucleotides was accomplished by incorporation of alkyne-modified photolabile nucleosides into DNA sequences, followed by a Cu(I) -catalyzed alkyne-azide cycloaddition with bis-azido linker molecules. We determined a range of ring sizes, in which the caged circular oligonucleotides exhibit superior duplex destabilizing properties. Specific binding of a full-length 90 nt C10 aptamer recognizing human Burkitt's lymphoma cells was then temporarily inhibited by locking the aptamer in a bicircularized structure...
November 29, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27893356/single-stranded-dna-aptamer-targeting-and-neutralization-of-anti-d-alloantibody-a-potential-therapeutic-strategy-for-haemolytic-diseases-caused-by-rhesus-alloantibody
#13
Yinze Zhang, Fan Wu, Manni Wang, Naibao Zhuang, Huayou Zhou, Hua Xu
BACKGROUND: Rhesus (Rh) D antigen is the most important antigen in the Rh blood group system because of its strong immunogenicity. When RhD-negative individuals are exposed to RhD-positive blood, they may produce anti-D alloantibody, potentially resulting in delayed haemolytic transfusion reactions and Rh haemolytic disease of the foetus and newborn, which are difficult to treat. Inhibition of the binding of anti-D antibody with RhD antigens on the surface of red blood cells may effectively prevent immune haemolytic diseases...
November 11, 2016: Blood Transfusion, Trasfusione del Sangue
https://www.readbyqxmd.com/read/27892593/dual-mode-refractive-index-and-charge-sensing-to-investigate-complex-surface-chemistry-on-nanostructures
#14
Nikhil Bhalla, Doojin Lee, Shivani Sathish, Amy Q Shen
This work presents a novel dual-mode charge and refractive index sensitive device integrated with nanoplasmonic islands, for the first time, on insulator-semiconductor junctions. The developed nano-metal-insulator semiconductor (nMIS) sensor facilitates simultaneous detection of charge and mass changes on the nanoislands due to the binding of biomolecules. The charging of the nanoislands is traced by using the capacitive field-effect electrolyte-metal-insulator-semiconductor structure and the refractive index changes are quantified by measuring the change in the localized surface plasmon resonances of the nanoislands...
November 28, 2016: Nanoscale
https://www.readbyqxmd.com/read/27891685/the-dna-aptamer-binds-stemness-enriched-cancer-cells-in-pancreatic-cancer
#15
Yoon-Jin Kim, Hee Seung Lee, Dawoon E Jung, Jeong Mi Kim, Si Young Song
Pancreatic cancer remains one of the most common and lethal cancers. Most patients (80%) present with inoperable advanced pancreatic cancer at initial diagnosis, and their early diagnosis is a significant unmet challenge. Recent studies indicate that cancer, including pancreatic cancer, is initiated and propagated by cancer stem cells (CSCs). CSCs are responsible not only for the pathogenesis of cancer but also for the heterogeneity, malignant degree, anticancer therapy resistance, and recurrence of tumors...
November 28, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27890659/rna-nanoparticles-harboring-annexin-a2-aptamer-can-target-ovarian-cancer-for-tumor-specific-doxorubicin-delivery
#16
Fengmei Pi, Hui Zhang, Hui Li, Varatharasa Thiviyanathan, David G Gorenstein, Anil K Sood, Peixuan Guo
A novel modified nucleic acid nanoparticle harboring an annexin A2 aptamer for ovarian cancer cell targeting and a GC rich sequence for doxorubicin loading is designed and constructed. The system utilizes a highly stable three-way junction (3WJ) motif from phi29 packaging RNA as a core structure. A phosphorothioate-modified DNA aptamer targeting annexin A2, Endo28, was conjugated to one arm of the 3WJ. The pRNA-3WJ motif retains correct folding of attached aptamer, keeping its functions intact. It is of significant utility for aptamer-mediated targeted delivery...
November 24, 2016: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/27886773/a-novel-aptameric-biosensor-based-on-the-self-assembled-dna-ws2-nanosheet-architecture
#17
Aixue Li, Jian Zhang, Jichuan Qiu, Zhenhuan Zhao, Cheng Wang, Chunjiang Zhao, Hong Liu
It has been reported that tungsten disulfide (WS2) can bind single-stranded DNA (ssDNA) with high affinity while it has less affinity toward double stranded DNA (dsDNA). In this work, for the first time, the high affinity between WS2 and ssDNA was used to construct stable sensing interface for ATP detection. A DNA sequence with -SH at one end was first immobilized on Au electrode. WS2 nanosheets were immobilized on the SH-DNA/Au electrode surface due to the strong affinity between WS2 and ssDNA. Then the WS2 nanosheets were used to immobilize ATP binding aptamer (ABA) through the high affinity between WS2 and ssDNA, too...
January 15, 2017: Talanta
https://www.readbyqxmd.com/read/27886058/optical-aptamer-probes-of-fluorescent-imaging-to-rapid-monitoring-of-circulating-tumor-cell
#18
Ji Yeon Hwang, Sang Tae Kim, Ho-Seong Han, Kyunggon Kim, Jin Soo Han
Fluorescence detecting of exogenous EpCAM (epithelial cell adhesion molecule) or muc1 (mucin1) expression correlated to cancer metastasis using nanoparticles provides pivotal information on CTC (circulating tumor cell) occurrence in a noninvasive tool. In this study, we study a new skill to detect extracellular EpCAM/muc1 using quantum dot-based aptamer beacon (QD-EpCAM/muc1 ALB (aptamer linker beacon). The QD-EpCAM/muc1 ALB was designed using QDs (quantum dots) and probe. The EpCAM/muc1-targeting aptamer contains a Ep-CAM/muc1 binding sequence and BHQ1 (black hole quencher 1) or BHQ2 (black hole quencher2)...
November 23, 2016: Sensors
https://www.readbyqxmd.com/read/27885761/a-stably-protonated-adenine-nucleotide-with-a-highly-shifted-pka-value-stabilizes-the-tertiary-structure-of-a-gtp-binding-rna-aptamer
#19
Antje C Wolter, A Katharina Weickhmann, Amir H Nasiri, Katharina Hantke, Oliver Ohlenschläger, Christoph H Wunderlich, Christoph Kreutz, Elke Duchardt-Ferner, Jens Wöhnert
RNA tertiary structure motifs are stabilized by a wide variety of hydrogen-bonding interactions. Protonated A and C nucleotides are normally not considered to be suitable building blocks for such motifs since their pKa values are far from physiological pH. Here, we report the NMR solution structure of an in vitro selected GTP-binding RNA aptamer bound to GTP with an intricate tertiary structure. It contains a novel kind of base quartet stabilized by a protonated A residue. Owing to its unique structural environment in the base quartet, the pKa value for the protonation of this A residue in the complex is shifted by more than 5 pH units compared to the pKa for A nucleotides in single-stranded RNA...
November 25, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27884158/rapid-visualization-of-latent-fingermarks-using-gold-seed-mediated-enhancement
#20
Chia-Hao Su, Chun-Chieh Yu, Fong-Yu Cheng
BACKGROUND: Fingermarks are one of the most important and useful forms of physical evidence in forensic investigations. However, latent fingermarks are not directly visible, but can be visualized due to the presence of other residues (such as inorganic salts, proteins, polypeptides, enzymes and human metabolites) which can be detected or recognized through various strategies. Convenient and rapid techniques are still needed to provide obvious contrast between the background and the fingermark ridges and to then visualize latent fingermark with a high degree of selectivity and sensitivity...
November 25, 2016: Journal of Nanobiotechnology
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