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Aptamers

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https://www.readbyqxmd.com/read/27933702/multiparameter-particle-display-mppd-a-quantitative-screening-method-for-the-discovery-of-highly-specific-aptamers
#1
Jinpeng Wang, Jingwen Yu, Qin Yang, John McDermott, Alexander Scott, Matthew Vukovich, Remy Lagrois, Qiang Gong, William Greenleaf, Michael Eisenstein, B Scott Ferguson, H Tom Soh
Aptamers are a promising class of affinity reagents because they are chemically synthesized, thus making them highly reproducible and distributable as sequence information rather than a physical entity. Although many high-quality aptamers have been previously reported, it is difficult to routinely generate aptamers that possess both high affinity and specificity. One of the reasons is that conventional aptamer selection can only be performed either for affinity (positive selection) or for specificity (negative selection), but not both simultaneously...
December 9, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27931100/photocaged-g-quadruplex-dnazyme-and-aptamer-by-postsynthetic-modification-on-phosphodiester-backbone
#2
Mengli Feng, Zhiyuan Ruan, Jiachen Shang, Lu Xiao, Aijun Tong, Yu Xiang
G-quadruplex-containing DNAzymes and aptamers are widely applied in many research fields because of their high stability and prominent activities versus the protein counterparts. In this work, G-quadruplex DNAs were equipped with photolabile groups to construct photocaged DNAzymes and aptamers. We incorporated TEEP-OH (thioether-enol phosphate, phenol substituted) into phosphodiester backbone of G-quadruplex DNA by a facile postsynthetic method to achieve efficient photocaging of their activities. Upon light irradiation, the peroxidase-mimicking activity of the caged G-quadruplex DNAzyme was activated, through the transformation of TEEP-OH into a native DNA phos-phodiester without any artificial scar...
December 9, 2016: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/27930845/isolation-and-characterization-of-rna-aptamers-against-a-proteasome-associated-deubiquitylating-enzyme-uch37
#3
Jung Hoon Lee, Min Jae Lee
Deubiquitylating (DUB) enzymes antagonize ubiquitin-dependent protein degradation both before and after the substrates are engaged with proteasomes. UCH37 is one of three proteasome-associated DUB enzymes in mammals and the only protease among them from the ubiquitin carboxyl-terminal hydrolase (UCH) family. Here, we report the identification of specific RNA aptamers for UCH37 through in vitro selection, and we describe their inhibitory effects on the DUB activity of UCH37. The RNA aptamers significantly delayed RPN13-mediated UCH37 activation and lowered total DUB activity of proteasomes, as measured by the hydrolysis of ubiquitin-rhodamine 110...
December 8, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27930344/specific-detection-of-biomolecules-in-physiological-solutions-using-graphene-transistor-biosensors
#4
Ning Gao, Teng Gao, Xiao Yang, Xiaochuan Dai, Wei Zhou, Anqi Zhang, Charles M Lieber
Nanomaterial-based field-effect transistor (FET) sensors are capable of label-free real-time chemical and biological detection with high sensitivity and spatial resolution, although direct measurements in high-ionic-strength physiological solutions remain challenging due to the Debye screening effect. Recently, we demonstrated a general strategy to overcome this challenge by incorporating a biomolecule-permeable polymer layer on the surface of silicon nanowire FET sensors. The permeable polymer layer can increase the effective screening length immediately adjacent to the device surface and thereby enable real-time detection of biomolecules in high-ionic-strength solutions...
December 5, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27924973/selection-of-aptamers-based-on-a-protein-microarray-integrated-with-a-microfluidic-chip
#5
Xiaohui Liu, Hui Li, Wenchao Jia, Zhu Chen, Danke Xu
We developed an efficient and fast method based on a protein microarray integrated with a microfluidic chip for the process of SELEX (systematic evolution of ligands by exponential enrichment). Lactoferrin from bovine milk was used as a target protein, while bovine serum albumin (BSA), α-lactalbumin, β-lactoglobulin and casein were used as negative proteins. They were separately dotted and immobilized to prepare the protein microarray and the resulting microarray was further integrated into a microfluidic chip for the SELEX (PMM-SELEX) process...
December 7, 2016: Lab on a Chip
https://www.readbyqxmd.com/read/27924950/molecular-gated-nanoporous-anodic-alumina-for-the-detection-of-cocaine
#6
Àngela Ribes, Elisabet Xifré-Pérez, Elena Aznar, Félix Sancenón, Teresa Pardo, Lluís F Marsal, Ramόn Martínez-Máñez
We present herein the use of nanoporous anodic alumina (NAA) as a suitable support to implement "molecular gates" for sensing applications. In our design, a NAA support is loaded with a fluorescent reporter (rhodamine B) and functionalized with a short single-stranded DNA. Then pores are blocked by the subsequent hybridisation of a specific cocaine aptamer. The response of the gated material was studied in aqueous solution. In a typical experiment, the support was immersed in hybridisation buffer solution in the absence or presence of cocaine...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924617/cxcl12-sdf-1-dependent-retinal-migration-of-endogenous-bone-marrow-derived-stem-cells-improves-visual-function-after-pharmacologically-induced-retinal-degeneration
#7
Volker Enzmann, Stéphanie Lecaudé, Anna Kruschinski, Axel Vater
Mobilized bone marrow-derived stem cells (BMSC) have been discussed as an alternative strategy for endogenous repair. Thereby, different approaches for BMSC mobilization have been pursued. Herein, the role of a newly discovered oligonucleotide for retinal homing and regeneration capability of BMSCs was investigated in the sodium iodate (NaIO3) model of retinal degeneration. Mobilization was achieved in GFP-chimera with NOX-A12, a CXC-motif chemokine ligand 12 (CXCL12)/stromal cell-derived factor 1 (SDF-1)-neutralizing L-aptamer...
December 6, 2016: Stem Cell Reviews
https://www.readbyqxmd.com/read/27923103/noninvasive-microsurgery-using-aptamer-functionalized-magnetic-microdisks-for-tumor-cell-eradication
#8
Tatiana N Zamay, Galina S Zamay, Irina V Belyanina, Sergey S Zamay, Valery V Denisenko, Olga S Kolovskaya, Tatiana I Ivanchenko, Valentina L Grigorieva, Irina V Garanzha, Dmitry V Veprintsev, Yury E Glazyrin, Alexandr V Shabanov, Viktor Y Prinz, Vladimir A Seleznev, Alexey E Sokolov, Vladimir S Prokopenko, Petr D Kim, Ana Gargaun, Maxim V Berezovski, Anna S Zamay
Magnetomechanical cell disruption using nano- and microsized structures is a promising biomedical technology used for noninvasive elimination of diseased cells. It applies alternating magnetic field (AMF) for ferromagnetic microdisks making them oscillate and causing cell membrane disruption with cell death followed by apoptosis. In this study, we functionalized the magnetic microdisks with cell-binding DNA aptamers and guided the microdisks to recognize cancerous cells in a mouse tumor in vivo. Only 10 min of the treatment with a 100 Hz AMF was enough to eliminate cancer cells from a malignant tumor...
December 6, 2016: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/27918604/real-time-naked-eye-multiplex-detection-of-toxins-and-bacteria-using-aiegens-with-the-assistance-of-graphene-oxide
#9
Ruoyu Zhang, Xiaolei Cai, Guangxue Feng, Bin Liu
Toxins and bacteria in water or food pose a threat to human life and could potentially be exploited for bioterrorism. Real-time naked-eye detection of these contaminants is highly desirable to provide a direct and simple analytical method and address the challenges of the existing strategies. Using the detection of ricin and B. subtilis as an example, a naked-eye multiplex detection model is established. In this work, a green fluorogen with aggregation-induced emission (AIE) characteristics was encapsulated in silica nanoshells...
December 5, 2016: Faraday Discussions
https://www.readbyqxmd.com/read/27918487/integrating-deoxyribozymes-into-colorimetric-sensing-platforms
#10
REVIEW
Dingran Chang, Sandy Zakaria, Mimi Deng, Nicholas Allen, Kha Tram, Yingfu Li
Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection...
December 3, 2016: Sensors
https://www.readbyqxmd.com/read/27918423/potentiometric-aptasensing-of-vibrio-alginolyticus-based-on-dna-nanostructure-modified-magnetic-beads
#11
Guangtao Zhao, Jiawang Ding, Han Yu, Tanji Yin, Wei Qin
A potentiometric aptasensing assay that couples the DNA nanostructure-modified magnetic beads with a solid-contact polycation-sensitive membrane electrode for the detection of Vibrio alginolyticus is herein described. The DNA nanostructure-modified magnetic beads are used for amplification of the potential response and elimination of the interfering effect from a complex sample matrix. The solid-contact polycation-sensitive membrane electrode using protamine as an indicator is employed to chronopotentiometrically detect the change in the charge or DNA concentration on the magnetic beads, which is induced by the interaction between Vibrio alginolyticus and the aptamer on the DNA nanostructures...
December 2, 2016: Sensors
https://www.readbyqxmd.com/read/27916536/a-new-lateral-flow-strip-assay-lfsa-using-a-pair-of-aptamers-for-the-detection-of-vaspin
#12
Nurul Hanun Ahmad Raston, Van-Thuan Nguyen, Man Bock Gu
A new lateral flow strip assay (LFSA) using a pair of aptamers has been designed and successfully developed using a pair of aptamers-functionalized with gold nanoparticles (AuNPs). This new LFSA biosensor system utilizes a cognate aptamer duo binding to vaspin, a target protein, at the two different binding sites, and exhibited a sensitive and highly selective response to vaspin. A sandwich-type format in LFSA was developed based on biotin-labeled primary V1 aptamer immobilized on streptavidin coated membrane as a capturing probe and secondary V49 aptamer conjugated with AuNPs as a signaling probe...
November 28, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27914932/detection-of-human-immunodeficiency-virus-rnas-in-living-cells-using-spinach-rna-aptamers
#13
Brandon D Burch, Carolina Garrido, David M Margolis
Many techniques currently used to measure HIV RNA production in cells suffer from limitations that include high background signal or the potential to destroy cellular context. Fluorophore-binding RNA aptamers offer the potential for visualizing RNAs directly in living cells with minimal cellular perturbation. We inserted a sequence encoding a fluorophore-binding RNA aptamer, known as Spinach, into the HIV genome such that predicted RNA secondary structures in both Spinach and HIV were preserved. Chimeric HIV-Spinach RNAs were functionally validated in vitro by testing their ability to enhance the fluorescence of a conditional fluorophore (DFHBI), which specifically binds Spinach...
November 30, 2016: Virus Research
https://www.readbyqxmd.com/read/27911494/determining-functional-aptamer-protein-interaction-by-biolayer-interferometry
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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