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Dna aptamer

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https://www.readbyqxmd.com/read/27936442/label-free-colorimetric-detection-of-cancer-related-gene-based-on-two-step-amplification-of-molecular-machine
#1
Huo Xu, Dong Wu, Chen-Qiao Li, Zheng Lu, Xiao-Yun Liao, Jie Huang, Zai-Sheng Wu
Highly sensitive detection of K-ras gene is of great significance in biomedical research and clinical diagnosis. Here, we developed a colorimetric biosensing system for the detection of proto-oncogene K-ras based on enhanced amplification effect of DNA molecular machine, where dual isothermal circular strand-displacement amplification (D-SDA) occurs on two arms in one-to-one correspondence. Specifically, we designed a primer-locked hairpin probe (HP) and a primer-contained linear polymerization template (PPT)...
December 2, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27934108/multianalytical-study-of-the-binding-between-a-small-chiral-molecule-and-a-dna-aptamer-evidence-for-asymmetric-steric-effect-upon-3-versus-5-end-sequence-modification
#2
Lylian Challier, Rebeca Miranda-Castro, Bertrand Barbe, Claire Fave, Benoît Limoges, Eric Peyrin, Corinne Ravelet, Emmanuelle Fiore, Pierre Labbé, Liliane Coche-Guérente, Eric Ennifar, Guillaume Bec, Philippe Dumas, François Mavré, Vincent Noël
Nucleic acid aptamers are involved in a broad field of applications ranging from therapeutics to analytics. Deciphering the binding mechanisms between aptamers and small ligands is therefore crucial to improve and optimize existing applications and to develop new ones. Particularly interesting is the enantiospecific binding mechanism involving small molecules with nonprestructured aptamers. One archetypal example is the chiral binding between l-tyrosinamide and its 49-mer aptamer for which neither structural nor mechanistic information is available...
December 6, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/27933990/automated-enrichment-of-sulfanilamide-in-milk-matrices-by-utilization-of-aptamer-linked-magnetic-particles
#3
Christin Fischer, Constanze Kallinich, Sven Klockmann, Jil Schrader, Markus Fischer
The present work demonstrates the first automated enrichment approach for antibiotics in milk using specific DNA aptamers. First, aptamers toward the antibiotic sulfanilamide were selected and characterized regarding their dissociation constants and specificity toward relevant antibiotics via fluorescence assay and LC-MS/MS detection. The performed enrichment was automated using the KingFisherDuo and compared to a manual approach. Verifying the functionality, trapping was realized in different milk matrices: (i) 0...
December 7, 2016: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/27933702/multiparameter-particle-display-mppd-a-quantitative-screening-method-for-the-discovery-of-highly-specific-aptamers
#4
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
#5
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/27930344/specific-detection-of-biomolecules-in-physiological-solutions-using-graphene-transistor-biosensors
#6
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/27924950/molecular-gated-nanoporous-anodic-alumina-for-the-detection-of-cocaine
#7
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/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/27918487/integrating-deoxyribozymes-into-colorimetric-sensing-platforms
#9
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
#10
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/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
#11
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
#12
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
#13
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
#14
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/27898377/upconversion-nanoparticles-grafted-molybdenum-disulfide-nanosheets-platform-for-microcystin-lr-sensing
#15
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
#16
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/27897376/photo-tethers-for-the-multi-cyclic-conformational-caging-of-long-oligonucleotides
#17
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
#18
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/27891685/the-dna-aptamer-binds-stemness-enriched-cancer-cells-in-pancreatic-cancer
#19
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
#20
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 25, 2016: Nanomedicine: Nanotechnology, Biology, and Medicine
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