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Relevant bibliographies by topics / Thrombin binding aptamer

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Journal articles

Academic literature on the topic 'Thrombin binding aptamer'

Author: Grafiati

Published: 6 September 2023

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Journal articles on the topic "Thrombin binding aptamer"

1

Ponzo, Irene, Friederike M. Möller, Herwin Daub, and Nena Matscheko. "A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding." Molecules 24, no. 16 (2019): 2877. http://dx.doi.org/10.3390/molecules24162877.

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Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of aptamer–analyte interaction and aptamer folding, employing the thrombin-binding aptamer (TBA) as a model system. Thrombin-binding aptamer folding into a G-quadruplex and its binding to thrombin strongly depend on the type and concentration of ions present in solution. We o

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2

Kim, Jieun, Dajeong Kim, and Jong Bum Lee. "DNA aptamer-based carrier for loading proteins and enhancing the enzymatic activity." RSC Advances 7, no. 3 (2017): 1643–45. http://dx.doi.org/10.1039/c6ra25507h.

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Here, we synthesized DNA microparticles comprised of thrombin binding aptamers via rolling circle amplification (RCA). These DNA aptamer particles could successfully load a number of thrombins and the complexes have shown improved thrombin activity.

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3

Poturnayová, Alexandra, Maja Šnejdárková, and Tibor Hianik. "DNA aptamer configuration affects the sensitivity and binding kinetics of thrombin." Acta Chimica Slovaca 5, no. 1 (2012): 53–58. http://dx.doi.org/10.2478/v10188-012-0009-z.

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DNA aptamer configuration affects the sensitivity and binding kinetics of thrombinThrombin is serine protease involved in the coagulation cascade, which converts soluble fibrinogen into insoluble strands of fibrin - a matrix of the blood clot formation. Development of the sensitive method of the thrombin detection in nanomolar level is important for clinical practice. In this work we applied acoustic thickness shear mode method (TSM) for study the binding of human thrombin depending on DNA aptamer configuration. We compared sensitivity of detection and binding kinetics of the thrombin to the c

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4

Zhdanov, Gleb, Alexander Arutyunyuan, Alexey Kopylov, and Elena Zavyalova. "Energy Dissipation Hypothesis Applied to Enhance the Affinity of Thrombin Binding Aptamer." Biophysica 1, no. 2 (2021): 179–93. http://dx.doi.org/10.3390/biophysica1020014.

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Nucleic acid aptamers are artificial recognizing molecules that are capable of specific binding to a wide variety of targets. Aptamers are commonly selected from a huge library of oligonucleotides and improved by introducing several mutations or modular constructions. Although aptamers hold great promise as therapeutic and diagnostic tools, no simple approach to improve their affinity has been suggested yet. Our recent analysis of aptamer–protein complexes revealed that aptamer affinity correlates with the size of an amino acid sidechain in the protein interface that was explained by efficient

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5

Beyer, Stefan, Wendy U. Dittmer, Andreas Reuter, and Friedrich C. Simmel. "Controlled Release of Thrombin Using Aptamer-Based Nanodevices." Advances in Science and Technology 53 (October 2006): 116–21. http://dx.doi.org/10.4028/www.scientific.net/ast.53.116.

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Aptamers are DNA or RNA single strands that have been selected from random pools based on their ability to bind ligands. Like antibodies, aptamers are highly specific to their targets, and thus have many potential uses in biomedicine and biotechnology. We report here on the construction of a protein-binding molecular device based on a DNA aptamer, which can be instructed to hold or release the human blood-clotting factor, α-thrombin, depending on an operator DNA sequence addressing it. In the operation of this DNA nanodevice, the thrombin-binding DNA aptamer is switched between a binding and a

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6

Kolganova, Natalia A., Vladimir B. Tsvetkov, Andrey A. Stomakhin, Sergei A. Surzhikov, Edward N. Timofeev, and Irina V. Varizhuk. "Alpha-Deoxyguanosine to Reshape the Alpha-Thrombin Binding Aptamer." International Journal of Molecular Sciences 24, no. 9 (2023): 8406. http://dx.doi.org/10.3390/ijms24098406.

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Modification of DNA aptamers is aimed at increasing their thermodynamic stability, and improving affinity and resistance to biodegradation. G-quadruplex DNA aptamers are a family of affinity ligands that form non-canonical DNA assemblies based on a G-tetrads stack. Modification of the quadruplex core is challenging since it can cause complete loss of affinity of the aptamer. On the other hand, increased thermodynamic stability could be a worthy reward. In the current paper, we developed new three- and four-layer modified analogues of the thrombin binding aptamer with high thermal stability, wh

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7

Funck, Timon, Tim Liedl, and Wooli Bae. "Dual Aptamer-Functionalized 3D Plasmonic Metamolecule for Thrombin Sensing." Applied Sciences 9, no. 15 (2019): 3006. http://dx.doi.org/10.3390/app9153006.

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DNA nanotechnology offers the possibility to rationally design structures with emergent properties by precisely controlling their geometry and functionality. Here, we demonstrate a DNA-based plasmonic metamolecule that is capable of sensing human thrombin proteins. The chiral reconfigurability of a DNA origami structure carrying two gold nanorods was used to provide optical read-out of thrombin binding through changes in the displayed plasmonic circular dichroism. In our experiments, each arm of the structure was modified with one of two different thrombin-binding aptamers—thrombin-binding apt

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8

Seelam Prabhakar, Preethi, Richard A. Manderville, and Stacey D. Wetmore. "Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations." Molecules 24, no. 16 (2019): 2908. http://dx.doi.org/10.3390/molecules24162908.

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Aptamers are functional nucleic acids that bind to a range of targets (small molecules, proteins or cells) with a high affinity and specificity. Chemically-modified aptamers are of interest because the incorporation of novel nucleobase components can enhance aptamer binding to target proteins, while fluorescent base analogues permit the design of functional aptasensors that signal target binding. However, since optimally modified nucleoside designs have yet to be identified, information about how to fine tune aptamer stability and target binding affinity is required. The present work uses mole

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9

Zeng, Xinling, Qing Zhou, Liyan Wang, et al. "A Fluorescence Kinetic-Based Aptasensor Employing Stilbene Isomerization for Detection of Thrombin." Materials 14, no. 22 (2021): 6927. http://dx.doi.org/10.3390/ma14226927.

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It is important to detect thrombin due to its physiological and pathological roles, where rapid and simple analytical approaches are needed. In this study, an aptasensor based on fluorescence attenuation kinetics for the detection of thrombin is presented, which incorporates the features of stilbene and aptamer. We designed and synthesized an aptasensor by one-step coupling of stilbene compound and aptamer, which employed the adaptive binding of the aptamer with thrombin to cause a change in stilbene fluorescence attenuation kinetics. The sensor realized detection of thrombin by monitoring the

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10

Russo Krauss, Irene, Andrea Pica, Antonello Merlino, Lelio Mazzarella, and Filomena Sica. "Duplex–quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer." Acta Crystallographica Section D Biological Crystallography 69, no. 12 (2013): 2403–11. http://dx.doi.org/10.1107/s0907444913022269.

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Potent second-generation thrombin aptamers adopt a duplex–quadruplex bimodular folding and recognize thrombin exosite II with very high affinity and specificity. A sound model of these oligonucleotides, either free or in complex with thrombin, is not yet available. Here, a structural study of one of these aptamers, HD22-27mer, is presented. The crystal structure of this aptamer in complex with thrombin displays a novel architecture in which the helical stem is enchained to a pseudo-G-quadruplex. The results also underline the role of the residues that join the duplex and quadruplex motifs and

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