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Journal articles on the topic 'Thrombin binding aptamer'

Author: Grafiati

Published: 6 September 2023

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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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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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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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11

Smith, Mark H., and Daniel Fologea. "Kinetic Exclusion Assay of Biomolecules by Aptamer Capture." Sensors 20, no. 12 (2020): 3442. http://dx.doi.org/10.3390/s20123442.

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DNA aptamers are short nucleotide oligomers selected to bind a target ligand with affinity and specificity rivaling that of antibodies. These remarkable features recommend aptamers as candidates for analytical and therapeutic applications that traditionally use antibodies as biorecognition elements. Numerous traditional and emerging analytical techniques have been proposed and successfully implemented to utilize aptamers for sensing purposes. In this work, we exploited the analytical capabilities offered by the kinetic exclusion assay technology to measure the affinity of fluorescent aptamers

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12

Mao, Yu, Jimmy Gu, Dingran Chang, et al. "Evolution of a highly functional circular DNA aptamer in serum." Nucleic Acids Research 48, no. 19 (2020): 10680–90. http://dx.doi.org/10.1093/nar/gkaa800.

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Abstract Circular DNA aptamers are powerful candidates for therapeutic applications given their dramatically enhanced biostability. Herein we report the first effort to evolve circular DNA aptamers that bind a human protein directly in serum, a complex biofluid. Targeting human thrombin, this strategy has led to the discovery of a circular aptamer, named CTBA4T-B1, that exhibits very high binding affinity (with a dissociation constant of 19 pM), excellent anticoagulation activity (with the half maximal inhibitory concentration of 90 pM) and high stability (with a half-life of 8 h) in human ser

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13

Kotkowiak, Weronika, Zofia Jahnz-Wechmann, and Anna Pasternak. "A Comprehensive Analysis of the Thrombin Binding Aptamer Containing Functionalized Pyrrolo-2’-deoxycytidines." Pharmaceuticals 14, no. 12 (2021): 1326. http://dx.doi.org/10.3390/ph14121326.

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Aptamers constitute an answer for the growing need for targeted therapy development. One of the most well-known representatives of this group of compounds is thrombin binding aptamers (TBA) targeted towards thrombin. The TBA inhibitory activity is determined by its spatial arrangement, which consists of two G-tetrads linked by two shorter TT loops and one longer TGT loop and folds into a unimolecular, antiparallel G-quadruplex structure. Interesting properties of the aptamer can be further improved via the introduction of a number of chemical modifications. Herein, a comprehensive analysis of

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14

Rakhmetova, S. Yu, S. P. Radko, O. V. Gnedenko, N. V. Bodoev, A. S. Ivanov, and A. I. Archakov. "Photoaptamer heterodimeric constructs as a new approach to enhance the efficiency of formation of photocrosslinking with a target protein." Biomeditsinskaya Khimiya 56, no. 1 (2010): 72–81. http://dx.doi.org/10.18097/pbmc20105601072.

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Using two DNA aptamers selectively recognizing anion-binding exosites 1 and 2 of thrombin as a model, it has been demonstrated that their conjugation by a poly-(dT)-linker (ranging from 5 to 65 nt in length) to produce aptamer heterodimeric constructs results into affinity enhancement. The apparent dissociation constant (Kdapp) measured at the optical biosensor Biacore-3000 for complexes of thrombin with the heterodimeric constructs reached minimum values (Kdapp = 0,2-0,4 nМ) which were approximately 30-fold less than for the complexes with the primary aptamers. A photoaptamer heterodimeric co

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15

Martin, Jennifer A., Peter A. Mirau, Yaroslav Chushak, et al. "Single-Round Patterned DNA Library Microarray Aptamer Lead Identification." Journal of Analytical Methods in Chemistry 2015 (2015): 1–8. http://dx.doi.org/10.1155/2015/137489.

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A method for identifying an aptamer in a single round was developed using custom DNA microarrays containing computationally derived patterned libraries incorporating no information on the sequences of previously reported thrombin binding aptamers. The DNA library was specifically designed to increase the probability of binding by enhancing structural complexity in a sequence-space confined environment, much like generating lead compounds in a combinatorial drug screening library. The sequence demonstrating the highest fluorescence intensity upon target addition was confirmed to bind the target

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16

Valsangkar, Vibhav, Sweta Vangaveti, Goh Woon Lee, et al. "Structural and Binding Effects of Chemical Modifications on Thrombin Binding Aptamer (TBA)." Molecules 26, no. 15 (2021): 4620. http://dx.doi.org/10.3390/molecules26154620.

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The thrombin binding aptamer (TBA) is a promising nucleic acid-based anticoagulant. We studied the effects of chemical modifications, such as dendrimer Trebler and NHS carboxy group, on TBA with respect to its structures and thrombin binding affinity. The two dendrimer modifications were incorporated into the TBA at the 5′ end and the NHS carboxy group was added into the thymine residues in the thrombin binding site of the TBA G-quadruplex (at T4, T13 and both T4/T13) using solid phase oligonucleotide synthesis. Circular dichroism (CD) spectroscopy confirmed that all of these modified TBA vari

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17

Nagata, Madoka, Jinhee Lee, Stephen Henley, Kazunori Ikebukuro, and Koji Sode. "An Amine-Reactive Phenazine Ethosulfate (arPES)—A Novel Redox Probe for Electrochemical Aptamer-Based Sensor." Sensors 22, no. 5 (2022): 1760. http://dx.doi.org/10.3390/s22051760.

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Electrochemical aptamer-based biosensors (E-ABs) are attractive candidates for use in biomarker detection systems due to their sensitivity, rapid response, and design flexibility. There are only several redox probes that were employed previously for this application, and a combination of redox probes affords some advantages in target detection. Thus, it would be advantageous to study new redox probes in an E-AB system. In this study, we report the use of amine-reactive phenazine ethosulfate (arPES) for E-AB through its conjugation to the terminus of thrombin-binding aptamer. The constructed E-

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18

Hao, Lihua, and Qiang Zhao. "A fluorescein labeled aptamer switch for thrombin with fluorescence decrease response." Analytical Methods 7, no. 9 (2015): 3888–92. http://dx.doi.org/10.1039/c5ay00464k.

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19

Basnar, Bernhard, Roey Elnathan, and Itamar Willner. "Following Aptamer−Thrombin Binding by Force Measurements." Analytical Chemistry 78, no. 11 (2006): 3638–42. http://dx.doi.org/10.1021/ac052289e.

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20

Rakhmetova, S. Yu, S. P. Radko, O. V. Gnedenko, N. V. Bodoev, A. S. Ivanov, and A. I. Archakov. "Comparative termodynamic analysis of thrombin interaction with anti-thrombin aptamers and their heterodimeric construct." Biomeditsinskaya Khimiya 56, no. 3 (2010): 404–11. http://dx.doi.org/10.18097/pbmc20105603404.

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Aptamers interacting selectively with the anion-binding exosites 1 and 2 of thrombin were merged into dimeric oligonucleotide constructs with use of a poly-(dT)-linker of 35 nucleotides (nt) long. Complexes of thrombin with the aptamers and their hetero- and homodimeric constructs were measured using the optical biosensor Biacore-3000. KD values measured for the hetero- and homodimeric constructs were correspondingly 25-30- and 2-3-fold lower than those for the primary aptamers. Analysis of temperature dependencies of KD values within the temperature interval of 10°C-40°C has shown that the va

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21

Wei, Yani, Luhui Wang, Yingying Zhang, and Yafei Dong. "An Enzyme- and Label-Free Fluorescence Aptasensor for Detection of Thrombin Based on Graphene Oxide and G-Quadruplex." Sensors 19, no. 20 (2019): 4424. http://dx.doi.org/10.3390/s19204424.

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An enzyme- and label-free aptamer-based assay is described for the determination of thrombin. A DNA strand (S) consisting of two parts was designed, where the first (Sa) is the thrombin-binding aptamer and the second (Se) is a G-quadruplex. In the absence of thrombin, Sa is readily adsorbed by graphene oxide (GO), which has a preference for ss-DNA rather than for ds-DNA. Upon the addition of the N-methyl-mesoporphyrin IX (NMM), its fluorescence (with excitation/emission at 399/610 nm) is quenched by GO. In contrast, in the presence of thrombin, the aptamer will bind thrombin, and thus, be sepa

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22

Fadock, Kaila L., Richard A. Manderville, Purshotam Sharma, and Stacey D. Wetmore. "Optimization of fluorescent 8-heteroaryl-guanine probes for monitoring protein-mediated duplex → G-quadruplex exchange." Organic & Biomolecular Chemistry 14, no. 19 (2016): 4409–19. http://dx.doi.org/10.1039/c6ob00474a.

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In this study, we describe the thermal and optical properties of the thrombin binding aptamer (TBA) that has been modified at syn-G-tetrad postions with fluorescent 8-heteroaryl-2′-deoxyguanosine derivatives that light-up upon thrombin binding.

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23

Nikolaeva, P. A., R. V. Moryachkov, V. N. Raldugina, J. O. Naumova, T. M. Novikova, and V. A. Spiridonova. "Structural analysis of thrombin-binding G-aptamers in presence of bivalent ions." Siberian Medical Review, no. 5 (2022): 111–13. http://dx.doi.org/10.20333/25000136-2022-5-111-113.

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The aim of this study was to examine 3D structures of DNA aptamers, thrombin inhibitors. •The main objective was to study 3D structure 15TBA, RE31, NU172 aptamers using the small-angle X-ray scattering method. The size of 15TBA was 4.5 nm, which corresponds to a partially unfolded conformation. The CD spectrum of Nu172 in the presence of 50 mM strontium ions indicates the presence of an antiparallel G-quadruplex, the concentration o f which drops at 50°C. NU172 does not have a rigid structure, apparently due to the presence of a guanine residue in the GT loop. The NU172 aptamer does not form a

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24

Nagatoishi, Satoru, Noburu Isono, Kouhei Tsumoto, and Naoki Sugimoto. "Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding." Biochimie 93, no. 8 (2011): 1231–38. http://dx.doi.org/10.1016/j.biochi.2011.03.013.

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25

Pagano, Bruno, Luigi Martino, Antonio Randazzo, and Concetta Giancola. "Stability and Binding Properties of a Modified Thrombin Binding Aptamer." Biophysical Journal 94, no. 2 (2008): 562–69. http://dx.doi.org/10.1529/biophysj.107.117382.

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26

Pol, Laura, Laura Karen Acosta, Josep Ferré-Borrull, and Lluis F. Marsal. "Aptamer-Based Nanoporous Anodic Alumina Interferometric Biosensor for Real-Time Thrombin Detection." Sensors 19, no. 20 (2019): 4543. http://dx.doi.org/10.3390/s19204543.

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Aptamer biosensors are one of the most powerful techniques in biosensing. Achieving the best platform to use in aptamer biosensors typically includes crucial chemical modifications that enable aptamer immobilization on the surface in the most efficient manner. These chemical modifications must be well defined. In this work we propose nanoporous anodic alumina (NAA) chemically modified with streptavidin as a platform for aptamer immobilization. The immobilization of biotinylated thrombin binding aptamer (TBA) was monitored in real time by means of reflective interferometric spectroscopy (RIfS).

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Esposito, Veronica, Maria Scuotto, Antonella Capuozzo, et al. "A straightforward modification in the thrombin binding aptamer improving the stability, affinity to thrombin and nuclease resistance." Org. Biomol. Chem. 12, no. 44 (2014): 8840–43. http://dx.doi.org/10.1039/c4ob01475h.

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Introduction of inversion of polarity sites at the 5′- and/or 3′-end in the thrombin binding aptamer is a simple modification able to improve, at the same time, thermal stability, affinity to thrombin and nuclease resistance.

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Keijzer, Jordi F., Judith Firet, and Bauke Albada. "Site-selective and inducible acylation of thrombin using aptamer-catalyst conjugates." Chemical Communications 57, no. 96 (2021): 12960–63. http://dx.doi.org/10.1039/d1cc05446e.

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Functionalizing a protein-binding aptamer with an acylation catalyst leads to site-selective modification of the target protein in proximity to the aptamer–protein interface. This protein modification can be switched ON or OFF by an external trigger.

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Taira, Kenichi, Koichi Abe, Takayuki Ishibasi, Katsuaki Sato, and Kazunori Ikebukuro. "Control of Aptamer Function Using Radiofrequency Magnetic Field." Journal of Nucleic Acids 2011 (2011): 1–6. http://dx.doi.org/10.4061/2011/103872.

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Remote control of aptamer function has allowed us to control protein function in space and time. Here, we propose a novel control system for aptamer function by radiofrequency magnetic field- (RFMF-) induced local heating of a gold nanoparticle conjugated with an aptamer. In this study, we used a 31-mer thrombin-binding aptamer (TBA), which can inhibit thrombin activity, as a model aptamer. We evaluated the RFMF control of the inhibitory activity of a gold nanoparticle-conjugated TBA. To evaluate the effect of RFMF on enzymatic activity, we utilized a complementary DNA strand that maintains th

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Porschewski, Peter, Mira A. M. Grättinger, Kerstin Klenzke, Anja Erpenbach, Michael R. Blind, and Frank Schäfer. "Using Aptamers as Capture Reagents in Bead-Based Assay Systems for Diagnostics and Hit Identification." Journal of Biomolecular Screening 11, no. 7 (2006): 773–81. http://dx.doi.org/10.1177/1087057106292138.

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Most applications of xMAP™ (Luminex®) bead-based assay technology in diagnostics and drug discovery use immobilized antigens or antibodies. Here the authors describe the development of novel assay systems in which synthetic oligonucleotides that specifically bind and inhibit other biomolecules—so-called aptamers—are directly immobilized on beads. The robustness, specificity, and sensitivity of aptamer-based assays were demonstrated in a test system that detected human α-thrombin in serum samples. xMAP technology was also adapted to competitive screening formats where an aptamer/protein complex

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Ptitsyn, K. G., S. E. Novikova, Y. Y. Kiseleva, et al. "Use of DNA-aptamers for enrichment of low abundant proteins in cellular extracts for quntitative detection by selected reaction monitoring." Biomeditsinskaya Khimiya 64, no. 1 (2018): 5–9. http://dx.doi.org/10.18097/pbmc20186401005.

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The relationship between the amount of a target protein in a complex biological sample and its amount measured by selected reaction monitoring (SRM) mass spectrometry upon the affinity enrichment of target protein with aptamers immobilized on a solid phase was studied. Human thrombin added in known concentrations to cellular extracts derived from bacterial cells was used as model target protein. It has been demonstrated that the affinity enrichment of thrombin in cellular extracts by means of the thrombin-binding aptamer immobilized on the surface of magnetic microbeads results in an approxima

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Kim, Dajeong, Jieun Kim, and Jong Bum Lee. "An enzymatically self-assembled DNA patch for enhanced blood coagulation." Chemical Communications 56, no. 44 (2020): 5917–20. http://dx.doi.org/10.1039/d0cc00974a.

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Kretz, Colin A., Alan R. Stafford, James C. Fredenburgh, and Jeffrey I. Weitz. "Thrombin Aptamer HD1 Inhibits Prothrombin Activation by Binding Proexosite 1 on Prothrombin." Blood 106, no. 11 (2005): 1950. http://dx.doi.org/10.1182/blood.v106.11.1950.1950.

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Abstract Functional maturation of exosites 1 and 2 during prothrombin activation endows thrombin with its physiological activities. Thrombin exosite 1 binds ligands such as fibrinogen, the thrombin receptor, and hirudin, and orients them to the active site. In contrast, thrombin exosite 2 binds ligands such as heparin, platelet glycoprotein Iba, and the chondroitin sulfate moiety of thrombomodulin molecules; ligands that do not directly interact with the active site. Neither exosite is fully functional in prothrombin. Exosite 2 only becomes functional when fragment 2 is released. In contrast,

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Zavyalova and Kopylov. "Energy Transfer as A Driving Force in Nucleic Acid–Protein Interactions." Molecules 24, no. 7 (2019): 1443. http://dx.doi.org/10.3390/molecules24071443.

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Many nucleic acid–protein structures have been resolved, though quantitative structure-activity relationship remains unclear in many cases. Thrombin complexes with G-quadruplex aptamers are striking examples of a lack of any correlation between affinity, interface organization, and other common parameters. Here, we tested the hypothesis that affinity of the aptamer–protein complex is determined with the capacity of the interface to dissipate energy of binding. Description and detailed analysis of 63 nucleic acid–protein structures discriminated peculiarities of high-affinity nucleic acid–prote

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Nishimura, Jun-ichi, Angela D. Burnette, Milena Batchvarova та ін. "Blocking Adhesion of Sickle Erythrocytes to Endothelial αVβ3 Using RNA Aptamer." Blood 108, № 11 (2006): 688. http://dx.doi.org/10.1182/blood.v108.11.688.688.

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Abstract Vaso-occlusive crises are a major clinical feature of sickle cell disease (SCD), and the adhesion of sickle erythrocytes (SS-RBC) to vascular endothelium is crucial to the generation of vaso-occlusion. The αvβ3 integrin is a major endothelial ligand for SS-RBC. Soluble thrombospondin has been thought to serve as a bridging molecule between erythrocyte CD36 and endothelial αvβ3, and high-molecular-weight multimers of von Willebrand factor also promote SS-RBC adhesion to endothelial αvβ3. Our group recently identified SS-RBC adhesion to endothelium via ICAM-4 (LW, CD242)-αvβ3 interactio

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Hall, Scott, Craig Gibbs, and Lawrence Leung. "Identification of Critical Residues on Thrombin Mediating Its Interaction with Fibrin." Thrombosis and Haemostasis 86, no. 12 (2001): 1466–74. http://dx.doi.org/10.1055/s-0037-1616750.

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SummaryThrombin binding to fibrin may be important in localizing thrombin to the site of vascular injury. However, fibrin-bound thrombin retains its catalytic activity toward fibrinogen, and may be prothrombotic under certain conditions. A collection of 52 purified thrombin mutants was used to identify those residues mediating the thrombin-fibrin interaction. Comparison of fibrinogen clotting activity with fibrin binding activity identified twenty residues involved in fibrinogen recognition with four of these residues important in fibrin binding (Lys65, His66, Tyr71, Arg73). No mutant was iden

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Ali, Aysha, Gemma A. Bullen, Benjamin Cross, et al. "Light-controlled thrombin catalysis and clot formation using a photoswitchable G-quadruplex DNA aptamer." Chemical Communications 55, no. 39 (2019): 5627–30. http://dx.doi.org/10.1039/c9cc01540j.

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Ma, Xiao, Agnivo Gosai, Ganesh Balasubramanian, and Pranav Shrotriya. "Aptamer based electrostatic-stimuli responsive surfaces for on-demand binding/unbinding of a specific ligand." Journal of Materials Chemistry B 5, no. 20 (2017): 3675–85. http://dx.doi.org/10.1039/c6tb02386j.

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39

Diculescu, Victor Constantin, Ana-Maria Chiorcea-Paquim, Ramon Eritja, and Ana Maria Oliveira-Brett. "Thrombin-Binding Aptamer Quadruplex Formation: AFM and Voltammetric Characterization." Journal of Nucleic Acids 2010 (2010): 1–8. http://dx.doi.org/10.4061/2010/841932.

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The adsorption and the redox behaviour of thrombin-binding aptamer (TBA) and extended TBA (eTBA) were studied using atomic force microscopy and voltammetry at highly oriented pyrolytic graphite and glassy carbon. The different adsorption patterns and degree of surface coverage were correlated with the sequence base composition, presence/absence of K+, and voltammetric behaviour of TBA and eTBA. In the presence of K+, only a few single-stranded sequences present adsorption, while the majority of the molecules forms stable and rigid quadruplexes with no adsorption. Both TBA and eTBA are oxidized

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Kim, Hyun Woo, Young Min Rhee, and Seung Koo Shin. "Charge–dipole interactions in G-quadruplex thrombin-binding aptamer." Physical Chemistry Chemical Physics 20, no. 32 (2018): 21068–74. http://dx.doi.org/10.1039/c8cp03050b.

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Lai, Pei-Xin, Ju-Yi Mao, Binesh Unnikrishnan, et al. "Self-assembled, bivalent aptamers on graphene oxide as an efficient anticoagulant." Biomaterials Science 6, no. 7 (2018): 1882–91. http://dx.doi.org/10.1039/c8bm00288f.

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Frense, D., S. Kang, K. Schieke, et al. "Label-free impedimetric biosensor for thrombin using the thrombin-binding aptamer as receptor." Journal of Physics: Conference Series 434 (April 18, 2013): 012091. http://dx.doi.org/10.1088/1742-6596/434/1/012091.

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Zhang, Xiangyuan, Ruoxin Hu, and Na Shao. "Label-free sensing of thrombin based on quantum dots and thrombin binding aptamer." Talanta 107 (March 2013): 140–45. http://dx.doi.org/10.1016/j.talanta.2013.01.003.

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Pérez de Carvasal, Kévan, Claudia Riccardi, Irene Russo Krauss, et al. "Charge-Transfer Interactions Stabilize G-Quadruplex-Forming Thrombin Binding Aptamers and Can Improve Their Anticoagulant Activity." International Journal of Molecular Sciences 22, no. 17 (2021): 9510. http://dx.doi.org/10.3390/ijms22179510.

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In the search for optimized thrombin binding aptamers (TBAs), we herein describe the synthesis of a library of TBA analogues obtained by end-functionalization with the electron-rich 1,5-dialkoxy naphthalene (DAN) and the electron-deficient 1,8,4,5-naphthalenetetra-carboxylic diimide (NDI) moieties. Indeed, when these G-rich oligonucleotides were folded into the peculiar TBA G-quadruplex (G4) structure, effective donor–acceptor charge transfer interactions between the DAN and NDI residues attached to the extremities of the sequence were induced, providing pseudo-cyclic structures. Alternatively

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Hagiwara, Kenta, Yuuya Kasahara, Hiroto Fujita, and Masayasu Kuwahara. "Non-Equilibrium Capillary Electrophoresis of Equilibrium Mixtures-Based Affinity Separation and Selective Enrichment of a Long-Length DNA Aptamer." Australian Journal of Chemistry 69, no. 10 (2016): 1102. http://dx.doi.org/10.1071/ch16272.

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Non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a kinetic capillary electrophoresis method used for the affinity analysis of DNA binding to proteins or ligands as well as a rapid selection of DNA aptamers. However, long DNA strands (100-mer or more) are generally difficult to analyse by this method owing to their poor peak separation. Herein, we report optimized conditions (use of a neutral phosphate buffer with an ionic strength of 0.074 as a binding buffer and use of an 80-cm fused silica capillary with a 75-μm internal diameter) for the peak separation of a 100

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Prommapan, Plengchart, Nermina Brljak, Troy W. Lowry, David Van Winkle, and Steven Lenhert. "Aptamer Functionalized Lipid Multilayer Gratings for Label-Free Analyte Detection." Nanomaterials 10, no. 12 (2020): 2433. http://dx.doi.org/10.3390/nano10122433.

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Lipid multilayer gratings are promising optical biosensor elements that are capable of transducing analyte binding events into changes in an optical signal. Unlike solid state transducers, reagents related to molecular recognition and signal amplification can be incorporated into the lipid grating ink volume prior to fabrication. Here we describe a strategy for functionalizing lipid multilayer gratings with a DNA aptamer for the protein thrombin that allows label-free analyte detection. A double cholesterol-tagged, double-stranded DNA linker was used to attach the aptamer to the lipid gratings

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Nishimura, Jun-ichi, Angela D. Burnette, Sabah Oney, et al. "Blocking Adhesion of Sickle Erythrocytes to Endothelial P-Selectin Using an RNA Aptamer." Blood 110, no. 11 (2007): 147. http://dx.doi.org/10.1182/blood.v110.11.147.147.

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Abstract Vaso-occlusive crises are a major clinical feature of sickle cell disease (SCD), and the adhesion of sickle erythrocytes (SS-RBCs) to vascular endothelium is crucial to the generation of vaso-occlusion. SS-RBCs express many adhesion molecules. Adhesive SS-RBCs bind to endothelial cell P-selectin and other adhesion molecules, as well as extracellular matrix proteins. Thrombin causes endothelial retraction with exposure of proadhesive extracellular matrix components as well as upregulation of endothelial expression of P-selectin. Other investigators have shown that SS-RBCs can bind to P

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Avino, Anna, Carme Fabrega, Maria Tintore, and Ramon Eritja. "Thrombin Binding Aptamer, More than a Simple Aptamer: Chemically Modified Derivatives and Biomedical Applications." Current Pharmaceutical Design 18, no. 14 (2012): 2036–47. http://dx.doi.org/10.2174/138161212799958387.

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Pica, Andrea, Irene Russo Krauss, Antonello Merlino, Satoru Nagatoishi, Naoki Sugimoto, and Filomena Sica. "Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer." FEBS Journal 280, no. 24 (2013): 6581–88. http://dx.doi.org/10.1111/febs.12561.

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Kovačič, Matic, Peter Podbevšek, Hisae Tateishi-Karimata, Shuntaro Takahashi, Naoki Sugimoto, and Janez Plavec. "Thrombin binding aptamer G-quadruplex stabilized by pyrene-modified nucleotides." Nucleic Acids Research 48, no. 7 (2020): 3975–86. http://dx.doi.org/10.1093/nar/gkaa118.

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Abstract Guanine-rich regions of the human genome can adopt non-canonical secondary structures. Their role in regulating gene expression has turned them into promising targets for therapeutic intervention. Ligands based on polyaromatic moieties are especially suitable for targeting G-quadruplexes utilizing their size complementarity to interact with the large exposed surface area of four guanine bases. A predictable way of (de)stabilizing specific G-quadruplex structures through efficient base stacking of polyaromatic functional groups could become a valuable tool in our therapeutic arsenal. W

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