scholarly journals Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers

2021 ◽  
Vol 22 (16) ◽  
pp. 8868
Author(s):  
Katja Schilling-Loeffler ◽  
Rachel Rodriguez ◽  
Jacquelina Williams-Woods
Keyword(s):  
New Orleans ◽  
Dissociation Constants ◽  
Foodborne Pathogen ◽  
Hybrid Structure ◽  
Cd Spectroscopy ◽  
Assay Development ◽  
Dot Blot ◽  
Equilibrium Dissociation Constants ◽  
Norovirus Gii ◽  
Cd Studies

Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.

scholarly journals Structural and Binding Effects of Chemical Modifications on Thrombin Binding Aptamer (TBA)

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4620
Author(s):  
Vibhav Valsangkar ◽  
Sweta Vangaveti ◽  
Goh Woon Lee ◽  
Walid M. Fahssi ◽  
Waqas S. Awan ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Carboxy Group ◽  
Dissociation Constants ◽  
Solid Phase ◽  
Cd Spectroscopy ◽  
Chemical Modifications ◽  
Binding Preference ◽  
G Quadruplex ◽  
Equilibrium Dissociation Constants ◽  
Dynamics Simulations

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 variants fold into a stable G-quadruplex. The binding affinity of TBA variants with thrombin was measured by surface plasmon resonance (SPR). The binding patterns and equilibrium dissociation constants (KD) of the modified TBAs are very similar to that of the native TBA. Molecular dynamics simulations studies indicate that the additional interactions or stability enhancement introduced by the modifications are minimized either by the disruption of TBA–thrombin interactions or destabilization elsewhere in the aptamer, providing a rational explanation for our experimental data. Overall, this study identifies potential positions on the TBA that can be modified without adversely affecting its structure and thrombin binding preference, which could be useful in the design and development of more functional TBA analogues.

Altered plasma catecholamines and numbers of α- and β-adrenergic receptors in platelets and leucocytes in hyperthyroid patients normalized under antithyroid treatment

1985 ◽  
Vol 110 (1) ◽  
pp. 75-82 ◽  
Author(s):  
Dieter Ratge ◽  
Sabine Hansel-Bessey ◽  
Hermann Wisser
Keyword(s):  
Dissociation Constants ◽  
Plasma Catecholamines ◽  
Cyclic Adenosine Monophosphate ◽  
Adenosine Monophosphate ◽  
Plasma Norepinephrine ◽  
Thyroid State ◽  
Antithyroid Treatment ◽  
Equilibrium Dissociation Constants ◽  
Equilibrium Dissociation ◽  
Hyperthyroid Patients

Abstract. We measured plasma catecholamines, α- and β-adrenoreceptor numbers and the accumulation of cyclic adenosine monophosphate (cAMP) in the unstimulated state and in response to 10 μmol/l (-) isoproterenol in blood cells from 29 euthyroid controls and from 18 patients with spontaneous hyperthyroidism. In the thyrotoxic patients plasma norepinephrine (1.14 ± 0.5 nmol/l) and epinephrine (0.3 ±0.14 nmol/l) were significantly decreased compared with plasma norepinephrine (1.87 ± 0.7 nmol) and epinephrine (0.41 ± 0.19 nmol/l) in the controls (P < 0.01 and P < 0.05, respectively) and the values obtained in subjects rendered euthyroid by antithyroid treatment (P < 0.001, respectively). α-adrenoceptor density in platelet membranes obtained from patients in the hyperthyroid state (114 ± 38 sites per cell) was significantly decreased when compared with controls (159 ± 48 sites per cell, P < 0.01) and the values from patients under effective antithyroid treatment (136 ± 35 sites per cell, P < 0.01). On the contrary, a significant increase in β-adrenoceptor density in mononuclear leucocyte (MNL) membranes was found in hyperthyroid patients (1751 ± 237 sites/cell) when compared with controls (1510 ± 351 sites/cell, P < 0.05) and the same patients following antithyroid treatment (1455 ± 260 sites/cell, P < 0.001). The equilibrium dissociation constants (KD) did not change in hyperthyroidism. Basal cAMP concentrations in MNL were higher in untreated thyrotoxicosis (45 ± 18 pmol/106 cells/10 min) than in patients in the euthyroid state (35 ± 9 pmol/106 cells/10 min, P < 0.05). Our data support the hypothesis that the balance of α- and β-adrenoceptors depends on the thyroid state. However, before the reputed catecholamine supersensitivity in hyperthyroid man can be accepted, the relationship between alterations in adrenoceptors and the biological responsiveness to catecholamines has to be demonstrated in different human tissues.

scholarly journals Circular dichroism determination of class I MHC-peptide equilibrium dissociation constants

1997 ◽  
Vol 6 (8) ◽  
pp. 1771-1773 ◽  
Author(s):  
Chantal S. Morgan ◽  
James M. Holton ◽  
Barry D. Olafson ◽  
Pamela J. Bjorkman ◽  
Stephen L. Mayo
Keyword(s):  
Circular Dichroism ◽  
Dissociation Constants ◽  
Class I ◽  
Class I Mhc ◽  
Equilibrium Dissociation Constants ◽  
Equilibrium Dissociation ◽  
Circular Dichroïsm

Preparation and Characterization of Paclitaxel Imprinted Silica Nanoparticles

2011 ◽  
Vol 399-401 ◽  
pp. 1894-1897
Author(s):  
Jian Hua Li ◽  
Zong Jian Zheng ◽  
Shao Ping Fu ◽  
Jing Bo Zhu
Keyword(s):  
Silica Nanoparticles ◽  
Dissociation Constants ◽  
Sol Gel ◽  
Scatchard Analysis ◽  
Binding Properties ◽  
Imprinted Polymers ◽  
Sol Gel Process ◽  
Equilibrium Dissociation Constants ◽  
Equilibrium Dissociation

Highly selective molecularly imprinted layer-coated silica nanoparticles for paclitaxel were synthesized by molecular imprinting technique with a sol–gel process on the supporter of silica nanoparticles. The morphology of the obtained polymers was characterized by scanning electron microscopy (SEM). The binding properties of the imprinted polymers were evaluated through the equilibrium rebinding experiments. Scatchard analysis revealed that two classes of binding sites were formed in the imprinted polymers with equilibrium dissociation constants of 0.0509 g•L-1and 0.0094 g•L-1, respectively. Paclitaxel and its analogue were employed for selectivity tests. The results indicated that the imprinted polymers exhibited good selectivity and specificity toward paclitaxel.

Adrenal medullary regulation of rat renal cortical adrenergic receptors

1987 ◽  
Vol 253 (5) ◽  
pp. F1063-F1067
Author(s):  
P. R. Sundaresan ◽  
M. M. Guarnaccia ◽  
J. L. Izzo
Keyword(s):  
Adrenal Medulla ◽  
Adrenergic Receptors ◽  
Dissociation Constants ◽  
Specific Binding ◽  
Physiological State ◽  
Plasma Corticosterone ◽  
Beta Adrenergic Receptors ◽  
Beta Adrenergic ◽  
Equilibrium Dissociation Constants ◽  
Equilibrium Dissociation

The role of the adrenal medulla in the regulation of renal cortical adrenergic receptors was investigated in renal cortical particulate fractions from control rats and rats 6 wk after adrenal demedullation. The specific binding of [3H]prazosin, [3H]rauwolscine, and [125I]iodocyanopindolol were used to quantitate alpha 1-, alpha 2-, and beta-adrenergic receptors, respectively. Adrenal demedullation increased the concentration of all three groups of renal adrenergic receptors; maximal number of binding sites (Bmax, per milligram membrane protein) for alpha 1-, and alpha 2-, and beta-adrenergic receptors were increased by 22, 18.5, and 25%, respectively (P less than 0.05 for each). No differences were found in the equilibrium dissociation constants (KD) for any of the radioligands. Plasma corticosterone and plasma and renal norepinephrine levels were unchanged, whereas plasma epinephrine was decreased 72% by adrenal demedullation (P less than 0.01); renal cortical epinephrine was not detectable in control or demedullated animals. Our results suggest that, in the physiological state, the adrenal medulla modulates the number of renal cortical adrenergic receptors, presumably through the actions of a circulating factor such as epinephrine.

Further studies on the corticosteroid-receptor system of the nasal gland of the domestic duck (Anas platyrhynchos)

1983 ◽  
Vol 61 (7) ◽  
pp. 731-743 ◽  
Author(s):  
Thomas Sandor ◽  
Afzal Z. Mehdi ◽  
John A. DiBattista
Keyword(s):  
Ammonium Sulfate ◽  
Reaction Temperature ◽  
Rate Constants ◽  
Binding Sites ◽  
Dissociation Constants ◽  
Similar Data ◽  
Nuclear Binding ◽  
Ammonium Sulfate Precipitate ◽  
Equilibrium Dissociation Constants ◽  
Equilibrium Dissociation

The interaction of tritiated corticosterone with the nasal gland corticosterone receptor was investigated. Kinetic studies have shown that the association of [3H]corticosterone–receptor followed second-order reaction kinetics and the dissociation of the ligand from the receptor became "pseudo" first order in the presence of large excess of radioinert steroids at 0, 15, 25, and 35 °C. Similar data were obtained with an ammonium sulfate precipitate of the cytosol. Dissociation rate constants varied from 10−5 to 10−3 s−1 and the association rate constants varied from 0.5 × 104 to 3.8 × 105 M−1∙s−1, depending on the reaction temperature and the cytoplasmic receptor preparation. Equilibrium dissociation constants were in 10−8–10−9 M range. Equilibrium dissociation constants, calculated from kinetic data (kd/ka), showed a marked temperature dependence, while those obtained by saturation analysis varied much less with the reaction temperature. Data obtained in these experiments were used to calculate some thermodynamic parameters of the binding of corticosterone to the cytoplasmic receptor. The enthalpy of dissociation was 101.5 and 79.4 kJ∙mol−1 and the entropy of dissociation was 200 and 280 J∙mol−1∙degree−1 for the crude cytoplasmic receptor and the ammonium sulfate precipitate, respectively. From the equilibrium dissociation constants, the enthalpy and entropy of the equilibrium binding was calculated. Polynomial fitting of Ka values versus 1/T yielded enthalpy (ΔH) values from −0.9 to −88.8 kJ∙mol−1, depending on the nature of the receptor preparation. Entropy values were negative for kinetically derived equilibrium association constants from the crude cytosol at all temperatures and for 0 and 15 °C for the precipitate. Entropy values were positive for Ka values obtained from kinetic rates at 25 and 35 °C and for Ka's calculated from saturation analysis. Further experiments with the precipitate confirmed our previous contention that the nasal gland cytoplasmic corticosterone receptor metabolized the bound ligand to 11-dehydrocorticosterone, though the receptor preparation was corticosterone specific. The following hydrodynamic parameters were obtained on the binding macromolecule: molecular weight, 316 000; s20,w, 8.0; Stokes radius (rs), 77.3 Å (1 Å = 0.1 nm); total frictional ratio (f/f0), 1.71. The labeled receptor preparation translocated to homologous nuclear binding sites following heat activation and, at the nuclear binding sites, the ligand was almost exclusively in its oxidized form. Measurement of the nuclear steroid–receptor complex by exchange assay with [3H]corticosterone confirmed the presence of nuclear binding sites. From these studies, it was concluded that the nasal gland of the duck contains specific, glucocorticoid-type corticosterone receptors and that the effector steroid is probably 11-dehydrocorticosterone or a critical mixture of these two steroids, with the oxidized form predominating.

scholarly journals Generating Aptamers for Recognition of Virus-Infected Cells

2009 ◽  
Vol 55 (4) ◽  
pp. 813-822 ◽  
Author(s):  
Zhiwen Tang ◽  
Parag Parekh ◽  
Pete Turner ◽  
Richard W Moyer ◽  
Weihong Tan
Keyword(s):  
Infected Cell ◽  
Vaccinia Virus ◽  
Dissociation Constants ◽  
A549 Cells ◽  
Molecular Probes ◽  
Dna Aptamer ◽  
Live Cells ◽  
Selection Strategy ◽  
Infected Cells ◽  
Equilibrium Dissociation Constants

Abstract Background: The development of molecular probes capable of recognizing virus-infected cells is essential to meet the serious clinical, therapeutic, and national-security challenges confronting virology today. We report the development of DNA aptamers as probes for the selective targeting of virus-infected living cells. Methods: To create aptamer probes capable of recognizing virus-infected cells, we used cell-SELEX (systematic evolution of ligands via exponential enrichment), which uses intact infected live cells as targets for aptamer selection. In this study, vaccinia virus–infected and –uninfected lung cancer A549 cells were chosen to develop our model probes. Results: A panel of aptamers has been evolved by means of the infected cell–SELEX procedure. The results demonstrate that the aptamers bind selectively to vaccinia virus–infected A549 cells with apparent equilibrium dissociation constants in the nanomolar range. In addition, these aptamers can specifically recognize a variety of target infected cell lines. The aptamers’ target is most likely a viral protein located on the cell surface. Conclusions: The success of developing a panel of DNA-aptamer probes capable of recognizing virus-infected cells via a whole living cell–SELEX selection strategy may increase our understanding of the molecular signatures of infected cells. Our findings suggest that aptamers can be developed as molecular probes for use as diagnostic and therapeutic reagents and for facilitating drug delivery against infected cells.

scholarly journals Neuroleptics antagonize a calcium-activated potassium channel in airway smooth muscle.

1987 ◽  
Vol 89 (2) ◽  
pp. 339-352 ◽  
Author(s):  
J D McCann ◽  
M J Welsh
Keyword(s):  
Smooth Muscle ◽  
Airway Smooth Muscle ◽  
Dissociation Constants ◽  
Rank Order ◽  
K Channel ◽  
Airway Smooth Muscle Cells ◽  
Open Probability ◽  
K Channels ◽  
Channel Inhibition ◽  
Equilibrium Dissociation Constants

We examined the effect of neuroleptics on Ca-activated K channels from dog airway smooth muscle cells. Because these agents inhibit a variety of other Ca-mediated processes, it seemed possible that they might also inhibit Ca-activated K channels. In excised, inside-out patches, several neuroleptics potently and reversibly inhibited the K channel from the internal but not the external surface of the patch. Measurements of the effect on open probability and open- and closed-state durations support a simple kinetic model in which neuroleptics bind to and block the open channel. Inhibition by neuroleptics was moderately voltage dependent, with blockers less potent at hyperpolarizing voltages. The relationship between voltage and the dissociation constant for the blocker suggests that the binding site is one-third of the way across the channel's electrical field. Equilibrium dissociation constants for the drug-channel complex were: haloperidol, 1.0 +/- 0.1 microM; trifluoperazine, 1.4 +/- 0.1 microM; thioridazine, 2.4 +/- 0.1 microM; and chlorpromazine, 2.0 microM. This rank-order potency is different from their potency as calmodulin inhibitors, which suggests that neuroleptics bind to the channel rather than a calmodulin-channel complex.

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