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Author  |
Bottari, F.; Daems, E.; de Vries, A.-M.; Van Wielendaele, P.; Trashin, S.; Blust, R.; Sobott, F.; Madder, A.; Martins, J.C.; De Wael, K. |
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Title |
Do aptamers always bind? The need for a multifaceted analytical approach when demonstrating binding affinity between aptamer and low molecular weight compounds |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Journal Of The American Chemical Society |
Abbreviated Journal |
J Am Chem Soc |
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Volume |
142 |
Issue |
46 |
Pages |
jacs.0c08691-19630 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Medical Biochemistry |
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Abstract |
In this manuscript, we compare different analytical methodologies to validate or disprove the binding capabilities of aptamer sequences. This was prompted by the lack of a universally accepted and robust quality control protocol for the characterization of aptamer performances coupled with the observation of independent yet inconsistent data sets in the literature. As an example, we chose three aptamers with a reported affinity in the nanomolar range for ampicillin, a β-lactam antibiotic, used as biorecognition elements in several detection strategies described in the literature. Application of a well-known colorimetric assay based on aggregation of gold nanoparticles (AuNPs) yielded conflicting results with respect to the original report. Therefore, ampicillin binding was evaluated in solution using isothermal titration calorimetry (ITC), native nano-electrospray ionization mass spectrometry (native nESI-MS), and 1H-nuclear magnetic resonance spectroscopy (1H NMR). By coupling the thermodynamic data obtained with ITC with the structural information on the binding event given by native nESI-MS and 1H NMR we could verify that none of the ampicillin aptamers show any specific binding with their intended target. The effect of AuNPs on the binding event was studied by both ITC and 1H NMR, again without providing positive evidence of ampicillin binding. To validate the performance of our analytical approach, we investigated two well-characterized aptamers for cocaine/quinine (MN4), chosen for its nanomolar range affinity, and l-argininamide (1OLD) to show the versatility of our approach. The results clearly indicate the need for a multifaceted analytical approach, to unequivocally establish the actual detection potential and performance of aptamers aimed at small organic molecules. |
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Wos |
000592911000024 |
Publication Date |
2020-11-09 |
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Series Issue |
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Edition |
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ISSN |
0002-7863 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
15 |
Times cited |
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Open Access |
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Notes |
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Approved |
Most recent IF: 15; 2020 IF: 13.858 |
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Call Number |
UA @ admin @ c:irua:173136 |
Serial |
6488 |
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Author |
Borhani, A.H.; Berghmans, H.; Trashin, S.; De Wael, K.; Fago, A.; Moens, L.; Habibi-Rezaei, M.; Dewilde, S. |
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Title |
Kinetic properties and heme pocket structure of two domains of the polymeric hemoglobin of Artemia in comparison with the native molecule |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Biochimica et biophysica acta : proteins and proteomics |
Abbreviated Journal |
Bba-Proteins Proteom |
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Volume |
1854 |
Issue |
10a |
Pages |
1307-1316 |
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Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
In this project, we studied some physicochemical properties of two different globin domains of the polymeric hemoglobin of the brine shrimp Artemia salina and compared them with those of the native molecule. Two domains (AsHbC1D1 and AsHbC1D5) were cloned and expressed in BL21(DE3)pLysS strain of Escherichiacoli. The recombinant proteins as well as the native hemoglobin (AfHb) were purified from bacteria and frozen Artemia, respectively by standard chromatographic methods and assessed by SDS-PAGE. The heme environment of these proteins was studied by optical spectroscopy and ligand-binding kinetics (e.g. CO association and O2 binding affinity) were measured for the two recombinant proteins and the native hemoglobin. This indicates that the CO association rate for AsHbC1D1 is higher than that of AsHbC1D5 and AfHb, while the calculated P50 value for AsHbC1D1 is lower than that of AsHbC1D5 and AfHb. The geminate and bimolecular rebinding parameters indicate a significant difference between both domains. Moreover, EPR results showed that the heme pocket in AfHb is in a more closed conformation than the heme pocket in myoglobin. Finally, the reduction potential of − 0.13 V versus the standard hydrogen electrode was determined for AfHb by direct electrochemical measurements. It is about 0.06 V higher than the potential of the single domain AsHbC1D5. This work shows that each domain in the hemoglobin of Artemia has different characteristics of ligand binding. |
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Wos |
000362307500008 |
Publication Date |
2015-05-22 |
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Edition |
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ISSN |
1570-9639 |
ISBN |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
2.773 |
Times cited |
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Open Access |
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Notes |
; This work was supported by the general grant for visiting scholar of the Ministry of Science, Research and Technology of I. R. Iran and by the University of Antwerp. ; |
Approved |
Most recent IF: 2.773; 2015 IF: 2.747 |
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Call Number |
UA @ admin @ c:irua:125909 |
Serial |
5683 |
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Author |
Blidar, A.; Trashin, S.; Carrion, E.N.; Gorun, S.M.; Cristea, C.; De Wael, K. |
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Title |
Enhanced photoelectrochemical detection of an analyte triggered by its concentration by a singlet oxygen-generating fluoro photosensitizer |
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A1 Journal article |
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Year |
2020 |
Publication |
Acs Sensors |
Abbreviated Journal |
Acs Sensors |
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Volume |
5 |
Issue |
11 |
Pages |
3501-3509 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
The use of a photocatalyst (photosensitizer) which produces singlet oxygen instead of enzymes for oxidizing analytes creates opportunities for designing cost-efficient and sensitive photoelectrochemical sensors. We report that perfluoroisopropyl-substituted zinc phthalocyanine (F64PcZn) interacts specifically with a complex phenolic compound, the antibiotic rifampicin (RIF), but not with hydroquinone or another complex phenolic compound, the antibiotic doxycycline. The specificity is imparted by the selective preconcentration of RIF in the photocatalytic layer, as revealed by electrochemical and optical measurements, complemented by molecular modeling that confirms the important role of a hydrophobic cavity formed by the iso-perfluoropropyl groups of the photocatalyst. The preconcentration effect favorably enhances the RIF photoelectrochemical detection limit as well as sensitivity to nanomolar (ppb) concentrations, LOD = 7 nM (6 ppb) and 2.8 A.M-1.cm(-2), respectively. The selectivity to RIF, retained in the photosensitizer layer, is further enhanced by the selective removal of all unretained phenols via simple washing of the electrodes with pure buffer. The utility of the sensor for analyzing municipal wastewater was demonstrated. This first demonstration of enhanced selectivity and sensitivity due to intrinsic interactions of a molecular photocatalyst (photosensitizer) with an analyte, without use of a biorecognition element, may allow the design of related, robust, simple, and viable sensors. |
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Wos |
000595550100021 |
Publication Date |
2020-10-29 |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
2379-3694 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
8.9 |
Times cited |
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Open Access |
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Notes |
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Approved |
Most recent IF: 8.9; 2020 IF: NA |
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Call Number |
UA @ admin @ c:irua:176057 |
Serial |
7913 |
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Author |
Balashova, I.O.; Tolbin, A.Y.; Tarakanov, P.A.; Krot, A.R.; Fedorova, K., V; Sergeeva, I.A.; Trashin, S.A.; De Wael, K.; Pushkarev, V.E.; Koifman, M.O.; Ponomarev, G., V. |
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Title |
A covalently linked dyad based on zinc phthalocyanine and methylpheophorbide α : synthetic and physicochemical study |
Type |
A1 Journal article |
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Year |
2021 |
Publication |
Macroheterocycles |
Abbreviated Journal |
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Volume |
14 |
Issue |
1 |
Pages |
40-50 |
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Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
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Abstract |
The first covalently linked conjugate of metal phthalocyaninate and chlorin e(6) derivative has been obtained by transesterification of alpha-ketomethyl ester in methylpheophorbide a with zinc(II) 2-(2-hydroxymethylbenzyloxy)-9(10),16(17),23(24)-tri-tert-butylphthalocyaninate under mild conditions. The dyad exhibits a panchromatic nature revealing both the phthalocyanine and pheophorbide derived bands in the UV-Vis absorption spectrum. The H-1 NMR spectroscopy data combined with theoretical calculations indicate the presence of spatial intramolecular interactions between the phthalocyanine, pheophorbide and spacer fragments of the dyad allowing to forecast its enhanced nonlinear optical properties, as well as the characteristic energy transfer from the excited pheophorbide subunit to the phthalocyanine core. Indeed, when excited in the UV-Vis range, the conjugate shows red fluorescence with the spectral maximum at 686 nm, which is close to the one of the initial zinc phthalocyaninate. Furthermore, the dyad effectively generates singlet oxygen and, in the presence of polyvinylpyrrolidone (PVP) as biocompatible solubilizer, forms stable micellar saline solutions with the particles ranged in size between 40 and 100 nm. These nanoparticles represent promising third-generation photosensitizing systems for application in theranostics. |
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Wos |
000659682000003 |
Publication Date |
2021-06-25 |
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Additional Links |
UA library record; WoS full record |
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Times cited |
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Open Access |
OpenAccess |
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Notes |
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Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:179196 |
Serial |
7386 |
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Author |
Anaf, W.; Trashin, S.; Schalm, O.; van Dorp, D.; Janssens, K.; De Wael, K. |
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Title |
Electrochemical photodegradation study of semiconductor pigments : influence of environmental parameters |
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A1 Journal article |
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Year |
2014 |
Publication |
Analytical chemistry |
Abbreviated Journal |
Anal Chem |
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Volume |
86 |
Issue |
19 |
Pages |
9742-9748 |
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Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Antwerp Cultural Heritage Sciences (ARCHES) |
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Abstract |
Chemical transformations in paintings often induce discolorations, disturbing the appearance of the image. For an appropriate conservation of such valuable and irreplaceable heritage objects, it is important to have a good know-how on the degradation processes of the (historical) materials: which pigments have been discolored, what are the responsible processes, and which (environmental) conditions have the highest impact on the pigment degradation and should be mitigated. Pigment degradation is already widely studied, either by analyzing historical samples or by accelerated weathering experiments on dummies. However, in historic samples several processes may have taken place, increasing the complexity of the current state, while aging experiments are time-consuming due to the often extended aging period. An alternative method is proposed for a fast monitoring of degradation processes of semiconductor pigments, using an electrochemical setup mimicking the real environment and allowing the identification of harmful environmental parameters for each pigment. Examples are given for the pigments cadmium yellow (CdS) and vermilion (α-HgS). |
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Wos |
000343017100058 |
Publication Date |
2014-08-27 |
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ISSN |
0003-2700; 5206-882x |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
6.32 |
Times cited |
18 |
Open Access |
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Notes |
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Approved |
Most recent IF: 6.32; 2014 IF: 5.636 |
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Call Number |
UA @ admin @ c:irua:118834 |
Serial |
5593 |
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Author |
Alvarez-Martin, A.; Trashin, S.; Cuykx, M.; Covaci, A.; De Wael, K.; Janssens, K. |
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Title |
Photodegradation mechanisms and kinetics of Eosin-Y in oxic and anoxic conditions |
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A1 Journal article |
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Year |
2017 |
Publication |
Dyes and pigments |
Abbreviated Journal |
Dyes Pigments |
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Volume |
145 |
Issue |
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Pages |
376-384 |
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Keywords |
A1 Journal article; Pharmacology. Therapy; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Toxicological Centre |
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Abstract |
Lakes based on Eosin-Y are extensively used by 19th century artists. Unfortunately, the identification of these pigments in paintings is a difficult task because Eosin-Y degrades very fast under the influence of light. The characterization of the (photo)degradation products of Eosin-Y can be very useful for the identification of these pigments in historic works of art and related cultural heritage artifacts. Furthermore, knowledge on how different factors influence the discoloration process (e.g. different types of irradiation sources and presence/absence of oxygen) is a valuable tool for preventive conservation. To this aim we performed a study on the photodegradation of Eosin-Y in solution under different illumination and in both oxic and anoxic conditions. The photodegradation of Eosin-Y was monitored by UV-VIS spectrophotometry, LC-QTOFMS and electrochemistry techniques. Results indicated higher degradation rates, by a factor of 20 or higher, under illumination with wavelengths near to the main absorbance band of the red pigment. Two different degradation pathways are observed under the conditions studied. LC-QTOFMS and electrochemistry suggested that in the presence of oxygen the degradation mechanism is an oxidative process where the breakdown of the structure causes the total discoloration. Meanwhile under anoxic conditions, a debromination process takes place while the chromophore, and consequently the color of the molecule in solution, remains essentially intact. |
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Wos |
000405972900046 |
Publication Date |
2017-06-16 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0143-7208 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.473 |
Times cited |
18 |
Open Access |
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Notes |
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Approved |
Most recent IF: 3.473 |
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Call Number |
UA @ admin @ c:irua:144385 |
Serial |
5770 |
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