Records |
Author |
Daems, E. |
Title |
Shaping up oligonucleotides : aptamer-target recognition investigated by native mass spectrometry |
Type |
Doctoral thesis |
Year |
2021 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
|
Abbreviated Journal |
|
Volume |
|
Issue |
|
Pages |
235 p. |
Keywords |
Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
Abstract |
Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
|
Publication Date |
|
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
|
ISBN |
|
Additional Links |
UA library record |
Impact Factor |
|
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: NA |
Call Number |
UA @ admin @ c:irua:178116 |
Serial |
8517 |
Permanent link to this record |
|
|
|
Author |
Daems, E.; Moro, G.; Berghmans, H.; Moretto, L.M.; Dewilde, S.; Angelini, A.; Sobott, F.; De Wael, K. |
Title |
Native mass spectrometry for the design and selection of protein bioreceptors for perfluorinated compounds |
Type |
A1 Journal article |
Year |
2021 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Analyst |
Abbreviated Journal |
Analyst |
Volume |
146 |
Issue |
6 |
Pages |
2065-2073 |
Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
Abstract |
Biosensing platforms are answering the increasing demand for analytical tools for environmental monitoring of small molecules, such as per- and polyfluoroalkyl substances (PFAS). By transferring toxicological findings in bioreceptor design we can develop innovative pathways for biosensor design. Indeed, toxicological studies provide fundamental information about PFAS-biomolecule complexes that can help evaluate the applicability of the latter as bioreceptors. The toolbox of native mass spectrometry (MS) can support this evaluation, as shown by the two case studies reported in this work. The analysis of model proteins’ (i.e. albumin, haemoglobin, cytochrome c and neuroglobin) interactions with well-known PFAS, such as perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), demonstrated the potential of this native MS screening approach. In the first case study, untreated albumin and delipidated albumin were compared in the presence and absence of PFOA confirming that the delipidation step increases albumin affinity for PFOA without affecting protein stability. In the second case study, the applicability of our methodology to identify potential bioreceptors for PFOS/PFOA was extended to other proteins. Structurally related haemoglobin and neuroglobin revealed a 1 : 1 complex, whereas no binding was observed for cytochrome c. These studies have value as a proof-of-concept for a general application of native MS to identify bioreceptors for toxic compounds. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000631575100031 |
Publication Date |
2021-01-18 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0003-2654; 1364-5528 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
Impact Factor |
3.885 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 3.885 |
Call Number |
UA @ admin @ c:irua:177074 |
Serial |
8294 |
Permanent link to this record |
|
|
|
Author |
Moro, G.; Barich, H.; Driesen, K.; Montiel, N.F.; Neven, L.; Mendonca, C.D.; Thiruvottriyur Shanmugam, S.; Daems, E.; De Wael, K. |
Title |
Unlocking the full power of electrochemical fingerprinting for on-site sensing applications |
Type |
A1 Journal article |
Year |
2020 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Analytical And Bioanalytical Chemistry |
Abbreviated Journal |
Anal Bioanal Chem |
Volume |
|
Issue |
|
Pages |
1-14 |
Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
Abstract |
Electrochemical sensing for the semi-quantitative detection of biomarkers, drugs, environmental contaminants, food additives, etc. shows promising results in point-of-care diagnostics and on-site monitoring. More specifically, electrochemical fingerprint (EF)-based sensing strategies are considered an inviting approach for the on-site detection of low molecular weight molecules. The fast growth of electrochemical sensors requires defining the concept of direct electrochemical fingerprinting in sensing. The EF can be defined as the unique electrochemical signal or pattern, mostly recorded by voltammetric techniques, specific for a certain molecule that can be used for its quantitative or semi-quantitative identification in a given analytical context with specified circumstances. The performance of EF-based sensors can be enhanced by considering multiple features of the signal (i.e., oxidation or reduction patterns), in combination with statistical data analysis or sample pretreatments or by including electrode surface modifiers to enrich the EF. In this manuscript, some examples of EF-based sensors, strategies to improve their performances, and open challenges are discussed to unlock the full power of electrochemical fingerprinting for on-site sensing applications. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000523396300002 |
Publication Date |
2020-04-04 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1618-2642 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.3 |
Times cited |
3 |
Open Access |
|
Notes |
; The presented review is the result of a concerted effort and fruitful discussions among enthusiastic, young, and (for the occasion) female researchers of the AXES research group, each of them with specific expertise and background, under the guidance of the corresponding author. The authors acknowledge FWO-Flanders, BOF-UA, IOF-UA, FAPESP and EU for funding. ; |
Approved |
Most recent IF: 4.3; 2020 IF: 3.431 |
Call Number |
UA @ admin @ c:irua:168563 |
Serial |
6647 |
Permanent link to this record |
|
|
|
Author |
Campos, R.; Thiruvottriyur Shanmugam, S.; Daems, E.; Ribeiro, R.; De Wael, K. |
Title |
Development of an electrochemiluminescent oligonucleotide-based assay for the quantification of prostate cancer associated miR-141-3p in human serum |
Type |
A1 Journal article |
Year |
2023 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Bioelectrochemistry: an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry |
Abbreviated Journal |
|
Volume |
153 |
Issue |
|
Pages |
108495-108496 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab) |
Abstract |
MicroRNAs (miRNAs) are small oligonucleotides (18–25 bases), biologically relevant for epigenetic regulation of key processes, particularly in association with cancer. Research effort has therefore been directed towards the monitoring and detection of miRNAs to progress (early) cancer diagnoses. Traditional detection strategies for miRNAs are expensive, with a lengthy time-to-result. In this study we develop an oligonucleotide-based assay using electrochemistry for the specific, selective and sensitive detection of a circulating miRNA (miR-141) associated with prostate cancer. In the assay, the excitation and readout of the signal are independent: an electrochemical stimulation followed by an optical readout. A ‘sandwich’ approach is incorporated, consisting of a biotinylated capture probe immobilised on streptavidin-functionalised surfaces and a detection probe labelled with digoxigenin. We show that the assay allows the detection of miR-141 in human serum, even in the presence of other miRNAs, with a LOD of 0.25 pM. The developed electrochemiluminescent assay has, therefore, the potential for efficient universal oligonucleotide target detection via the redesign of capture and detection probes. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
001031760700001 |
Publication Date |
2023-06-30 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1567-5394 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
Impact Factor |
5 |
Times cited |
|
Open Access |
Not_Open_Access: Available from 01.01.2024 |
Notes |
|
Approved |
Most recent IF: 5; 2023 IF: 3.346 |
Call Number |
UA @ admin @ c:irua:197615 |
Serial |
8849 |
Permanent link to this record |
|
|
|
Author |
Moro, G.; Campos, R.; Daems, E.; Moretto, L.M.; De Wael, K. |
Title |
Haem-mediated albumin biosensing : towards voltammetric detection of PFOA |
Type |
A1 Journal article |
Year |
2023 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Bioelectrochemistry: an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry |
Abbreviated Journal |
|
Volume |
152 |
Issue |
|
Pages |
108428-7 |
Keywords |
A1 Journal article; Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab) |
Abstract |
The haem group is a promising redox probe for the design of albumin-based voltammetric sensors. Among the endogenous ligands carried by human serum albumin (hSA), haem is characterised by a reversible redox behaviour and its binding kinetics strongly depend on hSA’s conformation, which, in turn, depends on the presence of other ligands. In this work, the potential applicability of haem, especially hemin, as a redox probe was first tested in a proof-of-concept study using perfluorooctanoic acid (PFOA) as model analyte. PFOA is known to bind hSA by occupying Sudlow’s I site (FA7) which is spatially related to the haem-binding site (FA1). The latter undergoes a conformational change, which is expected to affect hemin’s binding kinetics. To verify this hypothesis, hemin:albumin complexes in the presence/absence of PFOA were first screened by UV–Vis spectroscopy. Once the complex formation was verified, haem was further characterised via electrochemical methods to estimate its electron transfer kinetics. The hemin:albumin:PFOA system was studied in solution, with the aim of describing the multiple equilibria at stake and designing an electrochemical assay for PFOA monitoring. This latter could be integrated with protein-based bioremediation approaches for the treatment of per- and polyfluoroalkyl substances polluted waters. Overall, our preliminary results show how hemin can be applied as a redox probe in albumin-based voltammetric sensing strategies. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000971630400001 |
Publication Date |
2023-03-27 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1567-5394 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
Impact Factor |
5 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 5; 2023 IF: 3.346 |
Call Number |
UA @ admin @ c:irua:195069 |
Serial |
8876 |
Permanent link to this record |
|
|
|
Author |
Thiruvottriyur Shanmugam, S.; Campos, R.; Trashin, S.; Daems, E.; Carneiro, D.; Fraga, A.; Ribeiro, R.; De Wael, K. |
Title |
Singlet oxygen-based photoelectrochemical detection of miRNAs in prostate cancer patients’ plasma : a novel diagnostic tool for liquid biopsy |
Type |
A1 Journal article |
Year |
2024 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Bioelectrochemistry: an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry |
Abbreviated Journal |
|
Volume |
158 |
Issue |
|
Pages |
108698-108699 |
Keywords |
A1 Journal article; Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab) |
Abstract |
Dysregulation of miRNA expression occurs in many cancers, making miRNAs useful in cancer diagnosis and therapeutic guidance. In a clinical context using methods such as polymerase chain reaction (PCR), the limited amount of miRNAs in circulation often limits their quantification. Here, we present a PCR-free and sensitive singlet oxygen (1O2)-based strategy for the detection and quantification of miRNAs in untreated human plasma from patients diagnosed with prostate cancer. A target miRNA is specifically captured by functionalised magnetic beads and a detection oligonucleotide probe in a sandwich-like format. The formed complex is concentrated at the sensor surface via magnetic beads, providing an interface for the photoinduced redox signal amplification. The detection oligonucleotide probe bears a molecular photosensitiser, which produces 1O2 upon illumination, oxidising a redox reporter and creating a redox cycling loop, allowing quantification of pM level miRNA in diluted human plasma within minutes after hybridisation and without target amplification. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
|
Publication Date |
2024-04-04 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
1567-5394 |
ISBN |
|
Additional Links |
UA library record |
Impact Factor |
5 |
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: 5; 2024 IF: 3.346 |
Call Number |
UA @ admin @ c:irua:205281 |
Serial |
9229 |
Permanent link to this record |
|
|
|
Author |
Cánovas, R.; Daems, E.; Langley, A.R.; De Wael, K. |
Title |
Are aptamer-based biosensing approaches a good choice for female fertility monitoring? A comprehensive review |
Type |
A1 Journal article |
Year |
2023 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Biosensors and bioelectronics |
Abbreviated Journal |
|
Volume |
220 |
Issue |
|
Pages |
114881-18 |
Keywords |
A1 Journal article; Engineering sciences. Technology; Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab) |
Abstract |
The WHO estimates that 8–10% of couples are facing fertility problems, often due to inaccuracy in predicting the female's ovulation period controlled by four key hormones. The quantification and monitoring of such key hormones are crucial for the early identification of infertility, but also in improving therapeutic management associated with hormonal imbalance. In this review, we extensively summarize and discuss: i) drawbacks of laboratory methods for fertility testing (costly, invasive, complex) and commercially available point-of-care tests (measuring only one/two of the four key hormones), ii) the understanding of different biosensors for fertility monitoring, and iii) an in-depth classification and overview of aptamer-based sensing of the hormones of interest. This review provides insights on hormone detection strategies for fertility, with a focus on the classification of the current ‘aptasensing’ strategies, aiming to assist as a basic guide for the development of accurate fertility window monitoring tools based on aptamers. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000890547600004 |
Publication Date |
2022-11-07 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0956-5663 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
12.6 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 12.6; 2023 IF: 7.78 |
Call Number |
UA @ admin @ c:irua:191711 |
Serial |
8833 |
Permanent link to this record |
|
|
|
Author |
Daems, E.; Bassini, S.; Mariën, L.; Op de Beeck, H.; Stratulat, A.; Zwaenepoel, K.; Vandamme, T.; op de Beeck, K.; Koljenovic, S.; Peeters, M.; Van Camp, G.; De Wael, K. |
Title |
Singlet oxygen-based photoelectrochemical detection of single-point mutations in the KRAS oncogene |
Type |
University Hospital Antwerp |
Year |
2023 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Biosensors and bioelectronics |
Abbreviated Journal |
|
Volume |
249 |
Issue |
|
Pages |
115957-7 |
Keywords |
University Hospital Antwerp; A1 Journal article; Center for Oncological Research (CORE); Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab); Medical Genetics (MEDGEN) |
Abstract |
Single nucleotide point mutations in the KRAS oncogene occur frequently in human cancers, rendering them intriguing targets for diagnosis, early detection and personalized treatment. Current detection methods are based on polymerase chain reaction, sometimes combined with next-generation sequencing, which can be expensive, complex and have limited availability. Here, we propose a novel singlet oxygen (1O2)-based photoelectrochemical detection methodology for single-point mutations, using KRAS mutations as a case study. This detection method combines the use of a sandwich assay, magnetic beads and robust chemical photosensitizers, that need only air and light to produce 1O2, to ensure high specificity and sensitivity. We demonstrate that hybridization of the sandwich hybrid at high temperatures enables discrimination between mutated and wild-type sequences with a detection rate of up to 93.9%. Additionally, the presence of background DNA sequences derived from human cell-line DNA, not containing the mutation of interest, did not result in a signal, highlighting the specificity of the methodology. A limit of detection as low as 112 pM (1.25 ng/mL) was achieved without employing any amplification techniques. The developed 1O2-based photoelectrochemical methodology exhibits unique features, including rapidity, ease of use, and affordability, highlighting its immense potential in the field of nucleic acid-based diagnostics. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
001155075300001 |
Publication Date |
2023-12-23 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0956-5663 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
Impact Factor |
12.6 |
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: 12.6; 2023 IF: 7.78 |
Call Number |
UA @ admin @ c:irua:201875 |
Serial |
9092 |
Permanent link to this record |
|
|
|
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. |
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 |
Year |
2020 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Journal Of The American Chemical Society |
Abbreviated Journal |
J Am Chem Soc |
Volume |
142 |
Issue |
46 |
Pages |
jacs.0c08691-19630 |
Keywords |
A1 Journal article; Engineering sciences. Technology; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Medical Biochemistry |
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. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000592911000024 |
Publication Date |
2020-11-09 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0002-7863 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
15 |
Times cited |
|
Open Access |
|
Notes |
|
Approved |
Most recent IF: 15; 2020 IF: 13.858 |
Call Number |
UA @ admin @ c:irua:173136 |
Serial |
6488 |
Permanent link to this record |
|
|
|
Author |
Maso, L.; Trande, M.; Liberi, S.; Moro, G.; Daems, E.; Linciano, S.; Sobott, F.; Covaceuszach, S.; Cassetta, A.; Fasolato, S.; Moretto, L.M.; De Wael, K.; Cendron, L.; Angelini, A. |
Title |
Unveiling the binding mode of perfluorooctanoic acid to human serum albumin |
Type |
A1 Journal article |
Year |
2021 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Protein Science |
Abbreviated Journal |
Protein Sci |
Volume |
30 |
Issue |
4 |
Pages |
830-841 |
Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
Abstract |
Perfluorooctanoic acid (PFOA) is a toxic compound that is absorbed and distributed throughout the body by noncovalent binding to serum proteins such as human serum albumin (hSA). Though the interaction between PFOA and hSA has been already assessed using various analytical techniques, a high resolution and detailed analysis of the binding mode is still lacking. We report here the crystal structure of hSA in complex with PFOA and a medium-chain saturated fatty acid (FA). A total of eight distinct binding sites, four occupied by PFOAs and four by FAs, have been identified. In solution binding studies confirmed the 4:1 PFOA-hSA stoichiometry and revealed the presence of one high and three low affinity binding sites. Competition experiments with known hSA-binding drugs allowed locating the high affinity binding site in sub-domain IIIA. The elucidation of the molecular basis of the interaction between PFOA and hSA might provide not only a better assessment of the absorption and elimination mechanisms of these compounds in vivo but also have implications for the development of novel molecular receptors for diagnostic and biotechnological applications. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000625392600001 |
Publication Date |
2021-02-08 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0961-8368 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
2.523 |
Times cited |
|
Open Access |
Not_Open_Access |
Notes |
|
Approved |
Most recent IF: 2.523 |
Call Number |
UA @ admin @ c:irua:176725 |
Serial |
8714 |
Permanent link to this record |
|
|
|
Author |
Slavkovic, S.; Shoara, A.A.; Churcher, Z.R.; Daems, E.; De Wael, K.; Sobott, F.; Johnson, P.E. |
Title |
DNA binding by the antimalarial compound artemisinin |
Type |
A1 Journal article |
Year |
2022 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Scientific reports |
Abbreviated Journal |
|
Volume |
12 |
Issue |
1 |
Pages |
133 |
Keywords |
A1 Journal article; Pharmacology. Therapy; Engineering sciences. Technology; Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab) |
Abstract |
Artemisinin (ART) is a vital medicinal compound that is used alone or as part of a combination therapy against malaria. ART is thought to function by attaching to heme covalently and alkylating a range of proteins. Using a combination of biophysical methods, we demonstrate that ART is bound by three-way junction and duplex containing DNA molecules. Binding of ART by DNA is first shown for the cocaine-binding DNA aptamer and extensively studied using this DNA molecule. Isothermal titration calorimetry methods show that the binding of ART is both entropically and enthalpically driven at physiological NaCl concentration. Native mass spectrometry methods confirm DNA binding and show that a non-covalent complex is formed. Nuclear magnetic resonance spectroscopy shows that ART binds at the three-way junction of the cocaine-binding aptamer, and that binding results in the folding of the structure-switching variant of this aptamer. This structure-switching ability was exploited using the photochrome aptamer switch assay to demonstrate that ART can be detected using this biosensing assay. This study is the first to demonstrate the DNA binding ability of ART and should lay the foundation for further work to study implications of DNA binding for the antimalarial activity of ART. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000740510500120 |
Publication Date |
2022-01-07 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
2045-2322 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
|
Times cited |
|
Open Access |
OpenAccess |
Notes |
|
Approved |
no |
Call Number |
UA @ admin @ c:irua:184507 |
Serial |
8851 |
Permanent link to this record |
|
|
|
Author |
Daems, E.; Dewaele, D.; Barylyuk, K.; De Wael, K.; Sobott, F. |
Title |
Aptamer-ligand recognition studied by native ion mobility-mass spectrometry |
Type |
A1 Journal article |
Year |
2021 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Talanta |
Abbreviated Journal |
Talanta |
Volume |
224 |
Issue |
|
Pages |
121917 |
Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
Abstract |
The range of applications for aptamers, small oligonucleotide-based receptors binding to their targets with high specificity and affinity, has been steadily expanding. Our understanding of the mechanisms governing aptamer-ligand recognition and binding is however lagging, stymieing the progress in the rational design of new aptamers and optimization of the known ones. Here we demonstrate the capabilities and limitations of native ion mobility-mass spectrometry for the analysis of their higher-order structure and non-covalent interactions. A set of related cocaine-binding aptamers, displaying a range of folding properties and ligand binding affinities, was used as a case study in both positive and negative electrospray ionization modes. Using carefully controlled experimental conditions, we probed their conformational behavior and interactions with the high-affinity ligand quinine as a surrogate for cocaine. The ratios of bound and unbound aptamers in the mass spectra were used to rank them according to their apparent quinine-binding affinity, qualitatively matching the published ranking order. The arrival time differences between the free aptamer and aptamer-quinine complexes were consistent with a small ligand-induced conformational change, and found to inversely correlate with the affinity of binding. This mass spectrometry-based approach provides a fast and convenient way to study the molecular basis of aptamer-ligand recognition. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000600787800122 |
Publication Date |
2020-12-02 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0039-9140; 1873-3573 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
4.162 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 4.162 |
Call Number |
UA @ admin @ c:irua:174086 |
Serial |
7490 |
Permanent link to this record |
|
|
|
Author |
Daems, E.; Moro, G.; Campos, R.; De Wael, K. |
Title |
Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions |
Type |
A1 Journal article |
Year |
2021 |
Publication ![sorted by Publication field, ascending order (up)](img/sort_asc.gif) |
Trac-Trends In Analytical Chemistry |
Abbreviated Journal |
Trac-Trend Anal Chem |
Volume |
142 |
Issue |
|
Pages |
116311 |
Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation) |
Abstract |
Aptamers are promising biorecognition elements with a wide applicability from therapeutics to bio-sensing. However, to successfully use these biomolecules, a complete characterisation of their bindingperformance in the presence of the target is crucial. Several multi-analytical approaches have been re-ported including techniques to describe kinetic and thermodynamic aspects of the aptamer-targetinteraction, and techniques which allow an in-depth understanding of the aptamer-target structures.Recent literature shows the need of a critical data interpretation, a combination of characterisationtechniques and suggests the key role of the characterisation protocol design. Indeed, thefinal applicationof the aptamer should be considered before choosing the characterisation method. All the limitations andcapabilities of the analytical tools in use for aptamer characterisation should be taken into account. Here,we present a critical overview of the current methods and multi-analytical approaches to study aptamer-target binding, aiming to provide researchers with guidelines for the design of characterisation protocols. |
Address |
|
Corporate Author |
|
Thesis |
|
Publisher |
|
Place of Publication |
|
Editor |
|
Language |
|
Wos |
000682179000010 |
Publication Date |
2021-04-28 |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
Series Volume |
|
Series Issue |
|
Edition |
|
ISSN |
0165-9936; 1879-3142 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
8.442 |
Times cited |
|
Open Access |
OpenAccess |
Notes |
|
Approved |
Most recent IF: 8.442 |
Call Number |
UA @ admin @ c:irua:179407 |
Serial |
8203 |
Permanent link to this record |