TY - JOUR A1 - Sass, Stephan A1 - Stöcklein, Walter F. M. A1 - Klevesath, Anja A1 - Hurpin, Jeanne A1 - Menger, Marcus A1 - Hille, Carsten T1 - Binding affinity data of DNA aptamers for therapeutic anthracyclines from microscale thermophoresis and surface plasmon resonance spectroscopy JF - The analyst : the analytical journal of the Royal Society of Chemistry N2 - Anthracyclines like daunorubicin (DRN) and doxorubicin (DOX) play an undisputed key role in cancer treatment, but their chronic administration can cause severe side effects. For precise anthracycline analytical systems, aptamers are preferable recognition elements. Here, we describe the detailed characterisation of a single-stranded DNA aptamer DRN-10 and its truncated versions for DOX and DRN detection. Binding affinities were determined from surface plasmon resonance (SPR) and microscale thermophoresis (MST) and combined with conformational data from circular dichroism (CD). Both aptamers displayed similar nanomolar binding affinities to DRN and DOX, even though their rate constants differed as shown by SPR recordings. SPR kinetic data unravelled a two-state reaction model including a 1 : 1 binding and a subsequent conformational change of the binding complex. This model was supported by CD spectra. In addition, the dissociation constants determined with MST were always lower than that from SPR, and especially for the truncated aptamer they differed by two orders of magnitude. This most probably reflects the methodological difference, namely labelling for MST vs. immobilisation for SPR. From CD recordings, we suggested a specific G-quadruplex as structural basis for anthracycline binding. We concluded that the aptamer DRN-10 is a promising recognition element for anthracycline detection systems and further selected aptamers can be also characterised with the combined methodological approach presented here. Y1 - 2019 U6 - https://doi.org/10.1039/c9an01247h SN - 0003-2654 SN - 1364-5528 VL - 144 IS - 20 SP - 6064 EP - 6073 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Sabrowski, Wiebke A1 - Dreymann, Nico A1 - Möller, Anja A1 - Czepluch, Denise A1 - Albani, Patricia P. A1 - Theodoridis, Dimitrios A1 - Menger, Marcus M. T1 - The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer JF - Scientific reports N2 - The emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ss-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ss-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ss-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ss-lactamase 1 expressing Enterobacteriaceae. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-12062-2 SN - 2045-2322 VL - 12 IS - 1 PB - Macmillan Publishers Limited, part of Springer Nature CY - London ER - TY - JOUR A1 - Menger, Marcus A1 - Yarman, Aysu A1 - Erdössy, Júlia A1 - Yildiz, Huseyin Bekir A1 - Gyurcsányi, Róbert E. A1 - Scheller, Frieder W. T1 - MIPs and Aptamers for Recognition of Proteins in Biomimetic Sensing JF - Biosensors : open access journal N2 - Biomimetic binders and catalysts have been generated in order to substitute the biological pendants in separation techniques and bioanalysis. The two major approaches use either "evolution in the test tube" of nucleotides for the preparation of aptamers or total chemical synthesis for molecularly imprinted polymers (MIPs). The reproducible production of aptamers is a clear advantage, whilst the preparation of MIPs typically leads to a population of polymers with different binding sites. The realization of binding sites in the total bulk of the MIPs results in a higher binding capacity, however, on the expense of the accessibility and exchange rate. Furthermore, the readout of the bound analyte is easier for aptamers since the integration of signal generating labels is well established. On the other hand, the overall negative charge of the nucleotides makes aptamers prone to non-specific adsorption of positively charged constituents of the sample and the "biological" degradation of non-modified aptamers and ionic strength-dependent changes of conformation may be challenging in some application. KW - biomimetic recognition elements KW - aptamers KW - molecularly imprinted polymers KW - chemical sensors KW - aptasensors KW - in vitro selection KW - SELEX Y1 - 2016 U6 - https://doi.org/10.3390/bios6030035 SN - 2079-6374 VL - 6 SP - 4399 EP - 4413 PB - MDPI CY - Basel ER - TY - GEN A1 - Menger, Marcus A1 - Yarman, Aysu A1 - Erdőssy, Júlia A1 - Yildiz, Huseyin Bekir A1 - Gyurcsányi, Róbert E. A1 - Scheller, Frieder W. T1 - MIPs and aptamers for recognition of proteins in biomimetic sensing N2 - Biomimetic binders and catalysts have been generated in order to substitute the biological pendants in separation techniques and bioanalysis. The two major approaches use either "evolution in the test tube" of nucleotides for the preparation of aptamers or total chemical synthesis for molecularly imprinted polymers (MIPs). The reproducible production of aptamers is a clear advantage, whilst the preparation of MIPs typically leads to a population of polymers with different binding sites. The realization of binding sites in the total bulk of the MIPs results in a higher binding capacity, however, on the expense of the accessibility and exchange rate. Furthermore, the readout of the bound analyte is easier for aptamers since the integration of signal generating labels is well established. On the other hand, the overall negative charge of the nucleotides makes aptamers prone to non-specific adsorption of positively charged constituents of the sample and the "biological" degradation of non-modified aptamers and ionic strength-dependent changes of conformation may be challenging in some application. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 357 KW - biomimetic recognition elements KW - aptamers KW - molecularly imprinted polymers KW - chemical sensors KW - aptasensors KW - in vitro selection KW - SELEX Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400496 ER - TY - JOUR A1 - Dreymann, Nico A1 - Wuensche, Julia A1 - Sabrowski, Wiebke A1 - Moeller, Anja A1 - Czepluch, Denise A1 - Vu Van, Dana A1 - Füssel, Susanne A1 - Menger, Marcus M. T1 - Inhibition of Human Urokinase-Type Plasminogen Activator (uPA) Enzyme Activity and Receptor Binding by DNA Aptamers as Potential Therapeutics through Binding to the Different Forms of uPA JF - International journal of molecular sciences N2 - Urokinase-type plasminogen activator is widely discussed as a marker for cancer prognosis and diagnosis and as a target for cancer therapies. Together with its receptor, uPA plays an important role in tumorigenesis, tumor progression and metastasis. In the present study, systematic evolution of ligands by exponential enrichment (SELEX) was used to select single-stranded DNA aptamers targeting different forms of human uPA. Selected aptamers allowed the distinction between HMW-uPA and LMW-uPA, and therefore, presumably, have different binding regions. Here, uPAapt-02-FR showed highly affine binding with a K-D of 0.7 nM for HMW-uPA and 21 nM for LMW-uPA and was also able to bind to pro-uPA with a K-D of 14 nM. Furthermore, no cross-reactivity to mouse uPA or tissue-type plasminogen activator (tPA) was measured, demonstrating high specificity. Suppression of the catalytic activity of uPA and inhibition of uPAR-binding could be demonstrated through binding with different aptamers and several of their truncated variants. Since RNA aptamers are already known to inhibit uPA-uPAR binding and other pathological functions of the uPA system, these aptamers represent a novel, promising tool not only for detection of uPA but also for interfering with the pathological functions of the uPA system by additionally inhibiting uPA activity. KW - biomarker KW - cancer KW - cancer therapy KW - DNA aptamer KW - microscale thermophoresis (MST) KW - SELEX KW - surface plasmon resonance spectroscopy (SPR) KW - uPA KW - uPAR KW - urokinase Y1 - 2022 U6 - https://doi.org/10.3390/ijms23094890 SN - 1661-6596 SN - 1422-0067 VL - 23 IS - 9 PB - MDPI CY - Basel ER -