Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB
Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB

Functional Nucleic Acids - Aptamers

Magnetic robotic station - Aptamere
© Fraunhofer IZI-BB
Magnetic robotic station - Aptamere

The primary aim of the Working Group for Functional Nucleic Acids – Aptamers is to develop new and innovative products that are based on aptamers. This involves both the generation, synthesis and functionalization of aptamers, as well as their integration in various applications. At the same time, the goal is to work closely with industry and research institutes.

Aptamers are mainly short single-strand DNA and RNA molecules that exhibit the special property – much like antibodies – of highly affine and highly specific binding to target molecules. The extremely wide range of uses for aptamers in analytical, diagnostic and therapeutic applications makes them highly universal binding molecules.

Special focus is given to the production of new aptamers using an automated in-vitro selection process and an efficient monitoring and management process, as well as the development of aptamer-based detection methods, such as strip tests or so-called aptasensors.

APTACHIP – Aptamer array chip for monoclonal antibodies real time quantification in bioreactor (EuroTransBio)

Logo-EuroTransBio

The objective of the APTACHIP project is to develop an aptamer-based biosensor that will enable the real-time detection of biochemical species in the growth medium. To demonstrate proper function (proof of concept), the aptasensor will mainly be geared toward detecting monoclonal antibodies. This type of biosensor may be used in the future for the quantitative detection of different chemical species and, most importantly, for optimizing the supply of nutrients in a bioreactor. Following the project, further R&D services will be carried out to adapt the aptasensor concept for sectors other than the bioreactor market, specifically the areas of water testing, food safety and industrial process control.

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Methods

  • Methods for generating highly affine and highly specific RNA and DNA aptamers
  • Semi-automatic in-vitro selection process for the enrichment of target-affine nucleic acid pools, including an effective monitoring and management process
  • Sequence analysis of nucleic acid pools
  • Characterization and optimization of aptamer sequences
  • Diversity analysis of nucleic acid pools (DANA)
  • Fluorescence-based aptamer binding assay (FLAA)
  • Surface plasmon resonance (SPR) binding studies
  • Microscale thermophoresis (MST) binding studies
  • Flow cytometry (FACS) binding studies
  • Synthesis of RNA and DNA aptamers, including chemical modifications

 

 

 

Equipment

  • Security level 1 and 2 molecular-biological laboratories
  • KingFisher Duo Magnetic particle processor for SELEX process with plate function
  • KingFisher BioSprint 15 for SELEX process
  • PCR Workstation with HEPA filter
  • Spectrophotometer UV/VIS
  • Microtiter plates fluorimeter
  • Microtiter plate spectrophotometer
  • Biacore (X, TM T200)
  • Nanotemper (Monolith NT.115)

 

 

 

  • Fraunhofer-Institut IKTS-MD, Dresden
  • GeSIM mbH, Grosserkmannsdorf
  • Ipratech, Belgien
  • Multitel, Belgien

  • Weidemann, H., Feger, D., Ehlert, J. E., Menger, M. M., & Krempien, R. C. (2023). Markedly divergent effects of Ouabain on a Temozolomide-resistant (T98G) vs. a Temozolomide-sensitive (LN229) Glioblastoma cell line. Discov Oncol, 14(1), 27. https://doi.org/10.1007/s12672-023-00633-2
  • Sabrowski, W., Stöcklein, W. F. M., & Menger, M. M. (2023). Immobilization-Free Determination of Dissociation Constants Independent of Ligand Size Using MicroScale Thermophoresis. In G. Mayer & M. M. Menger (Eds.), Nucleic Acid Aptamers: Selection, Characterization, and Application (2 ed., pp. 129-140). Humana. https://doi.org/10.1007/978-1-0716-2695-5_10
  • Mayer, G., & Menger, M. M. (2023). Preface. In G. Mayer & M. M. Menger (Eds.), Nucleic Acid Aptamers: Selection, Characterization, and Application (2 ed., pp. V-VI). Humana. https://doi.org/10.1007/978-1-0716-2695-5
  • Kerler, Y., Sass, S., Hille, C., & Menger, M. M. (2023). Determination of Aptamer Structure Using Circular Dichroism Spectroscopy. In G. Mayer & M. M. Menger (Eds.), Nucleic Acid Aptamers: Selection, Characterization, and Application (2 ed., pp. 119-128). Humana. https://doi.org/10.1007/978-1-0716-2695-5_9
  • Dreymann, N., Möller, A., & Menger, M. M. (2023). Label-Free Determination of the Kinetic Parameters of Protein-Aptamer Interaction by Surface Plasmon Resonance. In G. Mayer & M. M. Menger (Eds.), Nucleic Acid Aptamers: Selection, Characterization, and Application (2 ed., pp. 141-153). Humana. https://doi.org/10.1007/978-1-0716-2695-5_11
  • Schmidt, C., Kammel, A., Tanner, J. A., Kinghorn, A. B., Khan, M. M., Lehmann, W., Menger, M., Schedler, U., Schierack, P., & Rödiger, S. (2022). A multiparametric fluorescence assay for screening aptamer–protein interactions based on microbeads. Scientific Reports, 12(1), 2961. https://doi.org/10.1038/s41598-022-06817-0
  • Sabrowski, W., Dreymann, N., Möller, A., Czepluch, D., Albani, P. P., Theodoridis, D., & Menger, M. M. (2022). The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer. Scientific Reports, 12(1), 7936. https://doi.org/10.1038/s41598-022-12062-2
  • Dreymann, N., Wuensche, J., Sabrowski, W., Moeller, A., Czepluch, D., Vu Van, D., Fuessel S., & Menger, M. M. (2022). 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. International Journal of Molecular Sciences, 23(9).
  • Dreymann, N., Sabrowski, W., Danso, J., & Menger, M. M. (2022). Aptamer-Based Sandwich Assay Formats for Detection and Discrimination of Human High- and Low-Molecular-Weight uPA for Cancer Prognosis and Diagnosis. Cancers, 14(21).
  • Kutovyi, Y., Li, J., Zadorozhnyi, I., Hlukhova, H., Boichuk, N., Yehorov, D., Menger, M., &. Vitusevich, S. (2020). Highly Sensitive and Fast Detection of C-Reactive Protein and Troponin Biomarkers Using Liquidgated Single Silicon Nanowire Biosensors. MRS Advances, 5(16), 835-846. https://doi.org/10.1557/adv.2020.60
  • Kutovyi, Y., Hlukhova, H., Boichuk, N., Menger, M., Offenhäusser, A., & Vitusevich, S. (2020). Amyloid-beta peptide detection via aptamer-functionalized nanowire sensors exploiting single-trap phenomena. Biosensors and Bioelectronics, 154, 112053. https://doi.org/https://doi.org/10.1016/j.bios.2020.112053
  • Sass, S., Stöcklein, W. F. M., Klevesath, A., Hurpin, J., Menger, M., & Hille, C. (2019). Binding affinity data of DNA aptamers for therapeutic anthracyclines from microscale thermophoresis and surface plasmon resonance spectroscopy [10.1039/C9AN01247H]. Analyst, 144(20), 6064-6073. https://doi.org/10.1039/C9AN01247H
  • Hlukhova, H., Menger, M., Offenhäusser, A., & Vitusevich, S. (2018). Highly Sensitive Aptamer-Based Method for the Detection of Cardiac Biomolecules on Silicon Dioxide Surfaces. MRS Advances, 3(27), 1535-1541. https://doi.org/10.1557/adv.2018.332
  • Czepluch, D., & Menger, M. (2018). Highly specific aptamers for analytics and therapeutics. q&more. http://q-more.chemeurope.com/q-more-articles/259/highly-specific-aptamers-for-analytics-and-therapeutics.html
  • Bahner, N., Reich, P., Frense, D., Menger, M., Schieke, K., & Beckmann, D. (2018). An aptamer-based biosensor for detection of doxorubicin by electrochemical impedance spectroscopy. Analytical and Bioanalytical Chemistry, 410(5), 1453-1462. https://doi.org/10.1007/s00216-017-0786-8
  • Menger, M., Yarman, A., Erdőssy, J., Yildiz, H. B., Gyurcsányi, R. E., & Scheller, F. W. (2016). MIPs and Aptamers for Recognition of Proteins in Biomimetic Sensing. Biosensors, 6(3).
  • Hacht, A. v., Seifert, O., Menger, M., Schütze, T., Arora, A., Konthur, Z., Neubauer, P., Wagner, A., Weise, C., &. Kurreck, J. (2014). Identification and characterization of RNA guanine-quadruplex binding proteins. Nucleic Acids Research, 42(10), 6630-6644. https://doi.org/10.1093/nar/gku290
  • Schütze, T., Wilhelm, B., Greiner, N., Braun, H., Peter, F., Mörl, M., Erdmann, V.A., Lehrach, H., Konthur, Z., Menger, M., Arndt, P.F., Glökler, J. (2011). Probing the SELEX Process with Next-Generation Sequencing. PLOS ONE, 6(12), e29604. https://doi.org/10.1371/journal.pone.0029604
  • Schütze, T., Arndt, P. F., Menger, M., Wochner, A., Vingron, M., Erdmann, V. A., Lehrach, H., Kaps, C., & Glökler, J. (2010). A calibrated diversity assay for nucleic acid libraries using DiStRO—a Diversity Standard of Random Oligonucleotides. Nucleic Acids Research, 38(4), e23-e23. https://doi.org/10.1093/nar/gkp1108
  • Menger, M. (2009). Aptamere – Generierung und Applikation. GenomXPress 1.09, 9(1), 17-19.
  • Wochner, A., Menger, M., Orgel, D., Cech, B., Rimmele, M., Erdmann, V. A., & Glökler, J. (2008). A DNA aptamer with high affinity and specificity for therapeutic anthracyclines. Analytical Biochemistry, 373(1), 34-42. https://doi.org/https://doi.org/10.1016/j.ab.2007.09.007
  • Wochner, A., Menger, M., & Rimmele, M. (2007). Characterisation of aptamers for therapeutic studies. Expert Opinion on Drug Discovery, 2(9), 1205-1224. https://doi.org/10.1517/17460441.2.9.1205
  • Wochner, A., Cech, B., Menger, M., Erdmann, V. A., & Glökler, J. (2007). Semi-automated selection of DNA aptamers using magnetic particle handling. BioTechniques, 43(3), 344-353. https://doi.org/10.2144/000112532
  • Menger, M., Glökler, J., & Rimmele, M. (2006). Application of Aptamers in Therapeutics and for Small-Molecule Detection. In V. Erdmann, J. Barciszewski, & J. Brosius (Eds.), RNA Towards Medicine (pp. 359-373). Springer Berlin Heidelberg. https://doi.org/10.1007/3-540-27262-3_18