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

Aptamers – Smart Binding Molecules

From Selection to Application

Aptamers are short, single-stranded DNA or RNA molecules that, due to their distinct three-dimensional structures, bind with high affinity and specificity to targets such as proteins, small molecules, or entire cells. This unique capability makes them versatile binding molecules with exceptional adaptability and extensive applications in diagnostics, therapeutics, and environmental and food testing.

Fraunhofer IZI-BB has extensive expertise in the selection, optimization, and functionalization of custom-designed aptamers. The development process is based on automated in vitro selection (SELEX) and efficient monitoring and process control methods. Our extensive infrastructure, which includes an S2 and toxin laboratory as well as state-of-the-art cell culture facilities, enables the generation of aptamers for a wide variety of targets.

We place a particular emphasis on the development of innovative aptamer-based detection systems, such as lateral-flow tests or aptasensors, which enable rapid, precise, and cost-effective analysis with low detection limits. As a result, we provide modern biotechnology with powerful new tools capable of detecting virtually any type of target.

Chracteristics and Benefits of the Technology

  • Remarkable alternative to antibodies: Due to their simple chemical synthesis, high stability, and low immunogenicity, aptamers represent a cost-effective and versatile alternative to conventional antibodies.
  • Diagnostic biosensors: Aptamers are used as highly specific binding molecules in biosensors to detect small molecules, proteins, viruses, bacteria, and cells.
  • Imaging and detection: Aptamers can be conjugated with fluorescent dyes or nanoparticles to visualize biological structures.
  • Therapeutic applications: Aptamers serve as drug inhibitors by specifically binding to disease-relevant proteins or receptors and blocking their function.
  • Targeted drug delivery: Aptamers enable the precise targeting of specific cells or tissues, thereby supporting targeted drug delivery.
  • Research tools: Aptamers are valuable tools for studying molecular interactions, as they can even recognize immunogenic target molecules or specific protein conformations that are difficult to detect with antibodies.

 

Engage our expertise to drive your research forward.

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Our Contribution to Your Project

  • Development of customized DNA and RNA aptamers with high target affinity and selectivity.
  • Cell-based, capture-based, or classical SELEX – tailored to target and application.
  • Parallelized development that accounts for diverse application  conditions, increasing the prospects of success. 
  • Complete characterization of the aptamers via sequence analysis, binding kinetics, and affinity assays.

© Fraunhofer IZI-BB

 
  • Aptamer development against proteins, including protein expression services.
  • Even difficult to express  proteins, such as membrane proteins, can be produced.
  • Synthesis of recombinant proteins containing non-natural amino acids
  • Synthesis of individual protein domains

 

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Cell-free and cell-based protein synthesis –

In addition to conventional, cell-based production, another key focus at Fraunhofer IZI-BB is cell-free protein synthesis. This method not only enables faster production times and makes the synthesis process more cost-effective, but also makes the process more flexible and easier to control.

 

The SELEX Process for Aptamer Development

Illustration des SELEX-Prozesses

 

 

1) Starting library: A large, random collection of DNA or RNA sequences is synthesized.

2) Selection: The library is incubated with the desired target (e.g., protein, small molecule, cell), and only matching sequences bind. All remaining sequences are removed.

3) Enrichment: Bound sequences are separated from the target structure and subsequently amplified using PCR.

4) Repetition and sequencing: Several (~6–9) selection cycles are performed until highly specific aptamers are produced; sequencing is performed at the end.

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LinCA: Analysis of Central Nervous System Diseases

Unlocking the vast diagnostic potential of cerebrospinal fluid

© Fraunhofer IZI-BB
The iterative integration of “low-input cell capture,” “low-input metabolomics/proteomics,” and “low-input genomics/transcriptomics” in LinCA for the identification and validation of predictive biomarkers.

LinCA (Low‑input CSF Analysis) addresses the urgent need for sensitive biomarker methods, as reliable diagnostic and predictive markers are lacking for many diseases, particularly those affecting the central nervous system. Cerebrospinal fluid (CSF), due to its immediate proximity to the central nervous system, offers a high diagnostic potential. However, CFS samples require novel technologies due to low analyte concentrations. This project will create a modular low-input omics platform that combines innovative microfluidic separation of very low cell counts with fluorescence-based detection using selective, high-affinity aptamers, as well as state-of-the-art molecular analyses of minimal amounts of proteins, metabolites, and DNA. The platform will be validated in clinical networks based on two use cases: mutation detection in CSF for LM (leptomeningeal metastases) and the identification and validation of predictive biomarkers for disease progression in MS (multiple sclerosis). Potential clients range from pharmaceutical and biotech companies to diagnostic and cell sorting technology providers who benefit from new binding molecules, selective cell separation, and validated biomarker methods.

LEGIOPLAS: Measurement System with a Plasmonic Aptamer Sensor Chip

On-site analysis of Legionella contamination in potable water systems

Entwurf des mobilen Legionellen-Messsystems, das im BMBF-Verbundprojekt LEGIOPLAS entwickelt wird.
© ECH Elektrochemie Halle GmbH
Entwurf des mobilen Legionellen-Messsystems, das im BMBF-Verbundprojekt LEGIOPLAS entwickelt wird.

LEGIOPLAS is an interdisciplinary research project aimed at developing a mobile, photonics-based measurement system for the rapid detection of Legionella bacteria in drinking water. Instead of the conventional laboratory cultivation method (which takes approximately two weeks to yield results), a plasmonic sensor is designed to detect Legionella bacteria – including epidemiologically relevant subspecies such as Legionella pneumophila serogroup 1 – directly on-site and nearly in real time. To achieve this, novel nanophotonic structures are combined with specifically binding aptamers and integrated into a portable device with an automated measurement process. The system is intended to enable a rapid assessment of Legionella contamination, support early countermeasures, and thus make drinking water hygiene safer, more efficient, and more cost-effective. In the long term, the developed measurement principle can also be applied to other analytes relevant to public health. 

APTACHIP: Aptamer-based Biosensor

Aptamer array chip for real-time quantification of monoclonal antibodies in a bioreactor (EuroTransBio)

Logo-EuroTransBio

The goal of the APTACHIP project is to develop an aptamer-based biosensor capable of measuring biochemical species in a bioreactor’s medium in real time. To demonstrate its functionality (proof of concept), the aptasensor will initially be designed to detect monoclonal antibodies. In the future, this biosensor could be used for the quantitative detection of various chemical species and, above all, for optimizing the nutrient supply to a bioreactor. In addition to the bioreactor market, the aptasensor concept is to be adapted for use in the fields of water monitoring, food safety, and industrial process control through further development efforts following the project.

Methods

  • Target-adapted design of a nucleic acid starting library
  • Automated in vitro selection process (SELEX) for the enrichment of binders and simultaneous monitoring
  • Comprehensive characterization of the aptamers via sequence analysis, affinity studies (FLAA, EMSA, and FACS), and determination of binding constants (SPR, MST, and ITC)
  • Optimization of aptamers through truncation, mutagenesis, chemical modification, or “doped” SELEX
  • Validation of functionality in application-relevant models

 

Equipment

  • Molecular biology laboratories with biosafety levels S1 and S2
  • Beckman Coulter Biomek i7 (MC96, Span-8, Orbital Shaker, Peltier Heating and Shaking, Thermo KingFisher Presto, Alpaqua Magnum FLX Magnetic Plate, Biomel Pogo Tube Chiller, Wash Station MC96, Thermo ATC 96-Well Thermal PCR Cycler, BioTek Epoch 2 Spectrophotometer)
  • PCR UV3/HEPA Workstation from Analytik Jena
  • Illumina MiniSeqTM
  • Implen NP80
  • CLARIOstarPlus microtiter plate fluorometer from BMG Labtech
  • Cytiva Biacore 1S+
  • Nanotemper Monolith NT.115
  • Sony FACS SH800S
  • Malvern MicroCal PEAQ-ITC

 

 

 

Project LinCA
  • Fraunhofer ITMP, Frankfurt/Göttingen
  • Fraunhofer ITEM-R, Regensburg
Project APTACHIP
  • Fraunhofer IKTS, Dresden
  • GeSim GmbH
  • Ipratech SA – Belgium
  • Multitel asbl – Belgium

 

 

 

 

 

 

  • Reck J., Mihov K., Jakob T.H., Dreymann N., El Agami H., Plesshoff S., Mykhailiuk K., Weigel W., Jungmann P., Wiglenda T., Schleunitz A., Freund W., Kresse M., Weigel M., Qian T., Amberg M., Von Emden L., Winklhofer P., Keuer C., Schuler B., Zawadzki C., De Felipe D., Menger M.M., Kleinert M., Keil N., Schell M. (2025), Demonstration of a Si3N4 Microring Resonator-Based Aptasensor for Human Urokinase-type Plasminogen Activator (uPA) Detection in Point-of-Care Diagnostics, Annu Int Conf IEEE Eng Med Biol Soc, 2025:1-6, https://doi.org/10.1109/EMBC58623.2025.11253292.
  • De Pascali M.C., Dreymann N., Menger M.M., Rant U., Engelen W. (2025), Kinetic screening of nucleic acid ligand libraries for hit identification, binding mode characterization, and sequence optimization, Sensing and Bio-Sensing Research, 49, 100840, https://doi.org/10.1016/j.sbsr.2025.100840.
  • Subhashini N., Kerler Y., Menger M.M., Böhm O., Witte J., Stadler C., Griberman A. (2024), Enhancing Colorimetric Detection of Nucleic Acids on Nitrocellulose Membranes: Cutting-Edge Applications in Diagnostics and Forensics, Biosensors, 14(9), 430, https://doi.org/10.3390/bios14090430.
  • Menger M.M., Yarman A., Oktay A., Scheller F.W. (2023), Molekularer Abdruck oder Selektion bei der Erzeugung biomimetischer Specifyer, BIOspektrum (Heidelb.), 29(7), 806-809, https://doi.org/10.1007/s12268-023-2064-y.
  • 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
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  • 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