Functional Nucleic Acids – Aptamers

The Functional Nucleic Acids – Aptamers Unit aims at developing new innovative products on the basis of aptamers. This goal comprises the generation, synthesis and functionalization of aptamers as well as the integration in diverse applications. The unit thereby seeks a close collaboration with the industry and academic institutes.

Primarily, aptamers are short, single-stranded DNA and RNA molecules with the particular feature ofbinding high-affine and high-specific targets such as antibodies. The very broad capabilities of aptamers as binding molecules are used in analytical, diagnostic and therapeutic applications.

A focus is on the generation of new aptamers by using an automatic in vitro selection process as well as a monitoring and managing process. Additionally, the unit develops of aptamer-based detection methods such as lateral flow assays or so-called aptasensors.

Methods

  • Process for generation of high-affine and high-specific RNA and DNA Aptamers
  • Semi-automatic in vitro selection process for the enrichment of target-affine nucleic acids pools including an effective monitoring and managing process
  • Sequence analysis of nucleic acids pools
  • Characterization und optimization of aptamer sequences
  • Diversity assay for nucleic acids (DANA)
  • Fluorescence dye linked aptamer assay (FLAA)
  • Surface plasmon resonance (SPR) binding studies
  • MicroScale Thermophoresis (MST) binding studies
  • Fluorescence-activated cell sorting (FACS) binding studies
  • Synthesis of RNA and DNA Aptamers including chemical modifications

Equipment

  • Molecularbiological laboratory with safety level 1 and 2
  • KingFisher Duo Magnetic Partical Processor for SELEX process
  • KingFisher BioSprint 15 Magnetic Partical Processor for SELEX process
  • PCR workstation with HEPA filter
  • Spectral photometer UV/VIS
  • Microtiterplate fluorometer
  • Microtiterplate spectral photometer
  • Biacore (X, TM T200)
  • Nanotemper (Monolith NT.115)

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

The objective of the APTACHIP project is the development of an aptamer-based multiplexed sensor for real time monitoring of the product concentration produced by mammalian cells in the growth medium of a bioreactor. First of all monoclonal antibodies are used as a product in the process in order to demonstrate the functionality of the aptasensor (proof of principle). The sensor can be used prospectively for the quantitative detection of diverse chemical molecules and can improve the quality control and the production process. Additionally, the developed aptasensor concept can be adapted for the use in the areas of water control, food safety and industrial process control.

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

  • Menger M, Yarman A, Erdőssy J, Yildiz HB, Gyurcsányi RE, Scheller FW. MIPs and Aptamers for Recognition of Proteins in Biomimetic Sensing. Biosensors (Basel). 2016 Jul 18;6(3). pii: E35. DOI dx.doi.org/10.3390/bios6030035Article
  • Hacht AV, Seifert O, Menger M, Schütze T, Arora A, Konthur Z, Neubauer P, Wagner A, Weise C, Kurreck J. Identification and characterization of RNA guanine-quadruplex binding proteins. Nucleic Acids Res. (2014), 42 (10): 6630-6644; DOI dx.doi.org/10.1093/nar/gku290. PMID: 24771345.
  • Schütze T, Wilhelm B, Greiner N, Braun H, Peter F, Mörl M, Erdmann VA, Lehrach H, Konthur Z, Menger M, Arndt PF, Glökler J. Probing the SELEX Process with Next-Generation Sequencing. PLoS ONE. (2011), 6(12): e29604; DOI dx.doi.org/10.1371/journal.pone.0029604. PMID: 22242135.
  • Schütze T, Arndt PF, Menger M, Wochner A, Vingron M, Erdmann VA, Lehrach H, Kaps C, Glökler J. A calibrated diversity assay for nucleic acid libraries using DiStRO—a Diversity Standard of Random Oligonucleotides. Nucleic Acids Res. (2010), 38(4): e23; DOI dx.doi.org/10.1093/nar/gkp1108. PMID: 19965765.
  • Menger M. Aptamere – Generierung und Applikation. GenomXPress. (2009), 1.09: 17-19.
  • Wochner A, Menger M, Orgel D, Cech B, Rimmele M, Erdmann VA, Glökler J. A DNA aptamer with high affinity and specificity for therapeutic anthracyclines. Anal Biochem. (2008), 373(1): 34-42. PMID: 17931589.
  • Wochner A, Cech B, Menger M, Erdmann VA, Glökler J. Semi-automated selection of DNA aptamers using magnetic particle handling. Biotechniques. (2007), 43(3): 344, 346, 348 passim. PMID: 17907577.
  • Wochner A, Menger M, Rimmele M. Characterisation of aptamers for therapeutic studies. Expert Opin Drug Discov. (2007), 2(9): 1205-1224. PMID: 23496129.
  • Menger M, Glokler J, Rimmele M. Application of aptamers in therapeutics and for small-molecule detection. Handb Exp Pharmacol. (2006), (173): 359-373. PMID: 16594625.