Single molecule interactions studied by using a modified DNA sequencer: a comparison with surface plasmon resonance

In this study we established the principles for using a commercial off-the-shelf DNA sequencer (RS, Pacific Biosciences) to measure biomolecular interactions.1,2 Binding between single oligonucleotides immobilized at the bottom of a nanowell to a complementary DNA strand was used as a model system. The influence of the labeling dye on the hybridization of a 7mer oligonucleotide was investigated. The resulting association and dissociation rate constants (kon and koff) and the calculated dissociation constants (Kd) were compared to data obtained from surface plasmon resonance (SPR) measurements. In the present study we identified a good agreement of the determined kinetic constants by the two methods investigated. DOI: https://doi.org/10.1117/12.2002953 Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-90585 Published Version Originally published at: Sobek, Jens; Schauer, Stefan; Rehrauer, Hubert; Fischer, David; Patrignani, Andrea; Landgraf, Stephan; Schlapbach, Ralph (2013). Single molecule interactions studied by using a modified DNA sequencer: a comparison with surface plasmon resonance. In: SPIE, San Francisco, 2 February 2013 2 February 2013, 85960Y. DOI: https://doi.org/10.1117/12.2002953 Single-molecule interactions studied by using a modified DNA sequencer: A comparison with surface plasmon resonance data Jens Sobek*, Stefan Schauer, Hubert Rehrauer, David Fischer, Andrea Patrignani, Stephan Landgraf, Ralph Schlapbach Functional Genomics Center Zurich, Swiss Federal Institute of Technology Zurich/University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland. Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9/I, 8010 Graz, Austria. ABSTRACT In this study we established the principles for using a commercial off-the-shelf DNA sequencer (RS, Pacific Biosciences) to measure biomolecular interactions. Binding between single oligonucleotides immobilized at the bottom of a nanowell to a complementary DNA strand was used as a model system. The influence of the labeling dye on the hybridization of a 7mer oligonucleotide was investigated. The resulting association and dissociation rate constants (kon and koff) and the calculated dissociation constants (Kd) were compared to data obtained from surface plasmon resonance (SPR) measurements. In the present study we identified a good agreement of the determined kinetic constants by the two methods investigated.