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

Abstract

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 (k(on) and k(off)) and the calculated dissociation constants (K-d) 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.