Minimizing DNA microarrays to a single molecule per spot: using zero-mode waveguide technology to obtain kinetic data for a large number of short oligonucleotide hybridization reactions

Jens Sobek; Hubert Rehrauer; Gerrit Kuhn; Ralph Schlapbach

doi:10.1117/12.2213325

22 April 2016 Minimizing DNA microarrays to a single molecule per spot: using zero-mode waveguide technology to obtain kinetic data for a large number of short oligonucleotide hybridization reactions

Jens Sobek, Hubert Rehrauer, Gerrit Kuhn, Ralph Schlapbach

Author Affiliations +

Proceedings Volume 9725, Frontiers in Biological Detection: From Nanosensors to Systems VIII; 97250M (2016) https://doi.org/10.1117/12.2213325
Event: SPIE BiOS, 2016, San Francisco, California, United States

Abstract

We have shown recently that the hybridization of short oligonucleotides can be studied in a zero-mode waveguide nanostructure (ZMW) chip using a modified DNA sequencer.[1] Here we present an extension of this method enabling the parallel measurement of kinetic constants of a large number of hybridization reactions on a single chip. This can be achieved by immobilization of a mixture of oligonucleotides, which leads to a statistical and random distribution of single molecules in the 150’000 ZMWs of a SMRT™ cell. This setup is comparable to a classical microarray with ZMWs in place of spots but unknown allocation of probes. The probe surface density is reduced by a factor of ~10¹⁰allowing the study of hybridization in the absence of interactions with neighboring probes. Hybridization with a dye labelled oligonucleotide results in trains of fluorescence pulses from which interpulse durations (IPDs) and pulse widths (PWs) can be extracted. Since the identity of a probe in a ZMW is unknown, the immobilized oligonucleotide is sequenced in a subsequent step. After mapping the fluorescence traces to the sequence, the association and dissociation rate constant for each oligonucleotide can be calculated. By selecting suitable probes, the method can be used to determine rate constants of hybridization for a large number of mismatch oligonucleotides in a single measurement and at single-molecule level.

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Citation Download Citation

Jens Sobek, Hubert Rehrauer, Gerrit Kuhn, and Ralph Schlapbach "Minimizing DNA microarrays to a single molecule per spot: using zero-mode waveguide technology to obtain kinetic data for a large number of short oligonucleotide hybridization reactions", Proc. SPIE 9725, Frontiers in Biological Detection: From Nanosensors to Systems VIII, 97250M (22 April 2016); https://doi.org/10.1117/12.2213325

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