Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets

*Walter Schottky Institut, Technische Universität München, 85748 Garching, Germany;
^‡Fujitsu Laboratories Ltd., Atsugi 243-0197, Japan; and
^§Institut für Halbleitertechnik, Technische Universität Braunschweig, 38106 Braunschweig, Germany

Edited by Charles R. Cantor, Sequenom Inc., San Diego, CA, and approved September 10, 2007 (received for review April 30, 2007)

Abstract

We report a method to detect label-free oligonucleotide targets. The conformation of surface-tethered probe nucleic acids is modulated by alternating electric fields, which cause the molecules to extend away from or fold onto the biased surface. Binding (hybridization) of targets to the single-stranded probes results in a pronounced enhancement of the layer-height modulation amplitude, monitored optically in real time. The method features an exceptional detection limit of <3 × 10⁸ bound targets per cm² sensor area. Single base-pair mismatches in the sequences of DNA complements may readily be identified; moreover, binding kinetics and binding affinities can be determined with high accuracy. When driving the DNA to oscillate at frequencies in the kHz regime, distinct switching kinetics are revealed for single- and double-stranded DNA. Molecular dynamics are used to identify the binding state of molecules according to their characteristic kinetic fingerprints by using a chip-compatible detection format.

Footnotes

^†To whom correspondence should be addressed. E-mail: rant{at}wsi.tum.de
Author contributions: U.R., K.A., S.F., N.Y., M.T., and G.A. designed research; U.R., K.A., S.S., and E.P. performed research; U.R., S.S., and E.P. analyzed data; and U.R. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at www.pnas.org/cgi/content/full/0703974104/DC1.
Abbreviation:

Tm,

melting temperature.