A single-molecule barcoding system using nanoslits for DNA analysis

doi:10.1073/pnas.0611151104

A single-molecule barcoding system using nanoslits for DNA analysis

*Laboratory for Molecular and Computational Genomics, Laboratory of Genetics, and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706;
^†Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706;
^‡Complex Fluids Theory, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands; and
^§Department of Chemical and Biological Engineering, University of Wisconsin, 1415 Engineering Drive, Madison, WI 53706

Communicated by David E. Housman, Massachusetts Institute of Technology, Cambridge, MA, December 14, 2006 (received for review November 12, 2006)

Abstract

Molecular confinement offers new routes for arraying large DNA molecules, enabling single-molecule schemes aimed at the acquisition of sequence information. Such schemes can rapidly advance to become platforms capable of genome analysis if elements of a nascent system can be integrated at an early stage of development. Integrated strategies are needed for surmounting the stringent experimental requirements of nanoscale devices regarding fabrication, sample loading, biochemical labeling, and detection. We demonstrate that disposable devices featuring both micro- and nanoscale features can greatly elongate DNA molecules when buffer conditions are controlled to alter DNA stiffness. Furthermore, we present analytical calculations that describe this elongation. We also developed a complementary enzymatic labeling scheme that tags specific sequences on elongated molecules within described nanoslit devices that are imaged via fluorescence resonance energy transfer. Collectively, these developments enable scaleable molecular confinement approaches for genome analysis.

Footnotes

^¶To whom correspondence should be sent at the ∗ address. E-mail: dcschwartz{at}facstaff.wisc.edu
Author contributions: K.J., D.M.D., and D.C.S. designed research; K.J. and D.M.D. performed research; K.J., T.O., R.R., and D.F. contributed new reagents/analytic tools; K.J., D.M.D., T.O., J.J.d.P., M.D.G., and D.C.S. analyzed data; and K.J., D.M.D., T.O., and D.C.S. wrote the paper.
The authors declare no conflict of interest.
This article contains supporting information online at www.pnas.org/cgi/content/full/0611151104/DC1.
Abbreviations:

PDMS,

poly(dimethylsiloxane);

ddNTP,

dideoxyribonucleotide;

TE,

Tris–EDTA.