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Research Article

Deposition of DNA Rafts on Cationic SAMs on Silicon [100]

Koshala Sarveswaran,^† Wenchuang Hu,^‡ Paul W. Huber,^† Gary H. Bernstein,^§ and Marya Lieberman*^†

Departments of Chemistry and Biochemistry and of Electrical Engineering, University of Notre Dame, Notre Dame, Indiana 46556, and Department of Electrical Engineering, University of Texas at Dallas, Dallas, Texas 75083

Langmuir, 2006, 22 (26), pp 11279–11283

DOI: 10.1021/la0615948

Publication Date (Web): November 15, 2006

†

Department of Chemistry and Biochemistry, University of Notre Dame.

‡

University of Texas at Dallas.

Department of Electrical Engineering, University of Notre Dame.

To whom correspondence should be addressed. E-mail: mlieberm@ nd.edu.

Abstract

We demonstrate a guided self-assembly approach to the fabrication of DNA nanostructures on silicon substrates. DNA oligonucleotides self-assemble into “rafts” 8 × 37 × 2 nm in size. The rafts bind to cationic SAMs on silicon wafers. Electron-beam lithography of a thin poly(methyl methacrylate) (PMMA) resist layer was used to define trenches, and (3-aminopropyl)triethoxysilane (APTES), a cationic SAM precursor, was deposited from aqueous solution onto the exposed silicon dioxide at the trench bottoms. The remaining PMMA can be cleanly stripped off with dichloromethane, leaving APTES layers 0.7−1.2 nm in thickness and 110 nm in width. DNA rafts bind selectively to the resulting APTES stripes. The coverage of DNA rafts on adjacent areas of silicon dioxide is 20 times lower than on the APTES stripes. The topographic features of the rafts, measured by AFM, are identical to those of rafts deposited on wide-area SAMs. Binding to the APTES stripes appears to be very strong as indicated by “jamming” of the rafts at a saturation coverage of 42% and the stability to repeated AFM scanning in air.

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