Covalent attachment of shape-restricted DNA molecules on amine-functionalized Si(1 1 1) surface

In designing modern microelectronic and sensing devices based on biological molecules, the underlying scientific questions focus on the ability to form a well-defined and stable interface between biological molecules and the base of electrical devices. This manuscript addresses the ability to form such an interface between silicon and various DNA molecules placed on a chemically modified self-assembled monolayer (SAM). More importantly, this work explores the possibility of designing biochemical binding sites located at a predetermined distance from the solid semiconductor surface utilizing shape-restricted DNA molecules with strategically placed functional groups that can serve as anchors. Here, for the first time we combine microscopic and spectroscopic analytical techniques with the design of geometrically-restricted thiol-DNA molecules not only to prove the selective covalent binding of these molecules to the Si(1 1 1) surface modified with the 11-amino-1-undecene self-assembled monolayers but also to analyze the geometry of produced structures. Thus, a sharp and well-defined interface with a specific distance between the potential binding site and semiconductor surface for a biochemical sensor can be built. The binding between the thiol-DNA and the amino-groups terminating the monolayer is achieved by using a sulfo-succinimidyl 4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (SSMCC) crosslinker molecule. The shape-restricted thiol-DNA is anchored to the surface via the formation of covalent bonds, as confirmed by combining biochemical investigation with X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary-ion mass spectroscopy (ToF-SIMS). Atomic force microscopy (AFM) is used to compare the well-defined but non-specific binding of the designed DNA on mica with that of selective covalent binding on SAM-covered Si(1 1 1). This approach allows for unambiguous assignment of the nature of chemical interaction between the DNA molecules and the surface and for the design of covalently bound geometrically defined biointerfaces for future applications.