Quantitative Real-Time Measurements of DNA Hybridization with Alkylated Nonoxidized Silicon Nanowires in Electrolyte Solution

Abstract

The quantitative, real time detection of single stranded oligonucleotides with silicon nanowires (SiNWs) in physiologically relevant electrolyte solution is demonstrated. Debye screening of the hybridization event is minimized by utilizing electrostatically adsorbed primary DNA on an amine-terminated NW surface. Two surface functionalization chemistries are compared: an amine terminated siloxane monolayer on the native SiO 2 surface of the SiNW, and an amine terminated alkyl monolayer grown directly on a hydrogen-terminated SiNW surface. The SiNWs without the native oxide exhibit improved solution-gated field-effect transistor characteristics and a significantly enhanced sensitivity to single stranded DNA detection, with an accompanying two orders of magnitude improvement in the dynamic range of sensing. A model for the detection of analyte by SiNW sensors is developed and utilized to extract DNA binding kinetic parameters. Those values are directly compared with values obtained by the standard method of surface plasmon resonance (SPR), and demonstrated to be similar. The nanowires, however, are characterized by higher detection sensitivity. The implication is that Si NWs can be utilized to quantitate the solution phase concentration of biomolecules at low concentrations. This work also demonstrates the importance of surface chemistry for optimizing biomolecular sensing with silicon nanowires.

Screening-Limited Response of NanoBiosensors

“…concentration [1][2][3][4][5] instead of the linear dependence predicted from classical theory and observed in fluorescence measurements [9] (see the list of four puzzles in section I). Numerical solution of Eqs.…”

“…2c, [7]), and (iv) anomalous time-dependence of sensor response instead of the classical Langmuir-type response (Fig. 2d, [1,2]). …”

“…Functionalized Silicon Nanowire (Si-NW) devices have been used to demonstrate detection of DNA [1][2][3] and proteins [4][5] at very low concentrations (Fig. 1a).…”

“…2a, [1][2][3][4][5]), (ii) linear dependence on pH which is crucial for protein detection (Fig. 2b, [5,6]), (iii) non-linear dependence of sensitivity on electrolyte concentration (Fig.…”

Organic Surface Modification of Silicon Nanowire-Based Sensor Devices

“…For example, (3-aminopropyl)-dimethyl-ethoxysilane (APDMES, Figure 2, silane 1b) has been used in the modification of SiNW-based devices to bind a 16-mer ss-DNA (Bunimovich, 2006). In contrast to APTES (1a), APDMES (1b) is a mono-alkoxydimethylsilane, which is a crucial difference when it comes to the monolayer quality.…”