Polymerization-Amplified Optical DNA Detection on Porous Silicon Templates Dirk Holthausen, † Roshan B. Vasani, ‡ Steven J. P. McInnes, ‡ Amanda V. Ellis, † and Nicolas H. Voelcker* ,‡ † School of Chemical and Physical Sciences, Flinders University, Bedford Park, South Australia 5042, Australia ‡ Mawson Institute, University of South Australia, Mawson Lakes, South Australia 5095, Australia * S Supporting Information ABSTRACT: A porous silicon-based optical DNA sensor is described herein, which enables rapid DNA detection. The DNA sensor relies on the specificity of the DNA base pairing in conjunction with an interferometric optical signal amplification step based on polymer formation within the porous silicon layer to detect the DNA targets in a highly selective fashion. We demonstrate that it is possible to discriminate between DNA strands exhibiting even a single nucleotide mismatch using this sensor. D NA sensing has a variety of applications, especially in medical science, forensics, ecology, and biotechnology. 1-4 Currently, the methods used for detection of DNA rely on either DNA labeling or DNA amplification using polymerase chain reaction. While these methods are widely accepted, they are also time-consuming and require the use of very sophisticated and expensive instrumentation. As a result, over the last few decades a variety of studies have focused on the development of DNA sensors that would enable the detection of minute quantities of DNA over shorter time frames. 2,5-9 Additionally, the ability to selectively discriminate between even single nucleotide mismatches is desirable for the identification of point mutations and diseases. A recent development in the field of DNA sensing involves the formation of polymers by means of controlled radical polymerization methods such as atom transfer radical polymer- ization (ATRP) 10 or reversible addition-fragmentation chain transfer polymerization (RAFT) 11 to amplify the signal of the target DNA strand binding to a capture strand immobilized on surfaces. The use of controlled radical polymerization instead of conventional polymerization methods is advantageous as the polymer growth from surfaces has been shown to be linear with respect to time, 12 which may facilitate quantitative detection. Qian et al. have used an ATRP version that is less sensitive to oxygen called activators generated by electron transfer (AGET) to detect DNA binding. 13 In their work, DNA capture strands immobilized on gold surfaces were incubated with target DNA strands modified with an ATRP initiator. Following this, the surface was immersed in the monomer mix and allowed to polymerize. Quantitative detection of DNA hybridization was performed using ellipsometry. Porous silicon (pSi) has been extensively studied for use as a biosensing platform owing to its unique optical properties. White light incident on the pSi layer reflects off the air/pSi and the pSi/Si interfaces and undergoes interference to produce Fabry-Pe ́ rot fringes that can be obtained using interferometric reflectance spectroscopy (IRS) and that, when Fourier transformed, afford an effective optical thickness (EOT) value. 14 Changes within the porous environment results in a change in the EOT, which can be easily measured in real- time. 15 An added advantage of pSi is that the high surface area affords higher sensitivity as compared to flat surfaces. However, previous studies with pSi platforms have shown that detection of hybridization of cDNA strands using IRS is difficult unless the signal is amplified by pore degradation. 16 This in turn has the disadvantage that the amplification mechanism prevents the reuse of the sensor. Herein, we present a signal amplification mechanism using pSi as the optical sensing platform where polymer growth is detected in real-time. Our method uses IRS to monitor the polymer growth from ATRP initiator-modified target DNA strands hybridized to capture strands immobilized on the pSi surface. Scheme 1 shows the experimental procedure for the fabrication (Scheme 1A) and the DNA sequences used (Scheme 1B). The pSi template was produced by electrochemical etching of highly phosphorus doped n-type silicon in 5% aqueous hydrofluoric acid in the presence of a nonionic surfactant (NCW1001). Analysis of the etched surfaces using scanning electron microscopy (SEM) revealed pores of roughly 88 ± 21 nm in diameter and a pore depth of approximately 2.3 μm (Figure S1A,B, see SI). To minimize oxidation, the freshly etched samples were immediately hydrosilylated with undecylenic acid-N-hydrox- Received: February 6, 2012 Accepted: June 27, 2012 Letter pubs.acs.org/macroletters © XXXX American Chemical Society 919 dx.doi.org/10.1021/mz300064k | ACS Macro Lett. 2012, 1, 919-921