Biosensors and Bioelectronics 26 (2011) 2085–2089 Contents lists available at ScienceDirect Biosensors and Bioelectronics journal homepage: www.elsevier.com/locate/bios Size-controllable quartz nanostructure for signal enhancement of DNA chip Jung Suk Kim a,1 , Jae Bum Cho b,1 , Bo Gi Park c , Wonbae Lee d , Kyu Back Lee c,d,∗ , Min-Kyu Oh b,∗∗ a Department of Biomedical Engineering, College of Medicine, Korea University, Anam-dong 5-1, Seoul 136-705, Republic of Korea b Department of Chemical and Biological Engineering, Korea University, Anam-dong 5-1, Seoul 136-713, Republic of Korea c Department of Interdisciplinary Bio/Micro System Technology, College of Engineering, Korea University, Anam-dong 5-1, Seoul 136-713, Republic of Korea d Department of Biomedical Engineering, College of Health Science, Korea University, San-1, Jeongneung-3-dong, Seoul 136-703, Republic of Korea article info Article history: Received 16 June 2010 Received in revised form 5 September 2010 Accepted 6 September 2010 Available online 16 September 2010 Keywords: Nanostructured quartz Nanopillar DNA chip DNA sensor abstract A mask-free, cost-effective dry-etching method for the fabrication of height- and spacing-controlled, pillar-like nanostructures was established in order to detect DNA molecules. The height and spacing of the quartz nanostructure were regulated by successive O 2 and CF 4 reactive ion etching times. The height and spacing of the nanostructures were tuned between 118 and 269 nm and between 107 and 161 nm, respectively. Probe DNA was immobilized on the structure and hybridized with fluorescently-labeled target DNA. Increases in the height and spacing of the nanopillar structure positively correlated with the fluorescence intensity of bound DNA. Usage of the nanostructure increased the DNA detection limit by up to 100-fold. © 2010 Elsevier B.V. All rights reserved. 1. Introduction Recently, numerous studies on fabrication of nanostructures and their applications to biotechnology have been reported (Kaji et al., 2003; Ogawa et al., 2007; Oillic et al., 2007b; Rosi and Mirkin, 2005; Anandan et al., 2006). A nanopattern of well-defined height and spacing generally offers several advantages for improving the sensing ability of a biosensor with several reasons. The first is increased surface area with high aspect ratio for the immobiliza- tion of more sensing probes. Second, appropriate spacing between the immobilized probes on the nanostructure enhances the acces- sibility of target materials (Oillic et al., 2007b). Finally, in an optical sensing system, a patterned surface can reduce the quenching effect of fluorescent signal materials by controlling immobilization and spacing. The fabrication of silicon-based high-aspect-ratio nanos- tructures is performed either by nanolithography followed by deep RIE (Reactive Ion Etching) or nanomolding (Choi et al., 2009; Fu et al., 2009). However, such methods still remain costly and problem- atic in the point that those methods still require expensive masks or master molds, and the cost for fabricating a mask or a master mold increases exponentially as the required resolution gets smaller and smaller in nanometer scale. Therefore, production of a nanopattern with well-defined height and spacing via a simple low-cost method ∗ Corresponding author. Tel.: +82 2 940 2882; fax: +82 2 929 8044. ∗∗ Corresponding author. Tel.: +82 2 3290 3308; fax: +82 2 926 6102. E-mail addresses: kblee@korea.ac.kr (K.B. Lee), mkoh@korea.ac.kr (M.-K. Oh). 1 These authors contributed equally to this work. is a crucial requirement for the successful construction of a highly sensitive biosensor system. We previously developed an effective method for fabricating high-aspect-ratio pillar-like nanostructures on a quartz surface (Lee et al., 2010). Our method finely controls the spacing and height of the resulting nanopattern in nanometer-scale resolution over several centimeters by simple two-step reactive ion etching (RIE) with O 2 and CF 4 plasma without any expensive mask, additional equipment or complicated technology. The spacing was controlled by the O 2 RIE time, and the height and shape of features in the nanopattern were mainly controlled by CF 4 RIE time. DNA chips, also called as DNA microarrays, have been devel- oped to analyze the concentration of specific DNA of which the sequences are related to genetic disease, pathogenic microorgan- ism, or gene expression (Bittel et al., 2005; Cho et al., 2006; Ito et al., 2007; Wen et al., 2004). This technology using immobilized DNA oligonucleotides allows highly parallel analysis by hybridiza- tion process, after which the DNA chip is analyzed by various methods such as surface plasmon resonance, electrochemical sig- naling or fluorescence level (Ahmed et al., 2007; Bin Lim et al., 2008; Lao et al., 2009; Wakai et al., 2004). Although DNA chips have great potential as a high-throughput detection method, their sensitivity on planar substrates is not particularly high due to the limitation of mixing efficiency and probe immobilization capacity (Oillic et al., 2007a). Therefore, pillar-like nanostructures have been synthesized on solid substrate for the detection of biomolecules (Kuwabara et al., 2008; Murthy et al., 2008; Park et al., 2009). In this study, we controlled the height and spacing of pillar-like nanostructures and examined their impact on DNA detection sen- 0956-5663/$ – see front matter © 2010 Elsevier B.V. All rights reserved. doi:10.1016/j.bios.2010.09.010