IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS, VOL. 16, NO. 4, JULY/AUGUST 2010 967 Toward A Highly Specific DNA Biosensor: PNA-Modified Suspended-Core Photonic Crystal Fibers Enrico Coscelli, Michele Sozzi, Federica Poli, Davide Passaro, Annamaria Cucinotta, Member, IEEE, Stefano Selleri, Senior Member, IEEE, Roberto Corradini, and Rosangela Marchelli Abstract—The feasibility of a biosensor for DNA detection based on suspended-core photonic crystal fibers is investigated. The pos- sibility of functionalization of the hole surface, which allows DNA strand binding, is demonstrated, along with the selective detec- tion of DNA through hybridization of immobilized peptide nucleic acid probes with their full-complementary and mismatched DNA segments. Index Terms—Biosensor, DNA, peptide nucleic acid (PNA), pho- tonic crystal fiber (PCF). I. INTRODUCTION I N RECENT years, photonic crystal fibers (PCFs), also known as microstructured optical fibers or holey fibers, have been deeply studied because of a number of unique features [1], [2]. The cross-section of such fibers is defined by an array of air-holes, running throughout the whole length, in a ma- trix of dielectric material. The light-guiding properties can be tailored with unprecedented degrees of freedom with a proper design of air-holes, relative position, size, and shape, thus mak- ing PCFs suitable for a wide range of applications, including telecommunications systems, spectroscopy, microscopy, high- power devices, and sensing. PCFs can be divided into two main categories, hollow-core fibers and solid-core fibers, based on the different guiding mechanism that they rely on. Hollow-core PCFs provide light confinement in a low-refractive-index core exploiting the photonic bandgap mechanism, which is due to the presence of a periodic lattice of holes in the cladding. Solid- core PCFs can guide light either in a high-refractive-index core, through modified total internal reflection, or in a low-refractive- index core, again exploiting the photonic bandgap provided by the microstructured region [3], [4]. Recently, both kinds of PCFs have undergone extensive research, with the aim of exploiting their unique characteristics to produce highly sensitive chemical and biological sensors [5], [6]. In fact, air-holes can be easily Manuscript received July 30, 2009; revised August 21, 2009; accepted August 31, 2009. Date of publication October 6, 2009; date of current version August 6, 2010. This work was supported in part by the European Cooperation in Science and Technology 299 action optical FIbres DEdicated to Society and in part by the Safety, Technology and Innovation in the Agro-Food Industry Laboratory of the High Technology Network of Emilia-Romagna, Italy. E. Coscelli, M. Sozzi, F. Poli, D. Passaro, A. Cucinotta, and S. Selleri are with the Department of Information Engineering, University of Parma, Parma 43100, Italy (e-mail: stefano.selleri@unipr.it). R. Corradini and R. Marchelli are with the Department of Organic and Indus- trial Chemistry, University of Parma, Parma 43100, Italy. Color versions of one or more of the figures in this paper are available online at http://ieeexplore.ieee.org. Digital Object Identifier 10.1109/JSTQE.2009.2031923 inflated or filled with gases or liquids without compromising the fiber robustness, obtaining a very long interaction length, even in the presence of very limited quantity of sample. Moreover, a hollow-core PCF’s capability to obtain light confinement in a low-index core yields the possibility to realize sample-filled core sensors [7], [8]. Sensing can also be performed through solid-core fibers, exploiting the evanescent tails of the guided mode field. Even if these fibers provide a lower field–sample interaction with respect to the hollow-core fibers, due to the fact that only a small fraction of the optical power travels in the sample-filled region, their confinement losses are lower on a broader wavelength range. Moreover, it is possible to speed up the diffusion of the sample into the holes of solid-core fibers with the realization of side accesses [9], given the fact that the presence of a periodic cladding lattice is not required by their guiding mechanism. Among solid-core fibers, suspended-core PCFs (SC-PCFs) appear to be most promising for developing efficient biologi- cal sensors, due to their high evanescent-field power fraction, which can almost reach 30% at 1550 nm for a submicrometer core diameter [10], and the capability to be designed with large air holes, which facilitate the filling with samples. Applications of SC-PCFs spanning from chemical sensing of gases and liq- uids to biological species detection have already been reported [10]–[12]. A detailed description of SC-PCFs will be given in Section II. One of the most intriguing possible applications of SC-PCFs is the selective detection of DNA. Well-established DNA anal- ysis techniques are usually performed by immobilizing a single strand of DNA on a glass chip and checking the hybridization of this strand to its complementary. A so-called functionalization treatment is required in order to allow the binding of biological species to the glass surface [13]. Hybridization is then proved through the measurement of the fluorescence signal produced by the labeled sample. The ability to perform this kind of anal- ysis, by exploiting the SC-PCFs hole surfaces instead of glass chips and by recollecting the fluorescence signal into the fiber core, can lead to a significant improvement of the sensitivity, with respect to the present technology. In this paper, the functionalization of internal surfaces of the holes of a silica SC-PCF and preliminary experimental studies on selective DNA detection are reported. Selective detection of DNA strands has already been demonstrated with polymer optical fibers [14], which have the advantage, through proper modifications of their surface, of allowing biomolecules to be 1077-260X/$26.00 © 2009 IEEE