Synthesis of mixed-sequence oligonucleotides on mesoporous silicon: chemical strategies and material stability
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NANO EXPRESS
Open Access
Synthesis of mixed-sequence oligonucleotides on mesoporous silicon: chemical strategies and material stability Monica Terracciano1,2, Ilaria Rea1, Luca De Stefano1*, Ivo Rendina1, Giorgia Oliviero2, Fabrizia Nici2, Stefano D'Errico2, Gennaro Piccialli2 and Nicola Borbone2
Abstract Rapid screening tests in medical diagnostic and environmental analysis are often based on oligonucleotide biochips. In this paper, we studied the stability of functionalized mesoporous silicon supports in the solid-phase synthesis of oligonucleotides, exploiting several chemical procedures. A 19-mer mixed sequence has been successfully synthesized on aminosilane-modified porous silicon photonic structures. The process and the materials have been characterized by optical reflectivity, atomic force microscopy and high-performance liquid chromatography. Keywords: Mesoporous silicon functionalization; DNA synthesis; Deprotection conditions; Surface stability
Background DNA chip technology has greatly evolved over the last decade, moving from pure genomics towards a number of biotechnology applications such as human disease diagnostics [1], environmental monitoring and food control [2,3]. DNA chips can be classified as a special class of biosensors since they are realized by immobilization of single-stranded oligonucleotides (ONs), the bioprobe, on a transducer surface. Any molecular interaction between the bioprobe and its ligands, such as hybridization to the complementary DNA sequence or protein binding, is then transduced into an analytical signal by an electrochemical-, optical- or surface plasmon resonancebased or electrical device, depending on the specific technology used. Porous silicon (PSi) is by far one of the most popular transducer materials due to its peculiar physical and chemical properties [4]. PSi is fabricated by electrochemical etching of crystalline silicon in aqueous hydrofluoric acid. Depending on etch time, current density and acid concentration, several porous morphologies can be obtained, from micropores (average pore size 50 nm) [5]. The resulting sponge-like matrix possesses a very large specific * Correspondence: [email protected] 1 Institute for Microelectronics and Microsystems, National Council of Research, Naples 80131, Italy Full list of author information is available at the end of the article
surface area (up to 300 m2/cm3): gases and liquids can easily get into pores, thus changing the optical, chemical and electrical properties of PSi [6]. Even if electrochemical etching induces silicon dissolution, the resulting PSi surface is smooth enough to get very good quality optical devices, also in the case of multilayered structures [7]. Periodic, or quasi-periodic, alternation of high- and lowporosity layers is used for fabrication of Bragg reflectors, microcavities and Thue-Morse sequences: all these photonic devices exhibit resonance wavelengths that can be used as monitoring peak in quantifying biomolecular interaction from the optical point of view [8-10]. The PSi surface c
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