Design of photocontrollable DNA chip by self-assembled monolayer method

In this study, a new photocontrollable DNA chip was designed on Si(100) wafer. The photo-controllable substrate was prepared by azobenzene-containing self-assembled monolayers (SAMs) on the Si(100) via chemisorption of 3-glycidoxypropyltrimethoxysilane (GPTS) and 4-(4?-aminophenylazo)benzoic acid (APABA). Photosensitive APABA was synthesized by using Schündehütte method and characterized by FTIR, NMR and LC-MS. The azobenzene monolayers were formed on Si(100) surfaces by GPTS linkages. The modified surfaces were characterized by X-ray photoelectron spectroscopy (XPS), contact angle analysis and atomic force microscopy (AFM) techniques. The reversible photoswitching performances of APABA molecules were investigated by UV Spectroscopy in DMSO solution. In order to understand and control this reversible photoswitching mechanism, contact angle measurements were performed by using a variety of liquids after UV and visible light irradiation. These contact angle results were used to calculate the components of the APABA-modified surface energy under UV and visible light with the aid of the Lifshitz?van der Waals/acid?base approach. The total surface energies of photoswitchable surfaces after visible and UV light irradiation were calculated as 37.28 mJ/m2 and 36.95 mJ/m2, respectively. To prepare a photo-controllable DNA chip, Cy3 labeled amino-terminated single stranded probe-DNA arrays were then immobilized onto the photoswitchable surface. Using fluorescence microscopy, the probe-DNA concentration and the incubation time were investigated. The optimum hybridization conditions were studied with Cy5 labeled complementary-DNA using fluorescence microscopy. In addition, the photocontrolling of DNA hybridizations onto prepared surfaces were verified by confocal microscopy after vis and UV light irradiation. The percentenge hybridization ratios for the on and off state of the DNA chip were calculated as 61% and 5%, respectively. Furthermore, the theoretical calculations were performed by using Density Functional Theory (DFT). The binding mechanisms and energies of APABA molecules on the epoxy-terminated Si(100)-(2x2) surfaces were theoretically investigated. Firstly, two possible models for chemisorption site of the trans-APABA molecule on the epoxy-terminated surface were considered; (i) amino-site binding (Model 1) and (ii) carboxyl-site binding (Model 2). The results showed that the Model 1 was energetically more favorable than Model 2 by 0.43 eV. Secondly, trans-APABA molecule was folded at different angles to obtain cis-APABA molecule on the surface. As a result, trans-surfaces were found energetically more favorable than cis-surfaces by 1.65 eV.