Experimental and computational evidence for hydrogen bonding interaction between 2′-deoxyadenosine conjugate adduct and amino-terminated organic film on Si(001)

• DNA base adduct was immobilized onto amino-terminated silicon surface.
• Hydrogen bonds were observed between aminosilane molecules and deoxyribose ring.
• Fluorescent film was characterized by spectroscopy and microscopy techniques.

A simple method for immobilization of malonaldehyde-acetaldehyde conjugate adduct with DNA base onto an amino-terminated surface of silicon from water solution is proposed. The Si(001) surface which contains OH groups was modified with 3-aminopropyltrimethoxysilane (APTMS) to serve as a linker between the silica surface and the organic adduct. The 2′-deoxyadenosine adduct was adsorbed on the APTMS/Si surface from acetonitrile/water solution. This nucleoside derivative is stable under laboratory conditions and emits a natural fluorescence, allowing for its adsorption on the APTMS/Si surface to be easily verified by fluorescence microscopy, non-contact atomic force microscopy and attenuated total reflectance Fourier transform infrared spectroscopy. The degree of surface coverage by the adduct was evaluated by X-ray photoelectron spectroscopy (XPS). Analysis of the XPS spectra revealed bands at 400.2 eV and 533.1 eV which are characteristic of a hydrogen bonded –NH2 and –OH group. This observation implies that the free electron donating –NH2 groups from the APTMS layer makes hydrogen bonds with the fluorescent adduct and immobilize it on the surface. The wetting angle of the APTMS/Si surface before and after adsorption of the nucleoside derivative does not differ significantly, which points to the involvement of an – OH group from 2′-deoxyadenosine to be involved in hydrogen bonding. These experimental results were further supported using quantum chemical calculations to demonstrate that the 2′deoxyadenosine adduct makes hydrogen bonds with the APTMS molecule. Furthermore, this hydrogen bond involves the –NH2 group from APTMS and –OH group at carbon atoms C3 and C6 from the deoxyribose ring of 2′deoxyadenosine.