title: Influence of nanometric holes on the sensitivity of a waveguide-mode sensor: label-free nanosensor for the analysis of RNA aptamer-ligand interactions.
abstract: Evanescent-field-coupled (EFC) waveguide-mode sensors can be used to detect nucleic acids or proteins from the changes in the local index of refraction upon adsorption of the target molecule on a waveguide surface. We recently described an EFC waveguide-mode sensor in which nanometric holes on a waveguide film resulted in an improved sensitivity in the analysis of the interactions of biomolecules. In the present study, we have shown that sensitivity depends upon the diameter of the holes, where increase in diameter of holes increases spectral shift resulting in an improved sensitivity. Using this improved EFC waveguide-mode sensor, we could detect interactions between RNA and a small ligand, cyanocobalamin (vitamin B 12), and between RNA and a protein (human coagulation factor IXa). These two interactions were monitored on surfaces modified with biotin-streptavidin-biotin and N-(2-trifluoroethanesulfonatoethyl)- N-(methyl)triethoxysilylpropyl-3-amine, respectively.
authors.affiliation: Center for Applied Near Field Optics Research (CAN-FOR), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan. gopi-subashchandrabose@aist.go.jp
authors.forename: Subash C B
authors.initials: SC
authors.lastname: Gopinath
authors.forename: Koichi
authors.initials: K
authors.lastname: Awazu
authors.forename: Makoto
authors.initials: M
authors.lastname: Fujimaki
authors.forename: Katsuaki
authors.initials: K
authors.lastname: Sugimoto
authors.forename: Yoshimichi
authors.initials: Y
authors.lastname: Ohki
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Komatsubara
authors.forename: Junji
authors.initials: J
authors.lastname: Tominaga
authors.forename: Kailash C
authors.initials: KC
authors.lastname: Gupta
authors.forename: Penmetcha K R
authors.initials: PK
authors.lastname: Kumar
mesh_terms: D052157:Aptamers, Nucleotide / Q000032:analysis* / Q000378:metabolism*; D015374:Biosensing Techniques / Q000379:methods*; D001710:Biotin / Q000378:metabolism; D008024:Ligands; D036103:Nanotechnology / Q000295:instrumentation / Q000379:methods*; D011485:Protein Binding; D012680:Sensitivity and Specificity; D013194:Staining and Labeling; D019809:Streptavidin / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D001710:Biotin; D019809:Streptavidin