Influence of Nanometric Holes on the Sensitivity of a Waveguide-Mode Sensor: Label-Free Nanosensor for the Analysis of RNA Aptamer−Ligand Interactions

Subash C. B. Gopinath*†, Koichi Awazu*†, Makoto Fujimaki†, Katsuaki Sugimoto‡, Yoshimichi Ohki‡, Tetsuro Komatsubara§, Junji Tominaga†, Kailash C. Gupta and Penmetcha K. R. Kumar
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, Waseda University, Shinjuku, Tokyo 169-8555, Tandem Accelerator Complex, University of Tsukuba, Tsukuba 305-8577, Japan, Institute for Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi 110 007, India, and Institute for Biological Resources and Functions, AIST, Tsukuba, Ibaraki 305-8566, Japan
Anal. Chem., 2008, 80 (17), pp 6602–6609
DOI: 10.1021/ac800767s
Publication Date (Web): August 2, 2008
Copyright © 2008 American Chemical Society
* To whom correspondence should be addressed. E-mail: gopi-subashchandrabose@aist.go.jp.
,
†

National Institute of Advanced Industrial Science and Technology (AIST).

,
‡

Waseda University.

,
§

University of Tsukuba.

,

Delhi University.

,

Institute for Biological Resources and Functions (AIST).

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 B12), 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.

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History

  • Published In Issue September 01, 2008
  • Article ASAPAugust 02, 2008
  • Received: April 17, 2008
    Accepted: July 9, 2008

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