Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA
Author(s)
Varsanik, Jonathan S.; Teynor, William; LeBlanc, John; Clark, Heather A.; Krogmeier, Jeffrey; Yang, Tian; Crozier, Kenneth; Bernstein, Jonathan; ... Show more Show less
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This work describes the development and fabrication of a novel nanofluidic flow-through sensing chip that utilizes a plasmonic resonator to excite fluorescent tags with sub-wavelength resolution. We cover the design of the microfluidic chip and simulation of the plasmonic resonator using Finite Difference Time Domain (FDTD) software. The fabrication methods are presented, with testing procedures and preliminary results. This research is aimed at improving the resolution limits of the Direct Linear Analysis (DLA) technique developed by US Genomics [1]. In DLA, intercalating dyes which tag a specific 8 base-pair sequence are inserted in a DNA sample. This sample is pumped though a nano-fluidic channel, where it is stretched into a linear geometry and interrogated with light which excites the fluorescent tags. The resulting sequence of optical pulses produces a characteristic "fingerprint" of the sample which uniquely identifies any sample of DNA. Plasmonic confinement of light to a 100 nm wide metallic nano-stripe enables resolution of a higher tag density compared to free space optics. Prototype devices have been fabricated and are being tested with fluorophore solutions and tagged DNA. Preliminary results show evanescent coupling to the plasmonic resonator is occurring with 0.1 micron resolution, however light scattering limits the S/N of the detector. Two methods to reduce scattered light are presented: index matching and curved waveguides.
Date issued
2010-02Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer ScienceJournal
Proceedings of SPIE--the International Society for Optical Engineering, v. 7577
Publisher
SPIE
Citation
Varsanik, Jonathan et al. “Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA.” Plasmonics in Biology and Medicine VII. Ed. Tuan Vo-Dinh & Joseph R. Lakowicz. ©2010 SPIE
Version: Final published version
ISSN
0277-786X
Keywords
Plasmon resonance, Optical waveguide, Microfluidics, Sub-wavelength resolution