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Proceedings Paper

Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA
Author(s): Jonathan Varsanik; William Teynor; John LeBlanc; Heather Clark; Jeffrey Krogmeier; Tian Yang; Kenneth Crozier; Jonathan Bernstein
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Paper Abstract

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.

Paper Details

Date Published: 16 February 2010
PDF: 12 pages
Proc. SPIE 7577, Plasmonics in Biology and Medicine VII, 75770Q (16 February 2010); doi: 10.1117/12.841165
Show Author Affiliations
Jonathan Varsanik, Massachusetts Institute of Technology (United States)
The Charles Stark Draper Lab., Inc. (United States)
William Teynor, The Charles Stark Draper Lab., Inc. (United States)
John LeBlanc, The Charles Stark Draper Lab., Inc. (United States)
Heather Clark, The Charles Stark Draper Lab., Inc. (United States)
Jeffrey Krogmeier, U.S. Genomics (United States)
Tian Yang, Harvard Univ. (United States)
Kenneth Crozier, Harvard Univ. (United States)
Jonathan Bernstein, The Charles Stark Draper Lab., Inc. (United States)

Published in SPIE Proceedings Vol. 7577:
Plasmonics in Biology and Medicine VII
Tuan Vo-Dinh; Joseph R. Lakowicz, Editor(s)

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