Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA
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 Diff...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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SPIE
2010
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| Online Access: | http://hdl.handle.net/1721.1/58612 |
| _version_ | 1811084447893684224 |
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| author | Varsanik, Jonathan S. Teynor, William LeBlanc, John Clark, Heather A. Krogmeier, Jeffrey Yang, Tian Crozier, Kenneth Bernstein, Jonathan |
| author2 | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science |
| author_facet | Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Varsanik, Jonathan S. Teynor, William LeBlanc, John Clark, Heather A. Krogmeier, Jeffrey Yang, Tian Crozier, Kenneth Bernstein, Jonathan |
| author_sort | Varsanik, Jonathan S. |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T12:50:53Z |
| format | Article |
| id | mit-1721.1/58612 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T12:50:53Z |
| publishDate | 2010 |
| publisher | SPIE |
| record_format | dspace |
| spelling | mit-1721.1/586122022-09-28T10:25:22Z Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA Varsanik, Jonathan S. Teynor, William LeBlanc, John Clark, Heather A. Krogmeier, Jeffrey Yang, Tian Crozier, Kenneth Bernstein, Jonathan Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Varsanik, Jonathan S. Varsanik, Jonathan S. Plasmon resonance Optical waveguide Microfluidics Sub-wavelength resolution 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. Charles Stark Draper Laboratory Harvard Center for Microfluidic and Plasmonic Systems U.S. Genomics 2010-09-21T12:46:39Z 2010-09-21T12:46:39Z 2010-02 2010-01 Article http://purl.org/eprint/type/JournalArticle 0277-786X http://hdl.handle.net/1721.1/58612 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 en_US http://dx.doi.org/10.1117/12.841165 Proceedings of SPIE--the International Society for Optical Engineering, v. 7577 Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf SPIE SPIE |
| spellingShingle | Plasmon resonance Optical waveguide Microfluidics Sub-wavelength resolution Varsanik, Jonathan S. Teynor, William LeBlanc, John Clark, Heather A. Krogmeier, Jeffrey Yang, Tian Crozier, Kenneth Bernstein, Jonathan Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA |
| title | Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA |
| title_full | Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA |
| title_fullStr | Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA |
| title_full_unstemmed | Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA |
| title_short | Sub-wavelength plasmonic readout for direct linear analysis of optically tagged DNA |
| title_sort | sub wavelength plasmonic readout for direct linear analysis of optically tagged dna |
| topic | Plasmon resonance Optical waveguide Microfluidics Sub-wavelength resolution |
| url | http://hdl.handle.net/1721.1/58612 |
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