Reconfigurable on-chip molecular analysis using DNA operationsin micro-droplets

• Project/Area Number: 23700362
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: Osaka University
• Principal Investigator: OGURA Yusuke 大阪大学, 大学院・情報科学研究科, 准教授 (20346191)
• Project Period (FY): 2011 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2012: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2011: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
• Keywords: DNAコンピュータ / 光ピンセット / 生体生命情報学 / システムオンチップ / 情報システム

Research Abstract

We studied on-chip molecular analysis in which a processing procedure can be configured dynamically. Two logic operation systems were investigated for easy analysis of DNA information. A method for identifying liquid-based microreactors was constructed using fluorescence color encoding. We demonstrated local and selective induction of DNA reactions by optical manipulation of liquid-based microreactors, and execution of DNA logic operations inside the microreactors.

Research Products

• [Journal Article] Fluorescence resonance energy transfer-based molecular logic circuit using a DNA scaffold (2012)
  • Author(s): T. Nishimura, Y. Ogura, and J. Tanida
  • Journal Title: Applied Physics Letters Volume: 101 Issue: 23 Pages: 233703-233703
  • DOI: 10.1063/1.4769812
  • Peer Reviewed
• [Journal Article] Optofluidic DNA computation based on optically manipulated microdroplets (2012)
  • Author(s): T.Nishimura, Y.Ogura, J.Tanida
  • Journal Title: Microfluidics and Nanofluidics Volume: Vol. 13 Issue: 1 Pages: 1-7
  • DOI: 10.1007/s10404-012-0934-6
  • Peer Reviewed
• [Journal Article] フォトニックDNAナノマシン (2012)
  • Author(s): 小倉裕介,西村隆宏,谷田 純
  • Journal Title: 光学 Volume: Vol. 41 Pages: 90-92
  • NAID: 10030157320
• [Journal Article] Photonic Nanoscale Automaton Based On Photo-/Heat-Regulated DNA Displacement Reactions (2012)
  • Author(s): Hiroto Sakai, Yusuke Ogura, and Jun Tanida
  • Journal Title: International Journal of Unconventional Computing Volume: Vol.8 Pages: 207-220
  • Peer Reviewed
• [Journal Article] フォトニックDNAナノマシン (2012)
  • Author(s): 小倉裕介，西村隆宏，谷田 純
  • Journal Title: 光学 Volume: 41 Pages: 90-92
  • NAID: 10030157320
• [Journal Article] Photonic Nanoscale Automaton Based On Photo-/Heat-Regulated DNA Displacement Reactions (2012)
  • Author(s): Hiroto Sakai, Yusuke Ogura, Jun Tanida
  • Journal Title: International Journal of Unconventional Computing Volume: 印刷中
  • Peer Reviewed
• [Journal Article] Large-area manipulation of microdroplets by holographic optical tweezers based on a hybrid diffractive system (2011)
  • Author(s): Y. Ogura, Y. Kazayama, T. Nishimura, J. Tanida
  • Journal Title: Applied Optics Volume: Vol.50 Issue: 34 Pages: H36-H36
  • DOI: 10.1364/ao.50.000h36
  • Peer Reviewed
• [Journal Article] Spatially parallel control of DNA reactions in optically manipulated micro-droplets (2011)
  • Author(s): Y. Ogura, T. Nishimura and J. Tanida
  • Journal Title: Journal of Nanophotonics Volume: Vol. 5 Issue: 1 Pages: 51702-51702
  • DOI: 10.1117/1.3574171
  • Peer Reviewed
• [Journal Article] DNAコンピューティングの原理と展開 (2011)
  • Author(s): 倉裕介
  • Journal Title: 生産と技術 Volume: Vol. 63 Pages: 28-33
• [Journal Article] DNAコンピューティングの原理と展開" (2011)
  • Author(s): 小倉裕介
  • Journal Title: 生産と技術 Volume: 63 Pages: 28-33
  • NAID: 40018919506
• [Presentation] Optical Manipulation of Liquid-based Microreactors in Optofluidic DNA Computation (2013)
  • Author(s): Takahiro Nishimura, Yuki Kazayama, Yusuke Ogura, and Jun Tanida
  • Organizer: in Optical trapping applications
  • Place of Presentation: Hawaii, USA
  • Year and Date: 2013-04-17
• [Presentation] リポソーム内DNA論理演算の実証 (2013)
  • Author(s): 風山祐輝,小倉裕介,谷田純
  • Organizer: 第60回応用物理学会春期学術講演会
  • Place of Presentation: 神奈川工科大学
  • Year and Date: 2013-03-29
• [Presentation] 光プログラム可能なDNA論理演算法 (2013)
  • Author(s): 小倉裕介,浅川洋平,西村隆宏,谷田 純
  • Organizer: レーザ学会学術講演会第33回年次大会
  • Place of Presentation: 姫路商工会議所
  • Year and Date: 2013-01-30
• [Presentation] Photonic Nanoscale Logic Using Fluorescence Resonance Energy Transfer on a DNA Scaffold (2012)
  • Author(s): Yusuke Ogura, Takahiro Nishimura, Hirotsugu Yamamoto, Kenji Yamada, Jun Tanida
  • Organizer: in the Second Japan-Korea Workshop on Digital Holography and Information Photonics
  • Place of Presentation: Tokushima, Japan
  • Year and Date: 2012-11-19
• [Presentation] 蛍光カラー符号化に基づく液体マイクロリア図4 リポソームの融合手順. クターの識別法 (2012)
  • Author(s): 風山祐輝, 小倉裕介, 谷田 純
  • Organizer: 日本光学会年次学術講演会 Optics & Photonics Japan 2012
  • Place of Presentation: タワーホール船堀
  • Year and Date: 2012-10-24
• [Presentation] Functional molecular sensing using photonic DNA nano-processor (2012)
  • Author(s): Yusuke Ogura, Takahiro Nishimura, Hirotsugu Yamamoto, Kenji Yamada, Jun Tanida
  • Organizer: in the 1st International Workshop on Information Physics and Computing in Nano-scale Photonics and Materials
  • Place of Presentation: Orleans, France
  • Year and Date: 2012-09-07
• [Presentation] 蛍光共鳴エネルギー移動を利用した分子入力・光出力論理回路の実装 (2012)
  • Author(s): 西村隆宏, 小倉裕介, 山田憲嗣, 山本裕紹, 谷田 純
  • Organizer: 第59回応用物理学関係連合講演会
  • Place of Presentation: 早稲田大学
  • Year and Date: 2012-03-16
• [Presentation] 光ピンセットを用いた液体マイクロリアクターのインタラクティブ制御 (2012)
  • Author(s): 風山祐輝, 小倉裕介, 鈴木宏明, 谷田純
  • Organizer: レーザー学会学術講演会第32回年次大会
  • Place of Presentation: TKP仙台カンファレンスセンター
  • Year and Date: 2012-02-01
• [Presentation] 光ピンセットを用いた液体マイクロリアクターのインタラクティブ制御 (2012)
  • Author(s): 風山祐輝, 小倉裕介, 鈴木宏明, 谷田 純
  • Organizer: レーザー学会学術講演会第32回年次大会
  • Place of Presentation: ＴＫＰ仙台カンファレンスセンター（宮城県）
• [Presentation] 蛍光共鳴エネルギー移動を利用した分子入力・光出力論理回路の実装 (2012)
  • Author(s): 西村隆宏, 小倉裕介, 山田憲嗣, 山本裕紹, 谷田 純
  • Organizer: 第59回応用物理学関係連合講演会
  • Place of Presentation: 早稲田大学（東京都）
• [Presentation] 蛍光共鳴エネルギー移動を利用したスキャフォールドDNA論理演算 (2011)
  • Author(s): 西村隆宏, 小倉裕介, 山田憲嗣, 山本裕紹, 谷田 純
  • Organizer: 日本光学会年次学術講演会Optics & Photonics Japan 2011
  • Place of Presentation: 大阪大学
  • Year and Date: 2011-11-29
• [Presentation] 光とDNAの協調によるナノ情報処理 (2011)
  • Author(s): 小倉裕介, 西村隆宏, 酒井寛人, 山本裕紹, 山田憲嗣, 谷田 純
  • Organizer: 日本光学会年次学術講演会Optics & Photonics Japan 2011
  • Place of Presentation: 大阪大学
  • Year and Date: 2011-11-29
• [Presentation] Photonic DNA Processor: A Computing DNA-Nanomachine with Sensing and Acting Functions (2011)
  • Author(s): Yusuke Ogura
  • Organizer: in BIT's 1st Annual World Congress of Nano-S&T
  • Place of Presentation: Dalian, China
  • Year and Date: 2011-10-25
• [Presentation] Bio-molecular sensing by use of DNA that can be activated and reset via photonic signals (2011)
  • Author(s): 西村隆宏, 小倉裕介, 山本裕紹, 山田憲嗣, 谷田 純
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学
  • Year and Date: 2011-09-18
• [Presentation] DNA配列置換反応を用いた光入力型DNAオートマトンの実装モデル (2011)
  • Author(s): 酒井寛人, 小倉裕介, 谷田 純
  • Organizer: 2011年度秋季第72回応用物理学会学術講演会
  • Place of Presentation: 山形大学
  • Year and Date: 2011-08-31
• [Presentation] A photonic DNA processor: concept and implementation (2011)
  • Author(s): Takahiro. Nishimura, Yusuke Ogura, Kenji Yamada, Hirotsugu Yamamoto, and Jun Tanida
  • Organizer: SPIE Optics & Photonics 2011
  • Place of Presentation: San Diego, USA
  • Year and Date: 2011-08-23
• [Presentation] Optical Manipulation of Microdroplets by Use of a Spatial Light Modulator and a Static Computer Generated Hologram (2011)
  • Author(s): Yusuke Ogura, Yuki Kazayama, Takahiro Nishimura, Jun Tanida
  • Organizer: in Information Photonics 2011
  • Place of Presentation: Ottawa, Canada
  • Year and Date: 2011-05-19
• [Presentation] Evaluation of holographic optical tweezers based on a hybrid diffractive system for manipulating microdroplets (2011)
  • Author(s): Yuki Kazayama, Takahiro Nishimura, Yusuke Ogura, Jun Tanida
  • Organizer: in Digital Holography and Three-Dimensional Imaging 2011
  • Place of Presentation: University of Tokyo, Japan
  • Year and Date: 2011-05-11
• [Presentation] Prototype demonstration of a photonic DNA processor: a photonically-controlled DNA nanomachine of sensing, computing, and actuating (2011)
  • Author(s): Takahiro Nishimura, Yusuke Ogura, Kenji Yamada, Hirotsugu Yamamoto, and Jun Tanida
  • Organizer: in 8th Annual Conference on Foundations of Nanoscience
  • Place of Presentation: Snowbird, USA
  • Year and Date: 2011-04-14
• [Presentation] Prototype demonstration of a photonic DNA processor: a photonically-controlled DNA nanomachine of sensing, computing, and actuating (2011)
  • Author(s): Takahiro Nishimura, Yusuke Ogura, Kenji Yamada, Hirotsugu Yamamoto, Jun Tanida
  • Organizer: 8th Annual Conference on Foundations of Nanoscience
  • Place of Presentation: Snowbird, USA
• [Presentation] Evaluation of holographic optical tweezers based on a hybrid diffractive system for manipulating microdroplets (2011)
  • Author(s): Yuki Kazayama, Takahiro Nishimura, Yusuke Ogura, Jun Tanida
  • Organizer: Digital Holography and Three-Dimensional Imaging 2011
  • Place of Presentation: Univ. Tokyo, Tokyo
• [Presentation] Optical Manipulation of Microdroplets by Use of a Spatial Light Modulator and a Static Computer Generated Hologram (2011)
  • Author(s): Yusuke Ogura, Yuki Kazayama, Takahiro Nishimura, Jun Tanida
  • Organizer: Information Photonics 2011
  • Place of Presentation: Ottawa Convention Centre, Canada
• [Presentation] A photonic DNA processor: concept and implementation (2011)
  • Author(s): Takahiro. Nishimura, Yusuke Ogura, Kenji Yamada, Hirotsugu Yamamoto, Jun Tanida
  • Organizer: SPIE Optics & Photonics 2011(招待講演)
  • Place of Presentation: San Diego, USA
• [Presentation] Photonic DNA Processor: A Computing DNA-Nanomachine with Sensing and Acting Functions (2011)
  • Author(s): Yusuke Ogura
  • Organizer: BIT's 1st Annual World Congress of Nano-S\&T 2011
  • Place of Presentation: Dalian, China
• [Presentation] DNA配列置換反応を用いた光入力型DNAオートマトンの実装モデル (2011)
  • Author(s): 酒井寛人, 小倉裕介, 谷田 純
  • Organizer: 2011年度秋季第72回応用物理学会学術講演会
  • Place of Presentation: 山形大学（山形県）
• [Presentation] Bio-molecular sensing by use of DNA that can be activated and reset via photonic signals (2011)
  • Author(s): 西村隆宏, 小倉裕介, 山本裕紹, 山田憲嗣, 谷田 純
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学（兵庫県）
• [Presentation] 蛍光共鳴エネルギー移動を利用したスキャフォールドDNA論理演算 (2011)
  • Author(s): 西村隆宏, 小倉裕介, 山田憲嗣, 山本裕紹, 谷田 純
  • Organizer: Optics & Photonics Japan 2011
  • Place of Presentation: 大阪大学（大阪府）
• [Presentation] 光とDNAの協調によるナノ情報処理 (2011)
  • Author(s): 小倉裕介, 西村隆宏, 酒井寛人, 山本裕紹, 山田憲嗣, 谷田 純
  • Organizer: Optics & Photonics Japan 2011
  • Place of Presentation: 大阪大学（大阪府）
• [Presentation] Functional molecular sensing using photonic DNA nano-processor
  • Author(s): Yusuke Ogura, Takahiro Nishimura, Hirotsugu Yamamoto, Kenji Yamada, Jun Tanida
  • Organizer: 1st International Workshop on Information Physics and Computing in Nano-scale Photonics and Materials (IPCN)
  • Place of Presentation: University of Orleans, France
  • Invited
• [Presentation] Photonic Nanoscale Logic Using Fluorescence Resonance Energy Transfer on a DNA Scaffold
  • Author(s): Yusuke Ogura, Takahiro Nishimura, Hirotsugu Yamamoto, Kenji Yamada, Jun Tanida
  • Organizer: The Second Japan-Korea Workshop on Digital Holography and Information Photonics (DHIP) 2012
  • Place of Presentation: University of Tokushima, Japan
  • Invited
• [Presentation] Optical Manipulation of Liquid-based Microreactors in Optofluidic DNA Computation
  • Author(s): Takahiro Nishimura, Yuki Kazayama, Yusuke Ogura, Jun Tanida
  • Organizer: Optical trapping applications
  • Place of Presentation: Waikoloa Marriott Beach Resort and Spa, Hawaii, USA
  • Invited
• [Presentation] 蛍光カラー符号化に基づく液体マイクロリアクターの識別法
  • Author(s): 風山祐輝, 小倉裕介, 谷田 純
  • Organizer: 日本光学会年次学術講演会 Optics & Photonics Japan 2012
  • Place of Presentation: タワーホール船堀（東京都）
• [Presentation] 光プログラム可能なDNA論理演算法
  • Author(s): 小倉裕介，浅川洋平，西村隆宏，谷田 純
  • Organizer: レーザ学会学術講演会第33回年次大会
  • Place of Presentation: 姫路商工会議所（兵庫県）
• [Presentation] リポソーム内DNA論理演算の実証
  • Author(s): 風山祐輝，小倉裕介，谷田純
  • Organizer: 第60回応用物理学会春期学術講演会
  • Place of Presentation: 神奈川工科大学（神奈川県）