• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Investigation of hydration structures and surface charges on biomolecules by three-dimensional force mapping

Research Project

Project/Area Number 25286057
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Thin film/Surface and interfacial physical properties
Research InstitutionKyoto University

Principal Investigator

Kobayahi Kei  京都大学, 白眉センター, 特定准教授 (40335211)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2015: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2014: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2013: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
Keywords走査プローブ顕微鏡 / 原子間力顕微鏡 / FM-AFM / フォースマッピング / 固液界面
Outline of Final Research Achievements

We recently developed frequency-modulation atomic force microscopy (FM-AFM) in liquids and made it possible to explore solid-liquid interface properties such as the hydration structures and surface charges with a nanometer-scale resolution. In this project, we employed FM-AFM to study the hydration structures and surface charges of biomolecules such as DNA by using two-dimensional (2D) and three-dimensional (3D) force mapping techniques. We obtained a 3D frequency shift map on a plasmid DNA molecule in a buffer solution with 50 mM nickel chloride. The map showed complicated contrast patterns with a sub-nanometer-scale resolution, which reflect the hydration structures around the DNA molecule. We also obtained a 3D frequency shift map on a lambda DNA molecule adsorbed on a poly-L-lysine (PL) layer on a mica substrate in potassium chloride solutions. By analyzing the frequency shift versus distance curves, we estimated the charge density of the labmda DNA molecule and the PL layer.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (47 results)

All 2016 2015 2014 2013 Other

All Int'l Joint Research (1 results) Journal Article (13 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 13 results,  Acknowledgement Compliant: 3 results,  Open Access: 2 results) Presentation (32 results) (of which Int'l Joint Research: 4 results,  Invited: 2 results) Book (1 results)

  • [Int'l Joint Research] Aalto University(Finland)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Visualization of trapped charges being ejected from organic thin-film transistor channels by Kelvin-probe force microscopy during gate voltage sweeps2016

    • Author(s)
      Y. Yamagishi, K. Kobayashi, K. Noda, H. Yamada
    • Journal Title

      Applied Physics Letters

      Volume: 108 Issue: 9 Pages: 093302-093302

    • DOI

      10.1063/1.4943140

    • NAID

      120005844268

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular-scale quantitative charge density measurement of biological molecule by frequency modulation atomic force microscopy in aqueous solutions2015

    • Author(s)
      Kenichi Umeda, Kei Kobayashi, Noriaki Oyabu, Kazumi Matsushige, and Hirofumi Yamada
    • Journal Title

      Nanotechnology

      Volume: 26 Issue: 28 Pages: 285103-285103

    • DOI

      10.1088/0957-4484/26/28/285103

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Surface Potential Measurement of Fullerene Derivative/Copper Phthalocyanine on Indium Tin Oxide Electrode by Kelvin Probe Force Microscopy2015

    • Author(s)
      N. Satoh, M. Yamaki, K. Noda, S. Katori, K. Kobayashi, K. Matsushige, H. Yamada
    • Journal Title

      pn. J. Appl. Phys.

      Volume: 54 Issue: 8S1 Pages: 08KF06-08KF06

    • DOI

      10.7567/jjap.54.08kf06

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Local impedance measurement of an electrode/single-pentacene-grain interface by frequency-modulation scanning impedance microscopy2015

    • Author(s)
      T. Kimura, K. Kobayashi, and H. Yamada
    • Journal Title

      Journal of Applied Physics

      Volume: 118 Issue: 5 Pages: 055501-055501

    • DOI

      10.1063/1.4927921

    • NAID

      120005844267

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Atom-Resolved Analysis of an Ionic KBr(001) Crystal Surface Covered with a Thin Water Layer by Frequency Modulation Atomic Force Microscopy2015

    • Author(s)
      T. Arai, M.i Koshioka, K. Abe, M. Tomitori , R. Kokawa, M. Ohta, H. Yamada, K. Kobayashi, and N. Oyabu
    • Journal Title

      Langmuir

      Volume: 31 Issue: 13 Pages: 3876-3883

    • DOI

      10.1021/acs.langmuir.5b00087

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Practical aspects of Kelvin-probe force microscopy at solid/liquid interfaces in various liquid media2014

    • Author(s)
      K. Umeda, K. Kobayashi, N. Oyabu, Y. Hirata, K. Matsushige, and H. Yamada
    • Journal Title

      Journal of Applied Physics

      Volume: 116 Issue: 13 Pages: 134307-134307

    • DOI

      10.1063/1.4896881

    • NAID

      120005496652

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Accurate formula for dissipative interaction in frequency modulation atomic force microscopy2014

    • Author(s)
      K. Suzuki, K. Kobayashi, A. Labuda, K. Matsushige and H. Yamada
    • Journal Title

      Applied Physics Letters

      Volume: 105 Issue: 23 Pages: 233105-233105

    • DOI

      10.1063/1.4903484

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Direct Observation of the Influence of Additives on Calcite Hydration by Frequency Modulation Atomic Force Microscopy2014

    • Author(s)
      Y. Araki, K. Tsukamoto, R. Takagi, T. Miyashita, N. Oyabu, K. Kobayashi, and H. Yamada
    • Journal Title

      Crystal growth & design

      Volume: 14 Issue: 12 Pages: 6254-6260

    • DOI

      10.1021/cg500891j

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Photothermal excitation setup for a modified commercial atomic force microscope2014

    • Author(s)
      H. Adam, S. Rode, M. Schreiber, K. Kobayashi, H. Yamada, and A. Kuehnle
    • Journal Title

      Review of Scientific Instruments

      Volume: 85 Issue: 2

    • DOI

      10.1063/1.4864084

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular-scale investigations of structures and surface charge distribution of surfactant aggregates by three-dimensional force mapping2014

    • Author(s)
      K. Suzuki, K. Kobayashi, N. Oyabu, K. Matsushige, and H. Yamada
    • Journal Title

      The Journal of Chemical Physics

      Volume: 140 Issue: 5 Pages: 54704-54704

    • DOI

      10.1063/1.4863346

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Immunoactive two-dimensional self-assembly of monoclonal antibodies in aqueous solution revealed by atomic force microscopy2014

    • Author(s)
      S. Ido, H. Kimiya, K. Kobayashi, H. Kominami, K. Matsushige and H. Yamada
    • Journal Title

      Nature Materials

      Volume: 13 Issue: 3 Pages: 264-270

    • DOI

      10.1038/nmat3847

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Charge compensation by long-period reconstruction in strongly polar lithium niobate surfaces2013

    • Author(s)
      S. Sanna, S. Rode, R. Hoelscher, S. Klassen, C. Marutschke, K. Kobayashi, H. Yamada, W. G. Schmidt, and A. Kuehnle
    • Journal Title

      Physical Review B

      Volume: 88 Issue: 11

    • DOI

      10.1103/physrevb.88.115422

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Visualization of hydration layers on muscovite mica in aqueous solution by frequency-modulation atomic force microscopy2013

    • Author(s)
      K. Kobayashi, N. Oyabu, K. Kimura, S. Ido, K. Suzuki, T. Imai, K. Tagami, M. Tsukada, and H. Yamada
    • Journal Title

      The Journal of Chemical Physics

      Volume: 138 Issue: 18 Pages: 184704-184704

    • DOI

      10.1063/1.4803742

    • NAID

      120005439693

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Presentation] Molecular-scale analysis of hydration structures on heterogeneous surfaces by three-dimensional force mapping2015

    • Author(s)
      K. Umeda, K. Kobayashi, and H. Yamada
    • Organizer
      18th International Conference on Non-Contact Atomic Force Microscopy (NC-AFM 2015)
    • Place of Presentation
      Cassis, France
    • Year and Date
      2015-09-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Molecular-scale visualization of different DNA conformations by using FM-AFM2015

    • Author(s)
      H. Kominami, K. Kobayashi, and H. Yamada
    • Organizer
      18th International Conference on Non-Contact Atomic Force Microscopy (NC-AFM 2015)
    • Place of Presentation
      Cassis, France
    • Year and Date
      2015-09-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Visualization of biomolecules-solution interfaces by frequency modulation AFM and 3D force mapping2015

    • Author(s)
      H. Kominami, K. Kobayashi, and H. Yamada
    • Organizer
      17th International Scanning Probe Microscopy Conference (ISPM 2015)
    • Place of Presentation
      Rio de Janeiro, Brazil
    • Year and Date
      2015-06-21
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Relationship between surface structures/charges and local hydration structures studied by 3D-liquid-FM-AFM2015

    • Author(s)
      K. Umeda, K. Kobayashi, and H. Yamada
    • Organizer
      17th International Scanning Probe Microscopy Conference (ISPM 2015)
    • Place of Presentation
      Rio de Janeiro, Brazil
    • Year and Date
      2015-06-21
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] マイカ基板上に形成されるStreptavidin 2次元結晶の液中FM-AFM高分解能構造観察2015

    • Author(s)
      崔 子鵬, 宮本 眞之, 木南 裕陽, 小林 圭, 平田 芳樹, 山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] FM-AFMによる界面活性剤分子集合体構造の形成過程評価 (3)2015

    • Author(s)
      鈴木 一博, 小林 圭, 山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] 液中動作FM-AFMを用いたイオン液体の局所溶媒和構造と表面構造/電荷との相関に関する研究2015

    • Author(s)
      梅田 健一, 小林 圭, 山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-14
    • Related Report
      2014 Annual Research Report
  • [Presentation] 液中FM-AFMによる免疫グロブリンM(IgM)の抗原結合評価2015

    • Author(s)
      黄 雲飛, 木南 裕陽, 小林 圭, 山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-13
    • Related Report
      2014 Annual Research Report
  • [Presentation] 液中FM-AFMによる左巻きDNAの高分解能観察2015

    • Author(s)
      木南 裕陽, 小林 圭, 山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] FM-AFMによるStreptavidin 2次元結晶の液中高分解能観察2015

    • Author(s)
      宮本 眞之, 木南 裕陽, 崔 子鵬, 小林 圭, 山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] Molecular-scale visualization of DNA strands with non-B DNA conformations using FM-AFM in liquids2014

    • Author(s)
      H. Kominami, K. Kobayashi, and H. Yamada
    • Organizer
      22nd International Colloquium on Scanning Probe Microscopy (ICSPM22)
    • Place of Presentation
      Atagawa, Japan
    • Year and Date
      2014-12-11 – 2014-12-13
    • Related Report
      2014 Annual Research Report
  • [Presentation] Relationship between surface structures/charges and local hydration structures studied by FM-AFM in liquids2014

    • Author(s)
      K. Umeda, K. Kobayashi, and H. Yamada
    • Organizer
      The 7th International Symposium on Surface Science (ISSS-7)
    • Place of Presentation
      Matsue, Japan
    • Year and Date
      2014-11-03 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] Molecular-scale Visualization of Self-Assembled Structures of Biomolecules Using FM-AFM in Liquids2014

    • Author(s)
      H. Kominami, K. Kobayashi, and H. Yamada
    • Organizer
      The 7th International Symposium on Surface Science (ISSS-7)
    • Place of Presentation
      Matsue, Japan
    • Year and Date
      2014-11-03 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] High-resolution Imaging of IgM Antibody Molecules by FM-AFM in Aqueous Solutions2014

    • Author(s)
      Y. Huang, H. Kominami, K. Kobayashi, and H. Yamada
    • Organizer
      The 7th International Symposium on Surface Science (ISSS-7)
    • Place of Presentation
      Matsue, Japan
    • Year and Date
      2014-11-03 – 2014-11-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] 液中動作FM-AFMによる真核生物DNA複製の初期過程イメージング2014

    • Author(s)
      木南 裕陽, 日詰 光治, 荒木 弘之, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-20
    • Related Report
      2014 Annual Research Report
  • [Presentation] 液中動作FM-AFMによるIgG抗体分子6量体形成の抗体種依存性2014

    • Author(s)
      木南 裕陽, 井戸 慎一郎, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] 液中FM-AFMによる免疫グロブリンM(IgM)構造評価2014

    • Author(s)
      黄 雲飛, 木南 裕陽, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] Avidin-biotin相互作用のFM-AFMフォースマップ評価2014

    • Author(s)
      李 文尭, 鈴木 一博, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] 液中動作FM-AFMを用いた局所水和構造と表面構造/電荷の相関に関する研究(2)2014

    • Author(s)
      梅田 健一, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-19
    • Related Report
      2014 Annual Research Report
  • [Presentation] バイオセンシングに向けた機能性タンパク質のFM-AFM構造観察2014

    • Author(s)
      崔 子鵬, 木南 裕陽, 小林 圭, 平田 芳樹, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] Relationship between local hydration structures and surface structures/charges studied by liquid-FM-AFM2014

    • Author(s)
      K. Umeda, K. Kobayashi, and H. Yamada
    • Organizer
      The 17th International Conference on Non-Contact Atomic Force Microscopy
    • Place of Presentation
      Tsukuba, Japan
    • Year and Date
      2014-08-04 – 2014-08-08
    • Related Report
      2014 Annual Research Report
  • [Presentation] Molecular-scale Investigation of Antigen Binding to IgG Antibody Self-Assembly Using Frequency-Modulation AFM in Liquids2014

    • Author(s)
      H. Kominami, S. Ido, K. Kobayashi, and H. Yamada
    • Organizer
      International Conference on Nanoscience and Technology
    • Place of Presentation
      Colorado, USA
    • Year and Date
      2014-07-20 – 2014-07-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] Exploring Solid-Liquid Interfaces by Frequency Modulation Atomic Force Microscopy2014

    • Author(s)
      K. Kobayashi and H. Yamada
    • Organizer
      Atomic structure of nanosystems from first-principles simulations and microscopy experiments, Physics Boat Workshops
    • Place of Presentation
      Helsinki, Finland - Stockholm, Sweden
    • Year and Date
      2014-06-03 – 2014-06-05
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Exploring the SolidLiquid Interfaces by TwoDimensional and ThreeDimensional Force Mapping Techniques with Frequency Modulation Atomic Force Microscopy

    • Author(s)
      K. Kobayashi and H. Yamada
    • Organizer
      2013 MRS Fall Meeting and Exhibit (Symposium LL)
    • Place of Presentation
      Boston, USA
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Visualization of hydration structures at the interface between alkali halide crystal surface and aqueous solution

    • Author(s)
      F. Ito, K. Suzuki, K. Kobayashi, and H. Yamada
    • Organizer
      19th International Vacuum Congress (IVC-19) and International Conference on Nanoscience and Technology
    • Place of Presentation
      Paris, France
    • Related Report
      2013 Annual Research Report
  • [Presentation] Immunoactivity of IgG Antibody Assembly Investigated by FM-AFM

    • Author(s)
      H. Kominami, S. Ido, H. Kimiya, K. Kobayashi, and H. Yamada
    • Organizer
      12th International Conference on Atomically Controlled Surfaces, Interfaces and Nanostructures in conjunction with 21st International Colloquium on Scanning Probe Microscopy
    • Place of Presentation
      つくば国際会議場
    • Related Report
      2013 Annual Research Report
  • [Presentation] Surface Potential Mapping of Fullerene Ultrathin Films by FM-KFM

    • Author(s)
      A. Noda, K. Kobayashi, and H. Yamada
    • Organizer
      12th International Conference on Atomically Controlled Surfaces, Interfaces and Nanostructures in conjunction with 21st International Colloquium on Scanning Probe Microscopy
    • Place of Presentation
      つくば国際会議場
    • Related Report
      2013 Annual Research Report
  • [Presentation] 液中動作FM-AFMによるIgG抗体分子への抗原吸着評価

    • Author(s)
      木南裕陽, 井戸慎一郎, 木宮宏和, 小林圭, 山田啓文
    • Organizer
      第61回応用物理学会春季学術講演会
    • Place of Presentation
      青山学院大学相模原キャンパス
    • Related Report
      2013 Annual Research Report
  • [Presentation] FM-AFMの減衰係数導出法

    • Author(s)
      鈴木一博, 小林圭, 山田啓文
    • Organizer
      第61回応用物理学会春季学術講演会
    • Place of Presentation
      青山学院大学相模原キャンパス
    • Related Report
      2013 Annual Research Report
  • [Presentation] 液中動作FM-AFMを用いた局所水和構造と表面構造/電荷の相関に関する研究

    • Author(s)
      梅田健一, 小林圭, 山田啓文
    • Organizer
      第61回応用物理学会春季学術講演会
    • Place of Presentation
      青山学院大学相模原キャンパス
    • Related Report
      2013 Annual Research Report
  • [Presentation] Molecular-scale fluctuation of surfactant micelle structures on graphite

    • Author(s)
      K. Suzuki, K. Kobayashi, N. Oyabu, K. Matsushige, and H. Yamada
    • Organizer
      16th International Conference on Noncontact Atomic Force Microscopy (NC-AFM 2013)
    • Place of Presentation
      University of Maryland, USA
    • Related Report
      2013 Annual Research Report
  • [Presentation] Monotonic Damping in Nanoscopic Hydration Experiments Measured by Photothermal AFM

    • Author(s)
      A. Labuda, K. Kobayashi, K. Suzuki, H. Yamada, P. Gruetter, M. Lysy, D. Bocek, D.A. Walters, R. Proksch, and J.P. Cleveland
    • Organizer
      16th International Conference on Noncontact Atomic Force Microscopy (NC-AFM 2013)
    • Place of Presentation
      University of Maryland, USA
    • Related Report
      2013 Annual Research Report
  • [Book] Atomic Force Microscopy in Nanobiology2014

    • Author(s)
      High-Resolution Imaging of Biological Molecules by Frequency Modulation Atomic Force Microscopy
    • Total Pages
      16
    • Publisher
      Pan Stanford Publishing
    • Related Report
      2013 Annual Research Report

URL: 

Published: 2013-05-21   Modified: 2019-07-29  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi