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A new method to deal with biomacromolecularimage observed by atomic force microscopy

Ji Chao Zhang Ling-Yun Dou Shuo-Xing Wang Peng-Ye

A new method to deal with biomacromolecularimage observed by atomic force microscopy

Ji Chao, Zhang Ling-Yun, Dou Shuo-Xing, Wang Peng-Ye
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  • In this paper, we develop a new method to eliminate the background noise in the image of biomacromolecule with complex conformation in order to obtain highly effective and accurately quantitative information. By using this algorithm, we are able to deal with the atomic force microscopic imags of both linear DNA and branch DNA. Furthermore, our method can be extended to the study of the images in the other field.
    • Funds:
    [1]

    Rivetti C, Guthold M, Bustamante C 1996 J. Mol. Biol. 264 919

    [2]

    Wei Z Y, Zang L H, Li M, Fan W, Xu Y J 2005 Acta Phys. Sin. 54 4955(in Chinese)[魏志勇、臧黎慧、李 明、范 我、许玉杰 2005 物理学报 54 4955]

    [3]

    Rivetti C, Guthold M, Bustamante C 1999 EMBO J. 18 4464

    [4]

    Rivetti C, Codeluppi S 2001 Ultramicroscopy 87 55

    [5]

    Meng X, Benson K, Chada K, Huff E J, Schwartz D C 1995 Nat. Genet. 9 432

    [6]

    Liu Y Y, Don S X, Wang P Y, Xie P, Wang W C 2005 Acta Phys. Sin. 54 622(in Chinese)[刘玉颖、窦硕星、王鹏业、谢 平、王渭池 2005 物理学报 54 622]

    [7]

    Hamon L, Pastre D, Dupaigne P, Le Breton C, Le Cam E, Pietrement O 2007 Nucleic Acids Res. 35 e58

    [8]

    Ratcliff G C, Erie D A 2001 J. Am. Chem. Soc. 123 5632

    [9]

    Kada G, Kienberger F, Hinterdorfer P 2008 Nano Today 3 12

    [10]

    Hu H L, Zhang K, Wang Z X, Kong T, Hu Y, Wang X P 2007 Acta Phys. Sin. 56 1674(in Chinese)[胡海龙、张 琨、王振兴、孔 涛、胡 颖、王晓平 2007 物理学报 56 1674]

    [11]

    Fan K Q, Jia J Y, Zhu Y M, Liu X Y 2007 Acta Phys. Sin. 56 6345(in Chinese)[樊康旗、贾建援、朱应敏、刘小院 2007 物理学报 56 6345]

    [12]

    Zuccheri G, Dame R T, Aquila M, Muzzalupo I, Samori B 1998 Appl. Phys. A: Mater. Sci. Process. 66 S585

    [13]

    Lysetska M, Knoll A, Boehringer D, Hey T, Krauss G, Krausch G 2002 Nucleic Acids Res. 30 2686

    [14]

    Wiggins P A, Van der Heijden T, Moreno-Herrero F, Spakowitz A, Phillips R, Widom J, Dekker C, Nelson P C 2006 Nat. Nanotechnol. 1 137

    [15]

    Ficarra E, Benini L, Macii E, Zuccheri G 2005 IEEE Trans. Inf. Technol. Biomed. 9 508

    [16]

    Sanchez-Sevilla A, Thimonier J, Marilley M, Rocca-Serra J, Barbet J 2002 Ultramicroscopy 92 151

    [17]

    Solis F J, Bash R, Yodh J, Lindsay S M, Lohr D 2004 Biophys. J. 87 3372

    [18]

    Wang H, Bash R, Lindsay S M, Lohr D 2005 Biophys. J. 89 3386

  • [1]

    Rivetti C, Guthold M, Bustamante C 1996 J. Mol. Biol. 264 919

    [2]

    Wei Z Y, Zang L H, Li M, Fan W, Xu Y J 2005 Acta Phys. Sin. 54 4955(in Chinese)[魏志勇、臧黎慧、李 明、范 我、许玉杰 2005 物理学报 54 4955]

    [3]

    Rivetti C, Guthold M, Bustamante C 1999 EMBO J. 18 4464

    [4]

    Rivetti C, Codeluppi S 2001 Ultramicroscopy 87 55

    [5]

    Meng X, Benson K, Chada K, Huff E J, Schwartz D C 1995 Nat. Genet. 9 432

    [6]

    Liu Y Y, Don S X, Wang P Y, Xie P, Wang W C 2005 Acta Phys. Sin. 54 622(in Chinese)[刘玉颖、窦硕星、王鹏业、谢 平、王渭池 2005 物理学报 54 622]

    [7]

    Hamon L, Pastre D, Dupaigne P, Le Breton C, Le Cam E, Pietrement O 2007 Nucleic Acids Res. 35 e58

    [8]

    Ratcliff G C, Erie D A 2001 J. Am. Chem. Soc. 123 5632

    [9]

    Kada G, Kienberger F, Hinterdorfer P 2008 Nano Today 3 12

    [10]

    Hu H L, Zhang K, Wang Z X, Kong T, Hu Y, Wang X P 2007 Acta Phys. Sin. 56 1674(in Chinese)[胡海龙、张 琨、王振兴、孔 涛、胡 颖、王晓平 2007 物理学报 56 1674]

    [11]

    Fan K Q, Jia J Y, Zhu Y M, Liu X Y 2007 Acta Phys. Sin. 56 6345(in Chinese)[樊康旗、贾建援、朱应敏、刘小院 2007 物理学报 56 6345]

    [12]

    Zuccheri G, Dame R T, Aquila M, Muzzalupo I, Samori B 1998 Appl. Phys. A: Mater. Sci. Process. 66 S585

    [13]

    Lysetska M, Knoll A, Boehringer D, Hey T, Krauss G, Krausch G 2002 Nucleic Acids Res. 30 2686

    [14]

    Wiggins P A, Van der Heijden T, Moreno-Herrero F, Spakowitz A, Phillips R, Widom J, Dekker C, Nelson P C 2006 Nat. Nanotechnol. 1 137

    [15]

    Ficarra E, Benini L, Macii E, Zuccheri G 2005 IEEE Trans. Inf. Technol. Biomed. 9 508

    [16]

    Sanchez-Sevilla A, Thimonier J, Marilley M, Rocca-Serra J, Barbet J 2002 Ultramicroscopy 92 151

    [17]

    Solis F J, Bash R, Yodh J, Lindsay S M, Lohr D 2004 Biophys. J. 87 3372

    [18]

    Wang H, Bash R, Lindsay S M, Lohr D 2005 Biophys. J. 89 3386

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    [2] Lin Yu, Yang Guang-Can, Wang Yan-Wei. A dynamic light scattering study of counter-ions condensation on DNA. Acta Physica Sinica, 2013, 62(11): 118702. doi: 10.7498/aps.62.118702
    [3] Pang Xiao-Feng, Liu Sheng-Gang, Dong Rui-Xin, Yan Xun-Ling. The nonlinear characteristics study of the effect of salt on denaturation transi tion of DNA. Acta Physica Sinica, 2003, 52(12): 3197-3202. doi: 10.7498/aps.52.3197
    [4] Liu Yu-Ying, Dou Shuo-Xing, Wang Peng-Ye, Xie Ping, Wang Wei-Chi. Study of interactions between DNA and histone with molecular combing method. Acta Physica Sinica, 2005, 54(2): 622-627. doi: 10.7498/aps.54.622
    [5] Zhang Yi-Nan, Wang Li-Hua, Liu Hua-Jie, Fan Chun-Hai. DNA self-assembly-based fabrication of metallic nanostructures and related nanophotonics. Acta Physica Sinica, 2017, 66(14): 147101. doi: 10.7498/aps.66.147101
    [6] Song Jun, Chen Lei, Liu De-Sheng, Xie Shi-Jie. Study on the energy levels and electronic states of DNA molecules. Acta Physica Sinica, 2004, 53(8): 2792-2795. doi: 10.7498/aps.53.2792
    [7] Huang Lei, Bao Guang-Wei, Liu Yan-Zhu. Solution of the Kirchhoff equation for thin elastic rod under bending by constraint violation correction method. Acta Physica Sinica, 2005, 54(6): 2457-2462. doi: 10.7498/aps.54.2457
    [8] Ran Shi-Yong. Brownian motion in a harmonic trap: magnetic tweezers experiment and its simulation. Acta Physica Sinica, 2012, 61(17): 170503. doi: 10.7498/aps.61.170503
    [9] Zhang Xiang-Jun, Meng Yong-Gang, Wen Shi-Zhu. On micro scanning forces under the coupling deformation of atomic force microscope probe. Acta Physica Sinica, 2004, 53(3): 728-733. doi: 10.7498/aps.53.728
    [10] Qi Hao, Zhang Jing, Sun Run-Guang. . Acta Physica Sinica, 2002, 51(6): 1203-1207. doi: 10.7498/aps.51.1203
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Publishing process
  • Received Date:  21 January 2011
  • Accepted Date:  16 February 2011
  • Published Online:  15 September 2011

A new method to deal with biomacromolecularimage observed by atomic force microscopy

  • 1. Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China

Abstract: In this paper, we develop a new method to eliminate the background noise in the image of biomacromolecule with complex conformation in order to obtain highly effective and accurately quantitative information. By using this algorithm, we are able to deal with the atomic force microscopic imags of both linear DNA and branch DNA. Furthermore, our method can be extended to the study of the images in the other field.

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