DNA molecule manipulation by motor proteins for analysis at the single-molecule level


Massively parallel and individual DNA manipulation for analysis has been demonstrated by designing a fully self-assembled molecular system using motor proteins. DNA molecules were immobilized by trapping in a polyacrylamide gel replica, and were digested by a restriction enzyme, XhoI, for DNA analysis. One end of the λDNA was modified with biotin and the other end was modified with digoxin molecules by fragment labeling and ligation methods. The digoxin-functionalized end was immobilized on a glass surface coated with anti-digoxigenin antibody. The biotinylated end was freely suspended and experienced Brownian motion in a buffer solution. The free end was attached to a biotinylated microtubule via avidin–biotin biding and the DNA was stretched by a kinesin-based gliding assay. A stretched DNA molecule was fixed between the gel and coverslip to observe the cleavage of the DNA by the enzyme, which was supplied through the gel network structure. This simple process flow from DNA manipulation to analysis offers a new method of performing molecular surgery at the single-molecule scale.

DNA molecule manipulation by motor proteins for analysis at the single-molecule level

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7


  1. 1.

    Manz A, Graber N, Widmer HM (1990) Sens Actuators B1:244–248

    CAS  Google Scholar 

  2. 2.

    Yokokawa R, Yumi Y, Takeuchi S, Kon T, Fujita H (2006) Nanotechnology 17:289–294

    Article  CAS  Google Scholar 

  3. 3.

    Noji H, Yasuda R, Yoshida M, Kinosita K Jr (1997) Nature 386:299–302

    Article  CAS  Google Scholar 

  4. 4.

    Arata H, Noji H, Fujita H (2006) Appl Phys Lett 88:083902

    Article  CAS  Google Scholar 

  5. 5.

    Washizu M, Kurosawa O (1990) IEEE Trans Ind Applicat 26:1165–1172

    Article  CAS  Google Scholar 

  6. 6.

    Hoyer C, Monajembashi S, Greulich K (1996) J Biotechnol 52:65–73

    Article  CAS  Google Scholar 

  7. 7.

    Washizu M, Kurosawa O, Arai I, Suzuki S, Shimamoto N (1995) IEEE Trans Ind Applicat 31:447–456

    Article  CAS  Google Scholar 

  8. 8.

    Suzuki S, Yamanashi T, Tazawa S, Kurosawa O, Washizu M (1998) IEEE Trans Ind Applicat 34:75–83

    Article  CAS  Google Scholar 

  9. 9.

    Oana H, Ueda M, Washizu M (1999) Biochem Biophys Res Commun 265:140–143

    Article  CAS  Google Scholar 

  10. 10.

    Kabata H, Okada W, Washizu M (2000) Jpn J Appl Phys 1 39:7164–7171

    Article  CAS  Google Scholar 

  11. 11.

    Yamamoto T, Kurosawa O, Kabata H, Shimamoto N, Washizu M (2000) IEEE Trans Ind Appl 36:1010–1017

    Article  CAS  Google Scholar 

  12. 12.

    Lam L, Sakakihara S, Ishizuka K, Takeuchi S, Noji H (2007) Versatile acrylamide-based microchambers for single molecular assays and analysis. In: 11th Int Conf on Miniaturized Systems for Chemistry and Life Sciences (mTAS2007), vol 1, Paris, France, 2007, 7–11 Oct 2007, pp 649–651

  13. 13.

    Wenner JR, Williams MC, Rouzina I, Bloomfield VA (2002) Biophys J 82:3160–3169

    CAS  Google Scholar 

  14. 14.

    Smith SB, Finzi L, Bustamante C (1992) Science 258:1122–1126

    Article  CAS  Google Scholar 

  15. 15.

    Hashiguchi G, Goda T, Hosogi M, Hirano K, Kaji N, Baba Y, Kakushima K, Fujita H (2003) Anal Chem 75:4347–4350

    Article  CAS  Google Scholar 

  16. 16.

    Krishnan M, Monch I, Schwille P (2007) Nano Lett 7:1270–1275

    Article  CAS  Google Scholar 

  17. 17.

    Dinu CZ, Opitz J, Pompe W, Howard J, Mertig M, Diez S (2006) Small (Weinheim an der Bergstrasse, Germany) 2:1090–1098

    CAS  Google Scholar 

  18. 18.

    Diez S, Reuther C, Dinu C, Seidel R, Mertig M, Pompe W, Howard J (2003) Nano Lett 3:1251–1254

    Article  CAS  Google Scholar 

  19. 19.

    Lam L, Sakakihara S, Ishizuka K, Takeuchi S, Arata H, Fujita H, Noji H (2008) Biomed Microdev (published online) http://www.springerlink.com/content/hm06334xn2536682/?p=a3aeb6ac7f994acbadfb98a1c8012305&pi=0

  20. 20.

    Hiratsuka Y, Tada T, Oiwa K, Kanayama T, Uyeda TQ (2001) Biophys J 81:1555–1561

    CAS  Google Scholar 

  21. 21.

    Hess H, Clemmens J, Qin D, Howard J, Vogel V (2001) Nano Lett 1:235–239

    Article  CAS  Google Scholar 

  22. 22.

    Lin C-T, Kao M-T, Kurabayashi K, Meyhofer E (2006) Small (Weinheim an der Bergstrasse, Germany) 2:281–287

    CAS  Google Scholar 

  23. 23.

    Clemmens J, Hess H, Doot R, Matzke CM, Bachand GD, Vogel V (2004) Lab Chip 4:83–86

    Article  CAS  Google Scholar 

  24. 24.

    Hess H, Matzke CM, Doot RK, Clemmens J, Bachand GD, Bunker BC, Vogel V (2003) Nano Lett 3:1651–1655

    Article  CAS  Google Scholar 

  25. 25.

    van den Heuvel MG, de Graaff MP, Dekker C (2006) Science 312:910–914

    Article  CAS  Google Scholar 

  26. 26.

    Tarhan MC, Yokokawa R, Morin F, Takeuchi S, Kon T, Fujita H (2006) In: 19th IEEE Int Conf on Micro Electro Mechanical Systems, Istanbul, Turkey, 22–26 Jan 2006, pp 526–529

  27. 27.

    Hyman A, Drechsel D, Kellogg D, Salser S, Sawin K, Steffen P, Wordeman L, Mitchison T (1991) Methods Enzymol 196:478–485

    Article  CAS  Google Scholar 

  28. 28.

    Williams RC Jr, Lee JC (1982) Methods Enzymol 85(Pt B):376–485

    Article  CAS  Google Scholar 

  29. 29.

    Doyle PS, Ladoux B, Viovy JL (2000) Phys Rev Lett 84:4769–4772

    Article  CAS  Google Scholar 

  30. 30.

    Howard J, Hudspeth AJ, Vale R (1989) Nature 342:154–159

    Article  CAS  Google Scholar 

  31. 31.

    Bustamante C, Bryant Z, Smith SB (2003) Nature 421:423–427

    Article  CAS  Google Scholar 

  32. 32.

    Turner D, Chang C, Fang K, Cuomo P, Murphy D (1996) Anal Biochem 242:20–25

    Article  CAS  Google Scholar 

  33. 33.

    Yokokawa R, Takeuchi S, Kon T, Nishiura M, Sutoh K, Fujita H (2004) Nano Lett 4:2265–2270

    Article  CAS  Google Scholar 

Download references


This work was supported by the Ministry of Education, Science, Sports and Culture, with a Grant-in-Aid for Young Scientists (B), 19710111, 2007, and the Japan Securities Foundation, 2005–2007. The authors thank Prof. Hiroyuki Noji and Dr. Liza Lam of The Institute of Scientific and Industrial Research (ISIR), Osaka University, Japan for technical help with the DNA immobilization for the enzymatic reaction. The authors would also like to acknowledge Mr. Mauricio Cordero of the Institute of Industrial Science, The University of Tokyo for his critical reading of this manuscript.

Author information



Corresponding author

Correspondence to Ryuji Yokokawa.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Yokokawa, R., Miwa, J., Tarhan, M.C. et al. DNA molecule manipulation by motor proteins for analysis at the single-molecule level. Anal Bioanal Chem 391, 2735 (2008). https://doi.org/10.1007/s00216-008-2125-6

Download citation


  • DNA
  • Molecular surgery
  • Motor protein
  • Nanomanipulation