Skip to content


  • Nano Review
  • Open Access

Stretching and immobilization of DNA for studies of protein–DNA interactions at the single-molecule level

  • 1,
  • 2,
  • 2 and
  • 1Email author
Nanoscale Research Letters20072:185

  • Received: 13 March 2007
  • Accepted: 30 March 2007
  • Published:


Single-molecule studies of the interactions of DNA and proteins are important in a variety of biological or biotechnology processes ranging from the protein’s search for its DNA target site, DNA replication, transcription, or repair, and genome sequencing. A critical requirement for single-molecule studies is the stretching and immobilization of otherwise randomly coiled DNA molecules. Several methods for doing so have been developed over the last two decades, including the use of forces derived from light, magnetic and electric fields, and hydrodynamic flow. Here we review the immobilization and stretching mechanisms for several of these techniques along with examples of single-molecule DNA–protein interaction assays that can be performed with each of them.


  • DNA
  • Single-molecule
  • Proteins
  • DNA–protein interactions


Authors’ Affiliations

Department of Chemical Engineering, University of Michigan, Ann Arbor, 48109, MI, USA
Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, MI, USA


  1. Kabata H, Kurosawa O, Arai I, Washizu M, Margarson SA, Glass RE, Shimamoto N: Science. 1993, 262: 1561. ; COI number [1:CAS:528:DyaK2cXkslakug%3D%3D]; Bibcode number [1993Sci...262.1561K] 10.1126/science.8248804View ArticleGoogle Scholar
  2. Harada Y, Funatsu T, Murakami K, Nonoyama Y, Ishihama A, Yanagida T: Biophys. J.. 1999, 76: 709. View ArticleGoogle Scholar
  3. Greene EC, Mizuuchi K: Mol. Cell. 2002, 9: 1079. COI number [1:CAS:528:DC%2BD38XksFKjtb0%3D] 10.1016/S1097-2765(02)00514-2View ArticleGoogle Scholar
  4. Gueroui Z, Place C, Freyssingeas E, Berge B: Proc. Natl. Acad. Sci. USA. 2002, 99: 6005. ; COI number [1:CAS:528:DC%2BD38XjslWgurY%3D]; Bibcode number [2002PNAS...99.6005G] 10.1073/pnas.092561399View ArticleGoogle Scholar
  5. Tagenfeldt JO, Printz C, Cao H, Chou S, Reisner WW, Riehn R, Wang YM, Cox EC, Sturm JC, Silberzan P, Austin RH: Proc. Natl. Acad. Sci. USA. 2004, 101: 10979. Bibcode number [2004PNAS..10110979T] Bibcode number [2004PNAS..10110979T] 10.1073/pnas.0403849101View ArticleGoogle Scholar
  6. Shi W-X, Larson RG: Nano Lett.. 2005, 5: 2476. COI number [1:CAS:528:DC%2BD2MXht1SmtrfP] 10.1021/nl051783vView ArticleGoogle Scholar
  7. Guthold M, Zhu X, Rivetti C, Yang G, Thomson NH, Kasas S, Hansma HG, Smith B, Hansma PK, Bustamante C: Biophys. J.. 1999, 77: 2284. View ArticleGoogle Scholar
  8. Sattin BD, Goh MC: Biophys. J.. 2004, 87: 3430. COI number [1:CAS:528:DC%2BD2cXpslKgsbg%3D] 10.1529/biophysj.104.045567View ArticleGoogle Scholar
  9. Funatsu T, Harada Y, Tokunaga M, Saito K, Yanagida T: Nature. 1995, 374: 555. ; COI number [1:CAS:528:DyaK2MXkvVKqtro%3D]; Bibcode number [1995Natur.374..555F] 10.1038/374555a0View ArticleGoogle Scholar
  10. Lu HP, Xun L, Xie XS: Science. 1998, 282: 1877. ; COI number [1:CAS:528:DyaK1cXotVWju7c%3D]; Bibcode number [1998Sci...282.1877P] 10.1126/science.282.5395.1877View ArticleGoogle Scholar
  11. Harada Y, Ohara O, Takatsuki A, Itoh H, Shimamoto N, Kinosita K: Nature. 2001, 409: 113. ; COI number [1:CAS:528:DC%2BD3MXkt1akug%3D%3D]; Bibcode number [2001Natur.409..113H] 10.1038/35051126View ArticleGoogle Scholar
  12. Revyakin A, Ebright RH, Strick TR: Proc. Natl. Acad. Sci. USA. 2004, 101: 4776. ; COI number [1:CAS:528:DC%2BD2cXjsFCjtbc%3D]; Bibcode number [2004PNAS..101.4776R] 10.1073/pnas.0307241101View ArticleGoogle Scholar
  13. Marko JF, Siggia ED: Macromolecules. 1995, 28: 8759. COI number [1:CAS:528:DyaK2MXpsFWqu70%3D] 10.1021/ma00130a008View ArticleGoogle Scholar
  14. van Oijen AM, Blainey PC, Crampton DJ, Richardson CC, Ellenberger T, Xie XS: Science. 2003, 301: 1235. ; COI number [1:CAS:528:DC%2BD3sXmslShs7Y%3D]; Bibcode number [2003Sci...301.1235V] 10.1126/science.1084387View ArticleGoogle Scholar
  15. Washizu M, Kurosawa O: IEEE Trans. Ind. Appl.. 1990, 26: 1165. COI number [1:CAS:528:DyaK3MXltlWisLs%3D] 10.1109/28.62403View ArticleGoogle Scholar
  16. Bensimon A, Simon A, Chiffaudel A, Croquette V, Heslot F, Bensimon D: Science. 1994, 265: 2096. ; COI number [1:CAS:528:DyaK2cXmsVOgtLo%3D]; Bibcode number [1994Sci...265.2096B] 10.1126/science.7522347View ArticleGoogle Scholar
  17. Michalet X, Ekong R, Fougerousse F, Rousseaux S, Schurra C, Hornigold N, van Slegtenhorst M, Wolfe J, Povey S, Beckmann JS, Bensimon A: Science. 1997, 277: 1518. COI number [1:CAS:528:DyaK2sXlvVGktrc%3D] 10.1126/science.277.5331.1518View ArticleGoogle Scholar
  18. Doyle PS, Ladoux B, Viovy J-L: Phys. Rev. Lett.. 2000, 84: 4769. ; COI number [1:CAS:528:DC%2BD3cXjsVWgtrg%3D]; Bibcode number [2000PhRvL..84.4769D] 10.1103/PhysRevLett.84.4769View ArticleGoogle Scholar
  19. Dukkipati VR, Kim JH, Pang SW, Larson RG: Nano Lett.. 2006, 6: 2499. COI number [1:CAS:528:DC%2BD28XpvFKitr0%3D] Bibcode number [1986OptL...11..288A] 10.1021/nl0617484View ArticleGoogle Scholar
  20. Ashkin A, Dziedzic JM, Bjorkholm JE, Chu S: Opt. Lett.. 1986, 11: 288. ; ; View ArticleGoogle Scholar
  21. Perkins TT, Smith DE, Larson RG, Chu S: Science. 1995, 268: 83. ; COI number [1:CAS:528:DyaK2MXkvV2ks7Y%3D]; Bibcode number [1995Sci...268...83P] 10.1126/science.7701345View ArticleGoogle Scholar
  22. Larson RG, Perkins TT, Smith DE, Chu S: Phys. Rev. E. 1997, 55: 1764. Bibcode number [1997PhRvE..55.1794L] Bibcode number [1997PhRvE..55.1794L] 10.1103/PhysRevE.55.1794View ArticleGoogle Scholar
  23. Smith SB, Cui Y, Bustamante C: Science. 1996, 271: 795. ; COI number [1:CAS:528:DyaK28XptlyjtQ%3D%3D]; Bibcode number [1996Sci...271..795S] 10.1126/science.271.5250.795View ArticleGoogle Scholar
  24. Yin H, Wang MD, Svoboda K, Landick R, Block SM, Gelles J: Science. 1995, 270: 1653. ; COI number [1:CAS:528:DyaK2MXpvVCisb4%3D]; Bibcode number [1995Sci...270.1653Y] 10.1126/science.270.5242.1653View ArticleGoogle Scholar
  25. Davenport RJ, Wuite GJL, Landick R, Bustamante C: Science. 2000, 287: 2497. ; COI number [1:CAS:528:DC%2BD3cXitlKmtrg%3D]; Bibcode number [2000Sci...287.2497D] 10.1126/science.287.5462.2497View ArticleGoogle Scholar
  26. Forde NR, Izhaky D, Woodcock GR, Wuite GJL, Bustamante C: Proc. Natl. Acad. Sci. USA. 2002, 99: 11682. ; COI number [1:CAS:528:DC%2BD38XntFWqsbs%3D]; Bibcode number [2002PNAS...9911682F] 10.1073/pnas.142417799View ArticleGoogle Scholar
  27. van den Broek B, Noom MC, Wuite GJL: Nucleic. Acids Res.. 2005, 32: 3040.Google Scholar
  28. Skinner GM, Baumann CG, Quinn DM, Molloy JE, Hoggett JG: J. Biol. Chem.. 2004, 279: 3239. COI number [1:CAS:528:DC%2BD2cXmtlChsQ%3D%3D] 10.1074/jbc.M310471200View ArticleGoogle Scholar
  29. Gosse C, Croquette V: Biophys. J.. 2002, 82: 3314. COI number [1:CAS:528:DC%2BD38Xkt1SrsL0%3D] 10.1016/S0006-3495(02)75672-5View ArticleGoogle Scholar
  30. Smith SB, Finzi L, Bustamante C: Science. 1992, 258: 1122. ; COI number [1:CAS:528:DyaK3sXps1Cguw%3D%3D]; Bibcode number [1992Sci...258.1122S] 10.1126/science.1439819View ArticleGoogle Scholar
  31. Marko JF: Europhys. Lett.. 1997, 38: 183. ; COI number [1:CAS:528:DyaK2sXjtFKrtr4%3D]; Bibcode number [1997EL.....38..183M] 10.1209/epl/i1997-00223-5View ArticleGoogle Scholar
  32. Maier B, Bensimon D, Croquette V: Proc. Natl. Acad. Sci. USA. 2000, 97: 12002. ; COI number [1:CAS:528:DC%2BD3cXnvVSgtrk%3D]; Bibcode number [2000PNAS...9712002M] 10.1073/pnas.97.22.12002View ArticleGoogle Scholar
  33. Wuite GJL, Smith SB, Young M, Keller D, Bustamante C: Nature. 2000, 404: 103. ; COI number [1:CAS:528:DC%2BD3cXhvVyquro%3D]; Bibcode number [2000Natur.404..103W] 10.1038/35003614View ArticleGoogle Scholar
  34. Strick TR, Croquette V, Bensimon D: Nature. 2000, 404: 901. ; COI number [1:CAS:528:DC%2BD3cXjtVCrurc%3D]; Bibcode number [2000Natur.404..901S] 10.1038/35009144View ArticleGoogle Scholar
  35. Ramos A, Morgan H, Green NG, Castellanos A: J. Phys. D: Appl. Phys.. 1998, 31: 2338. ; COI number [1:CAS:528:DyaK1cXmtlyisLo%3D]; Bibcode number [1998JPhD...31.2338R] 10.1088/0022-3727/31/18/021View ArticleGoogle Scholar
  36. Cohen AE: Phys. Rev. Lett.. 2003, 91: 235506. ; COI number [1:CAS:528:DC%2BD3sXps1ajtbk%3D]; Bibcode number [2003PhRvL..91w5506C] 10.1103/PhysRevLett.91.235506View ArticleGoogle Scholar
  37. Walti C, Tosch P, Davies AG, Germishuizen WA, Kaminski CF: Appl. Phys. Lett.. 2006, 88: 153901. COI number [1:CAS:528:DC%2BD28XjvF2ju70%3D] 10.1063/1.2188587View ArticleGoogle Scholar
  38. Washizu M, Kimura Y, Kobayashi T, Kurosawa O, Matsumoto S, Mamine T: AIP Conf. Proc.. 2004, 725: 67. ; COI number [1:CAS:528:DC%2BD2cXptFSgsLs%3D]; Bibcode number [2004AIPC..725...67W] 10.1063/1.1805380View ArticleGoogle Scholar
  39. Namasivayam V, Larson RG, Burke DT, Burns MA: Anal. Chem.. 2002, 74: 3378. COI number [1:CAS:528:DC%2BD38XktlChtL0%3D] 10.1021/ac025551hView ArticleGoogle Scholar
  40. Ueda M, Yoshikawa K, Doi M: Polym. J.. 1997, 29: 1040. COI number [1:CAS:528:DyaK2sXotVGjt7c%3D] 10.1295/polymj.29.1040View ArticleGoogle Scholar
  41. Holzel R, Bier FF: IEE Proc. Nanobiotechnol.. 2003, 150: 47. COI number [1:CAS:528:DC%2BD2cXpvFymug%3D%3D] 10.1049/ip-nbt:20031006View ArticleGoogle Scholar
  42. Sung KE, Burns MA: Anal. Chem.. 2006, 78: 2939. COI number [1:CAS:528:DC%2BD28XivVels7s%3D] 10.1021/ac051662fView ArticleGoogle Scholar
  43. Zheng L, Brody JP, Burke PJ: Biosens. Bioelectron.. 2004, 20: 606. COI number [1:CAS:528:DC%2BD2cXos1Krtr4%3D] 10.1016/j.bios.2004.03.029View ArticleGoogle Scholar
  44. Germishuizen WA, Tosch P, Middelberg APJ, Walti C, Davies AG, Wirtz R, Pepper M: J. Appl. Phys.. 2005, 97: 014702. ; COI number [1:CAS:528:DC%2BD2cXhtFChs7fJ]; Bibcode number [2005JAP....97A4702G] 10.1063/1.1825627View ArticleGoogle Scholar
  45. Dukkipati VR, Pang SW: Appl. Phys. Lett.. 2007, 90: 083901. COI number [1:CAS:528:DC%2BD2sXis1CjtbY%3D] 10.1063/1.2535556View ArticleGoogle Scholar
  46. Kabata H, Okada W, Washizu M: Jpn. J. Appl. Phys.. 2000, 39: 7164. ; COI number [1:CAS:528:DC%2BD3MXlvFeqtA%3D%3D]; Bibcode number [2000JaJAP..39.7164K] 10.1143/JJAP.39.7164View ArticleGoogle Scholar
  47. Keren K, Berman RS, Buchstab E, Sivan U, Braun E: Science. 2003, 302: 1380. ; COI number [1:CAS:528:DC%2BD3sXptVCqu7Y%3D]; Bibcode number [2003Sci...302.1380K] 10.1126/science.1091022View ArticleGoogle Scholar
  48. Ha T, Zhuang X, Kim HD, Orr JW, Williamson JR, Chu S: Proc. Natl. Acad. Sci. USA. 1999, 96: 9077. ; COI number [1:CAS:528:DyaK1MXltVeqtL4%3D]; Bibcode number [1999PNAS...96.9077H] 10.1073/pnas.96.16.9077View ArticleGoogle Scholar
  49. Ha T, Rasnik I, Cheng W, Babcock HP, Gauss G, Lohman TM, Chu S: Nature. 2002, 419: 638. ; COI number [1:CAS:528:DC%2BD38Xns1Ontrc%3D]; Bibcode number [2002Natur.419..638H] 10.1038/nature01083View ArticleGoogle Scholar
  50. Blanchard SC, Kim HD, Gonzalez RL, Puglisi JD, Chu S: Proc. Natl. Acad. Sci. USA. 2004, 101: 12893. ; COI number [1:CAS:528:DC%2BD2cXnslClurg%3D]; Bibcode number [2004PNAS..10112893B] 10.1073/pnas.0403884101View ArticleGoogle Scholar
  51. Blainey PC, van Oijen AM, Banerjee A, Verdine GL, Xie XS: Proc. Natl. Acad. Sci. USA. 2006, 103: 5752. ; COI number [1:CAS:528:DC%2BD28XktFaisbs%3D]; Bibcode number [2006PNAS..103.5752B] 10.1073/pnas.0509723103View ArticleGoogle Scholar
  52. von Hippel PH, Berg OG: J. Biol. Chem.. 1989, 264: 675.Google Scholar
  53. Shimamoto N: J. Biol. Chem.. 1999, 274: 15293. COI number [1:CAS:528:DyaK1MXjsV2hu70%3D] 10.1074/jbc.274.22.15293View ArticleGoogle Scholar
  54. Jing J, Reed J, Huang J, Hu X, Clarke V, Edington J, Housman D, Anantharaman TS, Huff EJ, Mishra B, Porter B, Shenker A, Wolfson E, Hiort C, Kantor R, Aston C, Schwartz DC: Proc. Natl. Acad. Sci. USA. 1998, 95: 8046. ; COI number [1:CAS:528:DyaK1cXks1Sltbw%3D]; Bibcode number [1998PNAS...95.8046J] 10.1073/pnas.95.14.8046View ArticleGoogle Scholar
  55. Chopra M, Li L, Hu H, Burns MA, Larson RG: J. Rheol.. 2003, 47: 1111. COI number [1:CAS:528:DC%2BD3sXmvVWnsLY%3D] 10.1122/1.1595097View ArticleGoogle Scholar
  56. Deegan RD, Bakajin O, Dupont TF, Huber G, Nagel SR, Witten TA: Nature. 1997, 389: 827. ; COI number [1:CAS:528:DyaK2sXmvFSktrY%3D]; Bibcode number [1997Natur.389..827D] 10.1038/39827View ArticleGoogle Scholar
  57. Kim JH, Shi W-X, Larson RG: Langmuir. 2007, 23: 755. COI number [1:CAS:528:DC%2BD28Xht1Cnsr%2FK] 10.1021/la062505uView ArticleGoogle Scholar
  58. Yokota H, Johnson F, Lu H, Robinson RM, Belu AM, Garrison MD, Ratner BD, Trask BJ, Miller DL: Nucleic. Acids Res.. 1997, 25: 1064. COI number [1:CAS:528:DyaK2sXhvVant78%3D] 10.1093/nar/25.5.1064View ArticleGoogle Scholar
  59. Kwok PY, Xiao M: Hum. Mutat.. 2004, 23: 442. COI number [1:CAS:528:DC%2BD2cXkslyhsbg%3D] 10.1002/humu.20020View ArticleGoogle Scholar
  60. Slezak T, Kuczmarski T, Ott L, Torres C, Medeiros D, Smith J, Truitt B, Mulakken N, Lam M, Vitalis E, Zelma A, Zhou CE, Gardner S: Brief. Bioinform.. 2003, 4: 133. COI number [1:CAS:528:DC%2BD3sXmsFCht7s%3D] 10.1093/bib/4.2.133View ArticleGoogle Scholar
  61. Reisner W, Morton KJ, Riehn R, Wang YM, Yu Z, Rosen M, Sturm JC, Chou SY, Frey E, Austin RH: Phys. Rev. Lett.. 2005, 94: 196101. ; COI number [1:CAS:528:DC%2BD2MXksVCksbk%3D]; Bibcode number [2005PhRvL..94s6101R] 10.1103/PhysRevLett.94.196101View ArticleGoogle Scholar
  62. Brau RR, Tarsa PB, Ferrer JM, Lee P, Lang MJ: Biophys. J.. 2006, 91: 1069. COI number [1:CAS:528:DC%2BD28XnsFOjtLg%3D] 10.1529/biophysj.106.082602View ArticleGoogle Scholar
  63. Philippe P, Bensimon A, Schwob E: Genes Dev.. 2002, 16: 2479. COI number [1:CAS:528:DC%2BD38XnvVGjt74%3D] 10.1101/gad.232902View ArticleGoogle Scholar
  64. Guan J, Lee LJ: Proc. Natl. Acad. Sci. USA. 2005, 102: 18321. ; COI number [1:CAS:528:DC%2BD28Xpt1er]; Bibcode number [2005PNAS..10218321G] 10.1073/pnas.0506902102View ArticleGoogle Scholar
  65. Klein DCG, Gurevich L, Janssen JW, Kouwenhoven LP, Carbeck JD, Sohn LL: Appl. Phys. Lett.. 2001, 78: 2396. ; COI number [1:CAS:528:DC%2BD3MXislKltbc%3D]; Bibcode number [2001ApPhL..78.2396K] 10.1063/1.1365099View ArticleGoogle Scholar


© to the authors 2007