SpringerOpen Newsletter

Receive periodic news and updates relating to SpringerOpen.

Open Access Nano Review

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

JiHoon Kim1, VenkatRam Dukkipati2, Stella W Pang2 and Ronald G Larson1*

Author Affiliations

1 Department of Chemical Engineering, University of Michigan, Ann Arbor, 48109, MI, USA

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

For all author emails, please log on.

Nanoscale Research Letters 2007, 2:185-201  doi:10.1007/s11671-007-9057-5


The electronic version of this article is the complete one and can be found online at:


Received:13 March 2007
Accepted:30 March 2007
Published:18 April 2007

© 2007 to the authors

Abstract

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.

Keywords:
DNA; Single-molecule; Proteins; DNA–protein interactions

Nano Review

[1-65]

References

  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]

    Publisher Full Text OpenURL

  2. Harada Y, Funatsu T, Murakami K, Nonoyama Y, Ishihama A, Yanagida T:

    Biophys. J.. 1999, 76:709.

    COI number [1:CAS:528:DyaK1MXnsVansw%3D%3D]

    OpenURL

  3. Greene EC, Mizuuchi K:

    Mol. Cell. 2002, 9:1079.

    COI number [1:CAS:528:DC%2BD38XksFKjtb0%3D]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  6. Shi W-X, Larson RG:

    Nano Lett.. 2005, 5:2476.

    COI number [1:CAS:528:DC%2BD2MXht1SmtrfP]

    Publisher Full Text OpenURL

  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.

    COI number [1:CAS:528:DyaK1MXmtl2mtL4%3D]

    OpenURL

  8. Sattin BD, Goh MC:

    Biophys. J.. 2004, 87:3430.

    COI number [1:CAS:528:DC%2BD2cXpslKgsbg%3D]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  10. Lu HP, Xun L, Xie XS:

    Science. 1998, 282:1877.

    COI number [1:CAS:528:DyaK1cXotVWju7c%3D]; Bibcode number [1998Sci...282.1877P]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  13. Marko JF, Siggia ED:

    Macromolecules. 1995, 28:8759.

    COI number [1:CAS:528:DyaK2MXpsFWqu70%3D]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  15. Washizu M, Kurosawa O:

    IEEE Trans. Ind. Appl.. 1990, 26:1165.

    COI number [1:CAS:528:DyaK3MXltlWisLs%3D]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  19. Dukkipati VR, Kim JH, Pang SW, Larson RG:

    Nano Lett.. 2006, 6:2499.

    COI number [1:CAS:528:DC%2BD28XpvFKitr0%3D]

    Publisher Full Text OpenURL

  20. Ashkin A, Dziedzic JM, Bjorkholm JE, Chu S:

    Opt. Lett.. 1986, 11:288.

    COI number [1:CAS:528:DyaL28Xitlejurs%3D]; Bibcode number [1986OptL...11..288A]

    OpenURL

  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]

    Publisher Full Text OpenURL

  22. Larson RG, Perkins TT, Smith DE, Chu S:

    Phys. Rev. E. 1997, 55:1764.

    Bibcode number [1997PhRvE..55.1794L]

    Publisher Full Text OpenURL

  23. Smith SB, Cui Y, Bustamante C:

    Science. 1996, 271:795.

    COI number [1:CAS:528:DyaK28XptlyjtQ%3D%3D]; Bibcode number [1996Sci...271..795S]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  27. van den Broek B, Noom MC, Wuite GJL:

    Nucleic. Acids Res.. 2005, 32:3040. OpenURL

  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]

    Publisher Full Text OpenURL

  29. Gosse C, Croquette V:

    Biophys. J.. 2002, 82:3314.

    COI number [1:CAS:528:DC%2BD38Xkt1SrsL0%3D]

    Publisher Full Text OpenURL

  30. Smith SB, Finzi L, Bustamante C:

    Science. 1992, 258:1122.

    COI number [1:CAS:528:DyaK3sXps1Cguw%3D%3D]; Bibcode number [1992Sci...258.1122S]

    Publisher Full Text OpenURL

  31. Marko JF:

    Europhys. Lett.. 1997, 38:183.

    COI number [1:CAS:528:DyaK2sXjtFKrtr4%3D]; Bibcode number [1997EL.....38..183M]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  34. Strick TR, Croquette V, Bensimon D:

    Nature. 2000, 404:901.

    COI number [1:CAS:528:DC%2BD3cXjtVCrurc%3D]; Bibcode number [2000Natur.404..901S]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  36. Cohen AE:

    Phys. Rev. Lett.. 2003, 91:235506.

    COI number [1:CAS:528:DC%2BD3sXps1ajtbk%3D]; Bibcode number [2003PhRvL..91w5506C]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  39. Namasivayam V, Larson RG, Burke DT, Burns MA:

    Anal. Chem.. 2002, 74:3378.

    COI number [1:CAS:528:DC%2BD38XktlChtL0%3D]

    Publisher Full Text OpenURL

  40. Ueda M, Yoshikawa K, Doi M:

    Polym. J.. 1997, 29:1040.

    COI number [1:CAS:528:DyaK2sXotVGjt7c%3D]

    Publisher Full Text OpenURL

  41. Holzel R, Bier FF:

    IEE Proc. Nanobiotechnol.. 2003, 150:47.

    COI number [1:CAS:528:DC%2BD2cXpvFymug%3D%3D]

    Publisher Full Text OpenURL

  42. Sung KE, Burns MA:

    Anal. Chem.. 2006, 78:2939.

    COI number [1:CAS:528:DC%2BD28XivVels7s%3D]

    Publisher Full Text OpenURL

  43. Zheng L, Brody JP, Burke PJ:

    Biosens. Bioelectron.. 2004, 20:606.

    COI number [1:CAS:528:DC%2BD2cXos1Krtr4%3D]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  45. Dukkipati VR, Pang SW:

    Appl. Phys. Lett.. 2007, 90:083901.

    COI number [1:CAS:528:DC%2BD2sXis1CjtbY%3D]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  52. von Hippel PH, Berg OG:

    J. Biol. Chem.. 1989, 264:675. OpenURL

  53. Shimamoto N:

    J. Biol. Chem.. 1999, 274:15293.

    COI number [1:CAS:528:DyaK1MXjsV2hu70%3D]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  55. Chopra M, Li L, Hu H, Burns MA, Larson RG:

    J. Rheol.. 2003, 47:1111.

    COI number [1:CAS:528:DC%2BD3sXmvVWnsLY%3D]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  57. Kim JH, Shi W-X, Larson RG:

    Langmuir. 2007, 23:755.

    COI number [1:CAS:528:DC%2BD28Xht1Cnsr%2FK]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  59. Kwok PY, Xiao M:

    Hum. Mutat.. 2004, 23:442.

    COI number [1:CAS:528:DC%2BD2cXkslyhsbg%3D]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL

  62. Brau RR, Tarsa PB, Ferrer JM, Lee P, Lang MJ:

    Biophys. J.. 2006, 91:1069.

    COI number [1:CAS:528:DC%2BD28XnsFOjtLg%3D]

    Publisher Full Text OpenURL

  63. Philippe P, Bensimon A, Schwob E:

    Genes Dev.. 2002, 16:2479.

    COI number [1:CAS:528:DC%2BD38XnvVGjt74%3D]

    Publisher Full Text OpenURL

  64. Guan J, Lee LJ:

    Proc. Natl. Acad. Sci. USA. 2005, 102:18321.

    COI number [1:CAS:528:DC%2BD28Xpt1er]; Bibcode number [2005PNAS..10218321G]

    Publisher Full Text OpenURL

  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]

    Publisher Full Text OpenURL