Skip to main content

Advertisement

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

Article metrics

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.

[165]

References

  1. 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.8248804

  2. 2.

    Harada Y, Funatsu T, Murakami K, Nonoyama Y, Ishihama A, Yanagida T: Biophys. J.. 1999, 76: 709.

  3. 3.

    Greene EC, Mizuuchi K: Mol. Cell. 2002, 9: 1079. COI number [1:CAS:528:DC%2BD38XksFKjtb0%3D] 10.1016/S1097-2765(02)00514-2

  4. 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.092561399

  5. 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.0403849101

  6. 6.

    Shi W-X, Larson RG: Nano Lett.. 2005, 5: 2476. COI number [1:CAS:528:DC%2BD2MXht1SmtrfP] 10.1021/nl051783v

  7. 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.

  8. 8.

    Sattin BD, Goh MC: Biophys. J.. 2004, 87: 3430. COI number [1:CAS:528:DC%2BD2cXpslKgsbg%3D] 10.1529/biophysj.104.045567

  9. 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] 10.1038/374555a0

  10. 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.282.5395.1877

  11. 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] 10.1038/35051126

  12. 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.0307241101

  13. 13.

    Marko JF, Siggia ED: Macromolecules. 1995, 28: 8759. COI number [1:CAS:528:DyaK2MXpsFWqu70%3D] 10.1021/ma00130a008

  14. 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.1084387

  15. 15.

    Washizu M, Kurosawa O: IEEE Trans. Ind. Appl.. 1990, 26: 1165. COI number [1:CAS:528:DyaK3MXltlWisLs%3D] 10.1109/28.62403

  16. 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.7522347

  17. 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.277.5331.1518

  18. 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.84.4769

  19. 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/nl0617484

  20. 20.

    Ashkin A, Dziedzic JM, Bjorkholm JE, Chu S: Opt. Lett.. 1986, 11: 288. ; ;

  21. 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.7701345

  22. 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.55.1794

  23. 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.271.5250.795

  24. 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.270.5242.1653

  25. 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.287.5462.2497

  26. 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.142417799

  27. 27.

    van den Broek B, Noom MC, Wuite GJL: Nucleic. Acids Res.. 2005, 32: 3040.

  28. 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.M310471200

  29. 29.

    Gosse C, Croquette V: Biophys. J.. 2002, 82: 3314. COI number [1:CAS:528:DC%2BD38Xkt1SrsL0%3D] 10.1016/S0006-3495(02)75672-5

  30. 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.1439819

  31. 31.

    Marko JF: Europhys. Lett.. 1997, 38: 183. ; COI number [1:CAS:528:DyaK2sXjtFKrtr4%3D]; Bibcode number [1997EL.....38..183M] 10.1209/epl/i1997-00223-5

  32. 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.97.22.12002

  33. 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] 10.1038/35003614

  34. 34.

    Strick TR, Croquette V, Bensimon D: Nature. 2000, 404: 901. ; COI number [1:CAS:528:DC%2BD3cXjtVCrurc%3D]; Bibcode number [2000Natur.404..901S] 10.1038/35009144

  35. 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] 10.1088/0022-3727/31/18/021

  36. 36.

    Cohen AE: Phys. Rev. Lett.. 2003, 91: 235506. ; COI number [1:CAS:528:DC%2BD3sXps1ajtbk%3D]; Bibcode number [2003PhRvL..91w5506C] 10.1103/PhysRevLett.91.235506

  37. 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] 10.1063/1.2188587

  38. 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] 10.1063/1.1805380

  39. 39.

    Namasivayam V, Larson RG, Burke DT, Burns MA: Anal. Chem.. 2002, 74: 3378. COI number [1:CAS:528:DC%2BD38XktlChtL0%3D] 10.1021/ac025551h

  40. 40.

    Ueda M, Yoshikawa K, Doi M: Polym. J.. 1997, 29: 1040. COI number [1:CAS:528:DyaK2sXotVGjt7c%3D] 10.1295/polymj.29.1040

  41. 41.

    Holzel R, Bier FF: IEE Proc. Nanobiotechnol.. 2003, 150: 47. COI number [1:CAS:528:DC%2BD2cXpvFymug%3D%3D] 10.1049/ip-nbt:20031006

  42. 42.

    Sung KE, Burns MA: Anal. Chem.. 2006, 78: 2939. COI number [1:CAS:528:DC%2BD28XivVels7s%3D] 10.1021/ac051662f

  43. 43.

    Zheng L, Brody JP, Burke PJ: Biosens. Bioelectron.. 2004, 20: 606. COI number [1:CAS:528:DC%2BD2cXos1Krtr4%3D] 10.1016/j.bios.2004.03.029

  44. 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] 10.1063/1.1825627

  45. 45.

    Dukkipati VR, Pang SW: Appl. Phys. Lett.. 2007, 90: 083901. COI number [1:CAS:528:DC%2BD2sXis1CjtbY%3D] 10.1063/1.2535556

  46. 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.39.7164

  47. 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.1091022

  48. 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.96.16.9077

  49. 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/nature01083

  50. 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.0403884101

  51. 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.0509723103

  52. 52.

    von Hippel PH, Berg OG: J. Biol. Chem.. 1989, 264: 675.

  53. 53.

    Shimamoto N: J. Biol. Chem.. 1999, 274: 15293. COI number [1:CAS:528:DyaK1MXjsV2hu70%3D] 10.1074/jbc.274.22.15293

  54. 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.95.14.8046

  55. 55.

    Chopra M, Li L, Hu H, Burns MA, Larson RG: J. Rheol.. 2003, 47: 1111. COI number [1:CAS:528:DC%2BD3sXmvVWnsLY%3D] 10.1122/1.1595097

  56. 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] 10.1038/39827

  57. 57.

    Kim JH, Shi W-X, Larson RG: Langmuir. 2007, 23: 755. COI number [1:CAS:528:DC%2BD28Xht1Cnsr%2FK] 10.1021/la062505u

  58. 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/25.5.1064

  59. 59.

    Kwok PY, Xiao M: Hum. Mutat.. 2004, 23: 442. COI number [1:CAS:528:DC%2BD2cXkslyhsbg%3D] 10.1002/humu.20020

  60. 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/4.2.133

  61. 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.94.196101

  62. 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.106.082602

  63. 63.

    Philippe P, Bensimon A, Schwob E: Genes Dev.. 2002, 16: 2479. COI number [1:CAS:528:DC%2BD38XnvVGjt74%3D] 10.1101/gad.232902

  64. 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.0506902102

  65. 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] 10.1063/1.1365099

Download references

Author information

Correspondence to Ronald G Larson.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Kim, J., Dukkipati, V., Pang, S.W. et al. Stretching and immobilization of DNA for studies of protein–DNA interactions at the single-molecule level. Nanoscale Res Lett 2, 185 (2007) doi:10.1007/s11671-007-9057-5

Download citation

Keywords

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