AFM volumetric methods for the characterization of proteins and nucleic acids

Methods

Volumn 60, Issue 2, 2013, Pages 113-121

  Fuentes Perez, Maria Eugenia ^a   Dillingham, Mark S ^b   Moreno Herrero, Fernando ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

Atomic force microscopy; Fiducial marker; Methods; Protein volumes; Single stranded DNA; Structural maintenance of chromosomes proteins

Indexed keywords

DNA; NUCLEIC ACID; PROTEIN; SINGLE STRANDED DNA;

ARTICLE; ARTIFACT; ATOMIC FORCE MICROSCOPY; DNA MARKER; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; IMAGE QUALITY; METHODOLOGY; NANOANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA BINDING; STOICHIOMETRY; TOPOGRAPHY; VOLUMETRY;

ALGORITHMS; DATA INTERPRETATION, STATISTICAL; DNA REPAIR; DNA REPLICATION; DNA, SINGLE-STRANDED; FIDUCIAL MARKERS; MICROSCOPY, ATOMIC FORCE; NUCLEIC ACID CONFORMATION; PARTICLE SIZE; PROTEIN CONFORMATION; PROTEINS;

EID: 84878229551     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.02.005     Document Type: Article

References (76)

1. Binnig G., Quate C.F., Gerber C. Phys. Rev. Lett. 1986, 56:930-933.
2. Putman A.J., van der Werf K.O., de Grooth B., van Hulst N.F., Greve J. Appl. Phys. Lett. 1994, 72:2454-2456.
3. Hansma P.K., Cleveland J.P., Radmacher M., Walters D.A., Hillner P.E., Bezanilla M., Fritz M., Vie D., Hansma H.G., Prater C.B., Massie J., Fukunaga L., Gurley J., Elings V. Appl. Phys. Lett. 1994, 64:1738-1740.
4. de Pablo P.J., Colchero J., Gómez-Herrero J., Baro A.M. Appl. Phys. Lett. 1998, 73:3300-3302.
5. Hansma H.G. Annu. Rev. Phys. Chem. 2001, 52:71-92.
6. Raab A., Han W., Badt D., Smith-Gill S.J., Lindsay S.M., Schindler H., Hinterdorfer P. Nat. Biotechnol. 1999, 17:901-905.
7. Grandbois M., Dettmann W., Benoit M., Gaub H.E. J. Histochem. Cytochem. 2000, 48:719-724.
8. Moreno-Herrero F., Colchero J., Gomez-Herrero J., Baro A.M. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 2004, 69:031915.
9. Hinterdorfer P., Garcia-Parajo M.F., Dufrene Y.F. Acc. Chem. Res. 2012, 45:327-336.
10. García R., Pérez R. Surf. Sci. Rep. 2002, 47:197-301.
11. Kasas S., Thomson N.H., Smith B.L., Hansma H.G., Zhu X., Guthold M., Bustamante C., Kool E.T., Kashlev M., Hansma P.K. Biochemistry 1997, 36:461-468.
12. Ando T., Kodera N., Takai E., Mayurama D., Saito K., Toda A. Proc. Natl. Acad. Sci. USA 2001, 98:12468-12472.
13. Moreno-Herrero F., de Jager M., Dekker N.H., Kanaar R., Wyman C., Dekker C. Nature 2005, 437:440-443.
14. Crampton N., Yokokawa M., Dryden D.T., Edwardson J.M., Rao D.N., Takeyasu K., Yoshimura S.H., Henderson R.M. Proc. Natl. Acad. Sci. USA 2007, 104:12755-12760.
15. Kodera N., Yamamoto D., Ishikawa R., Ando T. Nature 2010, 468:72-76.
16. Ando T., Uchihashi T., Fukuma T. Prog. Surf. Sci. 2008, 83:337-437.
17. Leuba S.H., Yang G., Robert C., Samori B., van Holde K., Zlatanova J., Bustamante C. Proc. Natl. Acad. Sci. USA 1994, 91:11621-11625.
18. Moreno-Herrero F., Herrero P., Colchero J., Baro A.M., Moreno F. FEBS Lett. 1999, 459:427-432.
19. Moreno-Herrero F., Perez M., Baro A.M., Avila J. Biophys. J. 2004, 86:517-525.
20. Lyubchenko Y.L., Shlyakhtenko L.S. Methods 2009, 47:206-213.
21. Shlyakhtenko L.S., Lushnikov A.Y., Lyubchenko Y.L. Biochemistry 2009, 48:7842-7848.
22. Pastre D., Hamon L., Sorel I., Le Cam E., Curmi P.A., Pietrement O. Langmuir 2010, 26:2618-2623.
23. Yeeles J.T., van Aelst K., Dillingham M.S., Moreno-Herrero F. Mol. Cell 2011, 42:806-816.
24. Cassina V., Seruggia D., Beretta G.L., Salerno D., Brogioli D., Manzini S., Zunino F., Mantegazza F. Eur. Biophys. J. 2011, 40:59-68.
25. Dufrene Y.F. Nat. Rev. Microbiol. 2008, 6:674-680.
26. Yu J., Warnke J., Lyubchenko Y.L. Nanomedicine 2011, 7:146-152.
27. Acerbi I., Luque T., Gimenez A., Puig M., Reguart N., Farre R., Navajas D., Alcaraz J. PLoS One 2012, 7:e32261.
28. Stolz M., Gottardi R., Raiteri R., Miot S., Martin I., Imer R., Staufer U., Raducanu A., Duggelin M., Baschong W., Daniels A.U., Friederich N.F., Aszodi A., Aebi U. Nat. Nanotechnol. 2009, 4:186-192.
29. Sotres J., Lindh L., Arnebrant T. Langmuir 2011, 27:13692-13700.
30. Hansma H.G., Hoh J.H. Annu. Rev. Biophys. Biomol. Struct. 1994, 23:115-139.
31. Braet F., Vermijlen D., Bossuyt V., De Zanger R., Wisse E. Ultramicroscopy 2001, 89:265-273.
32. Billingsley D.J., Bonass W.A., Crampton N., Kirkham J., Thomson N.H. Phys. Biol. 2012, 9:021001.
33. Bukharaev A.A., Berdunov N.V., Ovchinnikov D.V., Salikhov K.M. Scanning Microsc. 1998, 12:225-243.
34. Winzer A.T., Kraft C., Bhushan S., Stepanenko V., Tessmer I. Ultramicroscopy 2012, 121:8-15.
35. Santos S., Guang L., Souier T., Gadelrab K., Chiesa M., Thomson N.H. Rev. Sci. Instrum. 2012, 83:043707.
36. Santos S., Barcons V., Christenson H.K., Font J., Thomson N.H. PLoS One 2011, 6:e23821.
37. Moreno-Herrero F., Colchero J., Baro A.M. Ultramicroscopy 2003, 96:167-174.
38. Lyubchenko Y., Shlyakhtenko L., Harrington R., Oden P., Lindsay S. Proc. Natl. Acad. Sci. USA 1993, 90:2137-2140.
39. Bustamante C., Erie D.A., Keller D. Curr. Opin. Struct. Biol. 1994, 4:750-760.
40. Kienberger F., Costa L.T., Zhu R., Kada G., Reithmayer M., Chtcheglova L., Rankl C., Pacheco A.B., Thalhammer S., Pastushenko V., Heckl W.M., Blaas D., Hinterdorfer P. Biomaterials 2007, 28:2403-2411.
41. Schneider S.W., Larmer J., Henderson R.M., Oberleithner H. Pflugers Arch. 1998, 435:362-367.
42. Ratcliff G.C., Erie D.A. J. Am. Chem. Soc. 2001, 123:5632-5635.
43. Schlacher K., Leslie K., Wyman C., Woodgate R., Cox M.M., Goodman M.F. Mol. Cell 2005, 17:561-572.
44. Fuentes-Perez M.E., Gwynn E.J., Dillingham M.S., Moreno-Herrero F. Biophys. J. 2012, 102:839-848.
45. Wyman C., Rombel I., North A.K., Bustamante C., Kustu S. Science 1997, 275:1658-1661.
46. Schneider S., Folprecht G., Krohne G., Oberleithner H. Pflugers Arch. 1995, 430:795-801.
47. Henderson R.M., Schneider S., Li Q., Hornby D., White S.J., Oberleithner H. Proc. Natl. Acad. Sci. USA 1996, 93:8756-8760.
48. Ellis D.J., Dryden D.T., Berge T., Edwardson J.M., Henderson R.M. Nat. Struct. Biol. 1999, 6:15-17.
49. Berge T., Ellis D.J., Dryden D.T., Edwardson J.M., Henderson R.M. Biophys. J. 2000, 79:479-484.
50. Shlyakhtenko L.S., Gilmore J., Portillo A., Tamulaitis G., Siksnys V., Lyubchenko Y.L. Biochemistry 2007, 46:11128-11136.
51. Shlyakhtenko L.S., Lushnikov A.Y., Li M., Lackey L., Harris R.S., Lyubchenko Y.L. J. Biol. Chem. 2011, 286:3387-3395.
52. Neaves K.J., Cooper L.P., White J.H., Carnally S.M., Dryden D.T., Edwardson J.M., Henderson R.M. Nucleic Acids Res. 2009, 37:2053-2063.
53. Minh P.N., Devroede N., Massant J., Maes D., Charlier D. Nucleic Acids Res. 2009, 37:1463-1476.
54. Tang M., Cecconi C., Bustamante C., Rio D.C. J. Biol. Chem. 2007, 282:29002-29012.
55. Beerens N., Hoeijmakers J.H., Kanaar R., Vermeulen W., Wyman C. J. Biol. Chem. 2005, 280:4722-4729.
56. van der Linden E., Sanchez H., Kinoshita E., Kanaar R., Wyman C. Nucleic Acids Res. 2009, 37:1580-1588.
57. Pietrasanta L.I., Thrower D., Hsieh W., Rao S., Stemmann O., Lechner J., Carbon J., Hansma H. Proc. Natl. Acad. Sci. USA 1999, 96:3757-3762.
58. Horcas I., Fernandez R., Gomez-Rodriguez J.M., Colchero J., Gomez-Herrero J., Baro A.M. Rev. Sci. Instrum. 2007, 78:013705.
59. Cantor C.R., Schimmel P.R. Biophysical Chemistry. Part II. Techniques for the Study of Biological Structure and Function 1980, W.H. Freeman and company, New York.
60. Edstrom R.D., Meinke M.H., Yang X.R., Yang R., Elings V., Evans D.F. Biophys. J. 1990, 58:1437-1448.
61. Melby T.E., Ciampaglio C.N., Briscoe G., Erickson H.P. J. Cell Biol. 1998, 142:1595-1604.
62. Haering C.H., Lowe J., Hochwagen A., Nasmyth K. Mol. Cell 2002, 9:773-788.
63. Hirano M., Hirano T. Embo J. 2002, 21:5733-5744.
64. Garcia J., Cordeiro T.N., Prieto M.J., Pons M. Nucleic Acids Res. 2012, 40:10254-10262.
65. Atomic Force Microscopy in Liquids 2012, Wiley-VCH, Weinheim. A.M. Baro, R.G. Reifenberger (Eds.).
66. Taylor A., Smith G.R. Cell 1980, 22:447-457.
67. Dillingham M.S., Spies M., Kowalczykowski S.C. Nature 2003, 423:893-897.
68. Brown T.A., Cecconi C., Tkachuk A.N., Bustamante C., Clayton D.A. Genes Dev. 2005, 19:2466-2476.
69. Hamon L., Pastre D., Dupaigne P., Le Breton C., Le Cam E., Pietrement O. Nucleic Acids Res. 2007, 35:e58.
70. Yeeles J.T., Dillingham M.S. DNA Repair (Amst) 2010, 9:276-285.
71. Hormeno S., Ibarra B., Carrascosa J.L., Valpuesta J.M., Moreno-Herrero F., Arias-Gonzalez J.R. Biophys. J. 2011, 100:1996-2005.
72. Yeh J.I., Levine A.S., Du S., Chinte U., Ghodke H., Wang H., Shi H., Hsieh C.L., Conway J.F., Van Houten B., Rapic-Otrin V. Proc. Natl. Acad. Sci. USA 2012, 109:E2737-E2746.
73. Xu H., Beernink H.T., Morrical S.W. Nucleic Acids Res. 2010, 38:4821-4833.
74. Bastos M., Castro V., Mrevlishvili G., Teixeira J. Biophys. J. 2004, 86:3822-3827.
75. Ristic D., Modesti M., van der Heijden T., van Noort J., Dekker C., Kanaar R., Wyman C. Nucleic Acids Res. 2005, 33:3292-3302.
76. Umemura K., Okada T., Kuroda R. Scanning 2005, 27:35-43.