Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy

Methods

Volumn 29, Issue 2, 2003, Pages 175-187

  Yang, Yong ^a   Wang, Hong ^a,b   Erie, Dorothy A ^a,b  

^a University of North Carolina at Chapel Hill   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Association constants; Atomic force microscopy (AFM); DNA protein interactions; Force microscopy; Gene regulation; Protein protein interactions; Single molecule techniques; Solution imaging; Stoichiometry; Volume analysis

Indexed keywords

NUCLEIC ACID; PROTEIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; CONFORMATION; CRYSTAL; GENE CONTROL; MEASUREMENT; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; STOICHIOMETRY; THERMODYNAMICS;

AIR; DNA; FREEZING; IMAGE PROCESSING, COMPUTER-ASSISTED; MACROMOLECULAR SUBSTANCES; MAGNETICS; MICROSCOPY, ATOMIC FORCE; NANOTECHNOLOGY; NANOTUBES, CARBON; PROTEINS; SOLUTIONS;

EID: 0037328523     PISSN: 10462023     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1046-2023(02)00308-0     Document Type: Article

References (95)

1. Binnig G., Quate C.F., Gerber C. Phys. Rev. Lett. 56:1986;930-933.
2. Hansma P.K., Elings V.B., Marti O., Bracker C.E. Science. 242:1988;209-216.
3. Marti O., Elings V., Haugan M., Bracker C.E., Schneir J., Drake B., Gould S.A., Gurley J., Hellemans L., Shaw K.et al. J. Microsc. 152(Pt. 3):1988;803-809.
4. Radmacher M., Tillamnn R.W., Fritz M., Gaub H.E. Science. 257:1992;1900-1905.
5. Engel A., Muller D.J. Nat. Struct. Biol. 7:2000;715-718.
6. Zlatanova J., Lindsay S.M., Leuba S.H. Prog. Biophys. Mol. Biol. 74:2000;37-61.
7. Hansma H.G. Annu. Rev. Phys. Chem. 52:2001;71-92.
8. Fritzsche W., Takac L., Henderson E. Crit. Rev. Eukaryot. Gene Expr. 7:1997;231-240.
9. Henn A., Medalia O., Shi S.P., Steinberg M., Franceschi F., Sagi I. Proc. Natl. Acad. Sci. USA. 98:2001;5007-5012.
10. Bonin M., Oberstrass J., Lukacs N., Ewert K., Oesterschulze E., Kassing R., Nellen W. RNA. 6:2000;563-570.
11. Liphardt J., Onoa B., Smith S.B., Tinoco I.J.R., Bustamante C. Science. 292:2001;733-737.
12. Lyubchenko Y.L., Jacobs B.L., Lindsay S.M. Nucleic Acids Res. 20:1992;3983-3986.
13. Isralewitz B., Gao M., Schulten K. Curr. Opin. Struct. Biol. 11:2001;224-230.
14. Heymann J.B., Muller D.J., Mitsuoka K., Engel A. Curr. Opin. Struct. Biol. 7:1997;543-549.
15. Balashev K., Jensen T.R., Kjaer K., Bjornholm T. Biochimie. 83:2001;387-397.
16. Dufrene Y.F., Lee G.U. Biochim. Biophys. Acta. 1509:2000;14-41.
17. Dettmann W., Grandbois M., Andre S., Benoit M., Wehle A.K., Kaltner H., Gabius H.J., Gaub H.E. Arch. Biochem. Biophys. 383:2000;157-170.
18. Misevic G.N. Microsc. Res. Tech. 44:1999;304-309.
19. Marszalek P.E., Li H., Fernandez J.M. Nat. Biotechnol. 19:2001;258-262.
20. Willemsen O.H., Snel M.M., Cambi A., Greve J., De Grooth B.G., Figdor C.G. Biophys. J. 79:2000;3267-3281.
21. Lyubchenko Y.L., Jacobs B.L., Lindsay S.M., Stasiak A. Scanning Microsc. 9:1995;705-724. discussion 724-727.
22. Safinya C.R. Curr. Opin. Struct. Biol. 11:2001;440-448.
23. Oberleithner H., Geibel J., Guggino W., Henderson R.M., Hunter M., Schneider S.W., Schwab A., Wang W. Wien Klin Wochenschr. 109:1997;419-423.
24. Danker T., Oberleithner H. Pflugers Arch. 439:2000;671-681.
25. Henderson E. Prog. Surf. Sci. 46:1994;39-60.
26. Ohnesorge F.M., Horber J.K., Haberle W., Czerny C.P., Smith D.P., Binnig G. Biophys. J. 73:1997;2183-2194.
27. Morris V.J., Kirby A.R., Gunning A.P. Atomic Force Microscopy for Biologists. 1999;Imperial College Press.
28. Wagner P. FEBS Lett. 430:1998;112-115.
29. Hansma H.G., Laney D.E. Biophys. J. 70:1996;1933-1939.
30. Muller D.J., Amrein M., Engel A. J. Struct. Biol. 119:1997;172-188.
31. Lyubchenko Y.L., Oden P.I., Lampner D., Lindsay S.M., Dunker K.A. Nucleic Acids Res. 21:1993;1117-1123.
32. Stahlberg H., Fotiadis D., Scheuring S., Remigy H., Braun T., Mitsuoka K., Fujiyoshi Y., Engel A. FEBS Lett. 504:2001;166-172.
33. Mou J., Czajkowsky D.M., Zhang Y., Shao Z. FEBS Lett. 371:1995;279-282.
34. Guthold M., Zhu X., Rivetti C., Yang G., Thomson N.H., Kasas S., Hansma H.G., Smith B., Hansma P.K., Bustamante C. Biophys. J. 77:1999;2284-2294.
35. Osmulski P.A., Gaczynska M. J. Biol. Chem. 275:2000;13171-13174.
36. Oberleithner H., Schneider S., Bustamante J.O. Pflugers Arch. 432:1996;839-844.
37. Drake B., Prater C.B., Weisenhorn A.L., Gould S.A., Albrecht T.R., Quate C.F., Cannell D.S., Hansma H.G., Hansma P.K. Science. 243:1989;1586-1589.
38. Schulz A., Mucke N., Langowski J., Rippe K. J. Mol. Biol. 283:1998;821-836.
39. Nagami F., Zuccheri G., Samori B., Kuroda R. Anal. Biochem. 300:2002;170-176.
40. Muller D.J., Fotiadis D., Engel A. FEBS Lett. 430:1998;105-111.
41. Muller D.J., Dencher N.A., Meier T., Dimroth P., Suda K., Stahlberg H., Engel A., Seelert H., Matthey U. FEBS Lett. 504:2001;219-222.
42. Argaman M., Golan R., Thomson N.H., Hansma H.G. Nucleic Acids Res. 25:1997;4379-4384.
43. Jiao Y., Cherny D.I., Heim G., Jovin T.M., Schaffer T.E. J. Mol. Biol. 314:2001;233-243.
44. Berg O.G., Winter R.B., von Hippel P.H. Biochemistry. 20:1981;6929-6948.
45. Erie D.A., Yang G., Schultz H.C., Bustamante C. Science. 266:1994;1562-1566.
46. Rees W.A., Keller R.W., Vesenka J.P., Yang G., Bustamante C. Science. 260:1993;1646-1649.
47. Allan B.W., Garcia R., Maegley K., Mort J., Wong D., Lindstrom W., Beechem J.M., Reich N.O. J. Biol. Chem. 274:1999;19269-19275.
48. van Noort J., Orsini F., Eker A., Wyman C., de Grooth B., Greve J. Nucleic Acids Res. 27:1999;3875-3880.
49. Hun Seong G., Kobatake E., Miura K., Nakazawa A., Aizawa M. Biochem. Biophys. Res. Commun. 291:2002;361-366.
50. Rivetti C., Guthold M., Bustamante C. EMBO J. 18:1999;4464-4475.
51. Umemura K., Nagami F., Okada T., Kuroda R. Nucleic Acids Res. 28:2000;E39.
52. Margeat E., Le Grimellec C., Royer C.A. Biophys. J. 75:1998;2712-2720.
53. Rippe K., Guthold M., von Hippel P.H., Bustamante C. J. Mol. Biol. 270:1997;125-138.
54. Muller D.J., Engel A. Biophys. J. 73:1997;1633-1644.
55. Viani M.B., Schaffer T.E., Chand A., Rief M., Gaub H.E., Hansma P.K. J. Appl. Phys. 86:1999;2258-2262.
56. Oberleithner H., Schneider S., Larmer J., Henderson R.M. Kidney Blood Press. Res. 19:1996;142-147.
57. Scheuring S., Ringler P., Borgnia M., Stahlberg H., Muller D.J., Agre P., Engel A. EMBO J. 18:1999;4981-4987.
58. Schneider S.W., Larmer J., Henderson R.M., Oberleithner H. Pflugers Arch. 435:1998;362-367.
59. Xue Y., Ratcliff G.C., Wang H., Davis-Searles P.R., Gray M.D., Erie D.A., Redinbo M.R. Biochemistry. 41:2002;2901-2912.
60. Ratcliff G.C., Erie D.A. J. Am. Chem. Soc. 123:2001;5632-5635.
61. Wyman C., Rombel I., North A.K., Bustamante C., Kustu S. Science. 275:1997;1658-1661.
62. Hall M.C., Wang H., Erie D.A., Kunkel T.A. J. Mol. Biol. 312:2001;637-647.
63. Xia Y., Forsman K., Jass J., Uhlin B.E. Mol. Microbiol. 30:1998;513-523.
64. Bezanilla M., Drake B., Nudler E., Kashlev M., Hansma P.K., Hansma H.G. Biophys. J. 67:1994;2454-2459.
65. Viani M.B., Pietrasanta L.I., Thompson J.B., Chand A., Gebeshuber I.C., Kindt J.H., Richter M., Hansma H.G., Hansma P.K. Nat. Struct. Biol. 7:2000;644-647.
66. Stolz M., Stoffler D., Aebi U., Goldsbury C. J. Struct. Biol. 131:2000;171-180.
67. Rakowska A., Danker T., Schneider S.W., Oberleithner H. J. Membr. Biol. 163:1998;129-136.
68. Stoffler D., Goldie K.N., Feja B., Aebi U. J. Mol. Biol. 287:1999;741-752.
69. Oberleithner H., Schillers H., Wilhelmi M., Butzke D., Danker T. Pflugers Arch. 439:2000;251-255.
70. Ando T., Kodera N., Takai E., Maruyama D., Saito K., Toda A. Proc. Natl. Acad. Sci. USA. 98:2001;12468-12472.
71. Florin E.L., Moy V.T., Gaub H.E. Science. 264:1994;415-417.
72. Bustamante C., Macosko J.C., Wuite G.J. Nat. Rev. Mol. Cell Biol. 1:2000;130-136.
73. Heinz W.F., Hoh J.H. Trends Biotechnol. 17:1999;143-150.
74. Leckband D. Annu. Rev. Biophys. Biomol. Struct. 29:2000;1-26.
75. Tokunaga M., Aoki T., Hiroshima M., Kitamura K., Yanagida T. Biochem. Biophys. Res. Commun. 231:1997;566-569.
76. Luckham P.F., Smith K. Faraday Discuss. 1998;307-320. discussion 331-343.
77. Colton R.J., Engel A., Frommer J.E., Gaub H.E., Gewirth A.A., Guckenberger R., Rabe J., Heckl W.M., Parkinson B. Procedures in Scanning Probe Microscopies. 1998;Wiley, New York.
78. Lyubchenko Y.L., Gall A.A., Shlyakhtenko L.S., Harrington R.E., Jacobs B.L., Oden P.I., Lindsay S.M. J. Biomol. Struct. Dyn. 10:1992;589-606.
79. Clausen-Schaumann H., Seitz M., Krautbauer R., Gaub H.E. Curr. Opin. Chem. Biol. 4:2000;524-530.
80. Muller D.J., Fotiadis D., Scheuring S., Muller S.A., Engel A. Biophys. J. 76:1999;1101-1111.
81. Hafner J.H., Cheung C.L., Woolley A.T., Lieber C.M. Prog. Biophys. Mol. Biol. 77:2001;73-110.
82. Shao Z., Shi D., Somlyo A.V. Biophys. J. 78:2000;950-958.
83. Shao Z., Zhang Y. Ultramicroscopy. 66:1996;141-152.
84. Woolley A.T., Cheung C.L., Hafner J.H., Lieber C.M. Chem. Biol. 7:2000;193-204.
85. Mat-Arip Y., Garver K., Chen C., Sheng S., Shao Z., Guo P. J. Biol. Chem. 276:2001;32575-32584.
86. Stevens R.M.D., Frederick N.A., Smith B.L., Morse D.E., Stucky G.D., Hansma P.K. Nanotechnology. 11:2000;1-5.
87. Umemura K., Komatsu J., Uchihashi T., Choi N., Ikawa S., Nishinaka T., Shibata T., Nakayama Y., Katsura S., Mizuno A., Tokumoto H., Ishikawa M., Kuroda R. Biochem. Biophys. Res. Commun. 281:2001;390-395.
88. Han W., Lindsay S.M., Jing T. Appl. Phys. Lett. 69:1996;4111-4114.
89. Ratcliff G.C., Erie D.A., Superfine R. Appl. Phys. Lett. 72:1998;1911-1913.
90. Viani M.B., Schaffer T.E., Paloczi G.T., Pietrasanta L.I., Smith B.L., Thompson J.B., Richter M., Rief M., Gaub H.E., Plaxco K.W., Cleland A.N., Hansma H.G., Hansma P.K. Rev. Sci. Instrum. 70:1999;4300-4303.
91. Hodges A.R., Bussmann K.M., Hoh J.H. Rev. Sci. Instrum. 72:2001;3880-3883.
92. Guthold M., Falvo M., Matthews W.G., Paulson S., Mullin J., Lord S., Erie D., Washburn S., Superfine R., Brooks F.P., Taylor R.M. J. Mol. Graphics Modell. 17:2000;187-197.
93. Guthold M., Matthews G., Negishi A., Taylor R.M., Erie D., Brooks F.P. Jr., Superfine R. Surf. Interf. Anal. 27:1999;437-443.
94. Sincell M. Science. 290:2000;1530.
95. Guthold M., Bezanilla M., Erie D.A., Jenkins B., Hansma H.G., Bustamante C. Proc. Natl. Acad. Sci. USA. 91:1994;12927-12931.