Imaging of nucleic acids with atomic force microscopy

Methods

Volumn 54, Issue 2, 2011, Pages 274-283

  Lyubchenko, Yuri L ^a   Shlyakhtenko, Luda S ^a   Ando, Toshio ^b  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^b KANAZAWA UNIVERSITY   (Japan)

Author keywords

AFM; Atomic force microscopy; DNA dynamics; DNA nanostructures; High speed AFM; Holliday junctions; RNA assembly; RNA nanostructures

Indexed keywords

DNA; MICA; RNA;

A J MOUSE; ATOMIC FORCE MICROSCOPY; CONTROLLED STUDY; DNA STRUCTURE; MOLECULAR IMAGING; NANOTECHNOLOGY; PRIORITY JOURNAL; RELIABILITY; REPRODUCIBILITY; REVIEW; RNA STRUCTURE;

ALUMINUM SILICATES; DNA; DNA, CRUCIFORM; MICROSCOPY, ATOMIC FORCE; NUCLEIC ACID CONFORMATION; RNA; SILANES; SURFACE PROPERTIES; TIME-LAPSE IMAGING;

EID: 79958754967     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2011.02.001     Document Type: Review

References (109)

1. Seeman N.C. Mol. Biotechnol. 2007, 37:246-257.
2. Guo P. Nat. Nanotechnol. 2010, 5:833-842.
3. Guo P. J. Nanosci. Nanotechnol. 2005, 5:1964-1982.
4. Guo P., Coban O., Snead N.M., Trebley J., Hoeprich S., Guo S., Shu Y. Adv. Drug Deliv. Rev. 2010, 62:650-666.
5. Bustamante C., Vesenka J., Tang C.L., Rees W., Guthold M., Keller R. Biochemistry 1992, 31:22-26.
6. Lyubchenko Y.L., Jacobs B.L., Lindsay S.M. Nucleic Acids Res. 1992, 20:3983-3986.
7. Yang J., Takeyasu K., Shao Z. FEBS Lett. 1992, 301:173-176.
8. Vesenka J., Guthold M., Tang C.L., Keller D., Delaine E., Bustamante C. Ultramicroscopy 1992, 42-44(Pt B):1243-1249.
9. Allen M.J., Dong X.F., O'Neill T.E., Yau P., Kowalczykowski S.C., Gatewood J., Balhorn R., Bradbury E.M. Biochemistry 1993, 32:8390-8396.
10. Bustamante C., Erie D.A., Keller D. Curr. Opin. Struct. Biol. 1994, 4:750-760.
11. Mou J., Czajkowsky D.M., Zhang Y., Shao Z. FEBS Lett 1995, 371:279-282.
12. Bustamante C., Rivetti C., Keller D.J. Curr. Opin. Struct. Biol. 1997, 7:709-716.
13. Lyubchenko Y.L., Gall A.A., Shlyakhtenko L.S. Methods Mol. Biol. 2001, 148:569-578.
14. 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. 1992, 10:589-606.
15. Lyubchenko Y.L., Shlyakhtenko L.S., Aki T., Adhya S. Nucleic Acids Res. 1997, 25:873-876.
16. Bustamante C., Guthold M., Zhu X., Yang G. J. Biol. Chem. 1999, 274:16665-16668.
17. Shlyakhtenko L.S., Gall A.A., Filonov A., Cerovac Z., Lushnikov A., Lyubchenko Y.L. Ultramicroscopy 2003, 97:279-287.
18. Keller R.W., Keller D.J., Bear D., Vasenka J., Bustamante C. Ultramicroscopy 1992, 42-44(Pt B):1173-1180.
19. Hegner M., Wagner P., Semenza G. FEBS Lett. 1993, 336:452-456.
20. Wagner P., Kernen P., Hegner M., Ungewickell E., Semenza G. FEBS Lett. 1994, 356:267-271.
21. Wagner P., Hegner M., Kernen P., Zaugg F., Semenza G. Biophys. J. 1996, 70:2052-2066.
22. Medalia O., Englander J., Guckenberger R., Sperling J. Ultramicroscopy 2002, 90:103-112.
23. Yonghai S., Zhuang L., Zhiguo L., Gang W., Li W., Lanlan S. Microsc. Res. Tech. 2005, 68:59-64.
24. Ikai A. Surf. Sci. Rep. 1996, 26:261-332.
25. Wang T.-W., Lu H.-Y., Lou P.-J., Lin F.-H. Biomaterials 2008, 29:4447-4454.
26. Goksu E.I., Vanegas J.M., Blanchette C.D., Lin W.C., Longo M.L. Biochim. Biophys. Acta 2009, 1788:254-266.
27. Jiang X., Lin X. Electrochem. Commun. 2004, 6:873-879.
28. Oliveira Brett A.M., Chiorcea Paquim A.-M. Bioelectrochemistry 2005, 66:117-124.
29. Spagnoli C., Korniakov A., Ulman A., Balazs E.A., Lyubchenko Y.L., Cowman M.K. Carbohydr. Res. 2005, 340:929-941.
30. Adamcik J., Klinov D.V., Witz G., Sekatskii S.K., Dietler G. FEBS Lett. 2006, 580:5671-5675.
31. Dubrovin E.V., Gerritsen J.W., Zivkovic J., Yaminsky I.V., Speller S. Colloids Surf. B 2010, 76:63-69.
32. Lyubchenko Y.L., Shlyakhtenko L.S. Methods 2009, 47:206-213.
33. Lyubchenko Y.L., Shlyakhtenko L.S., Gall A.A. Methods Mol. Biol. 2009, 543:337-351.
34. Seeman N.C. Methods Mol. Biol. 2005, 303:143-166.
35. Chen C., Sheng S., Shao Z., Guo P. J. Biol. Chem. 2000, 275:17510-17516.
36. Liu Z., Li Z., Zhou H., Wei G., Song Y., Wang L. Micron 2005, 36:525-531.
37. Hansma H.G., Laney D.E. Biophys. J. 1996, 70:1933-1939.
38. Thomson N.H., Kasas S., Smith, Hansma H.G., Hansma P.K. Langmuir 1996, 12:5905-5908.
39. Dahlgren P.R., Lyubchenko Y.L. Biochemistry 2002, 41:11372-11378.
40. Zheng J., Li Z., Wu A., Zhou H. Biophys. Chem. 2003, 104:37-43.
41. 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.
42. Zhang K., Qi H., Li H., Liu Y., Chen W. Scanning 2009, 31:75-82.
43. Hansma H.G., Golan R., Hsieh W., Lollo C.P., Mullen-Ley P., Kwoh D. Nucleic Acids Res. 1998, 26:2481-2487.
44. Brack C. CRC Crit. Rev. Biochem. 1981, 10:113-169.
45. Thundat T., Allison D.P., Warmack R.J., Brown G.M., Jacobson K.B., Schrick J.J., Ferrell T.L. Scanning Microsc. 1992, 6:911-918.
46. Hansma H.G., Bezanilla M., Zenhausern F., Adrian M., Sinsheimer R.L. Nucleic Acids Res. 1993, 21:505-512.
47. Bezanilla M., Srinivas M., Laney D.E., Lyubchenko Y.L., Hansma H.G. Adsorption of DNA to Mica Silylated mica and Minerals: Characterization by Atomic Force Microscopy 1995, American Chemical Society, Washington, DC, ETATS-UNIS.
48. Pastre D., Pietrement O., Fusil S., Landousy F., Jeusset J., David M.O., Hamon L., Le Cam E., Zozime A. Biophys. J. 2003, 85:2507-2518.
49. Solis F.J. J. Chem. Phys. 2002, 117:9009-9015.
50. Das R., Mills T.T., Kwok L.W., Maskel G.S., Millett I.S., Doniach S., Finkelstein K.D., Herschlag D., Pollack L. Phys. Rev. Lett. 2003, 90:188103.
51. Cheng H., Zhang K., Libera J.A., Olvera de la Cruz M., Bedzyk M.J. Biophys. J. 2006, 90:1164-1174.
52. Kekicheff P., Marcelja S., Senden T.J., Shubin V.E. J. Chem. Phys. 1993, 99:6098-6113.
53. Han W., Dlakic M., Zhu Y.J., Lindsay S.M., Harrington R.E. Proc. Natl. Acad. Sci. USA 1997, 94:10565-10570.
54. Han W., Lindsay S.M., Dlakic M., Harrington R.E. Nature 1997, 386:563.
55. Wiggins P.A., van der Heijden T., Moreno-Herrero F., Spakowitz A., Phillips R., Widom J., Dekker C., Nelson P.C. Nat. Nanotechnol. 2006, 1:137-141.
56. Zuccheri G., Samori B. Methods Cell Biol. 2002, 68:357-395.
57. Vologodskii A., Cozzarelli N.R. Biophys. J. 1996, 70:2548-2556.
58. Cherny D.I., Jovin T.M. J. Mol. Biol. 2001, 313:295-307.
59. Lyubchenko Y.L., Blankenship R.E., Gall A.A., Lindsay S.M., Thiemann O., Simpson L., Shlyakhtenko L.S. Scanning Microsc. Suppl. 1996, 10:97-107. (discussion 07-09).
60. J. Liu, S. Guo, M. Cinier, L.S. Shlyakhtenko, Y. Shu, Chaoping Chen, G. Shen, P. Guo, ACS Nano, in press, doi:10.1021/nn1024658.
61. Lindsay S.M., Tao N.J., DeRose J.A., Oden P.I., Lyubchenko Yu L., Harrington R.E., Shlyakhtenko L. Biophys. J. 1992, 61:1570-1584.
62. Shlyakhtenko L.S., Miloseska L., Potaman V.N., Sinden R.R., Lyubchenko Y.L. Ultramicroscopy 2003, 97:263-270.
63. Lyubchenko Y.L., Shlyakhtenko L.S. Proc. Natl. Acad. Sci. USA 1997, 94:496-501.
64. Hsieh S., Chao W.-J., Hsieh C.-W. J. Nanosci. Nanotechnol. 2009, 9:2894-2901.
65. Shao Z., Mou J., Czajkowsky D.M., Yang J., Yuan J.-Y. Adv. Phys. 1996, 45:1-86.
66. Jing T.W., Jeffrey A.M., DeRose J.A., Lyubchenko Y.L., Shlyakhtenko L.S., Harrington R.E., Appella E., Larsen J., Vaught A., Rekesh D., et al. Proc. Natl. Acad. Sci. USA 1993, 90:8934-8938.
67. Rekesh D., Lyubchenko Y., Shlyakhtenko L.S., Lindsay S.M. Biophys. J. 1996, 71:1079-1086.
68. Ohshiro T., Maeda M. Chem. Commun. (Camb). 2010, 46:2581-2583.
69. Shapir E., Cohen H., Borovok N., Kotlyar A.B., Porath D. J. Phys. Chem. B 2006, 110:4430-4433.
70. Beebe T.P., Wilson T.E., Ogletree D.F., Katz J.E., Balhorn R., Salmeron M.B., Siekhaus W.J. Science 1989, 243:370-372.
71. Arscott P.G., Lee G., Bloomfield V.A., Evans D.F. Nature 1989, 339:484-486.
72. Lee G., Arscott P.G., Bloomfield V.A., Evans D.F. Science 1989, 244:475-477.
73. Clemmer C.R., Beebe T.P. Science 1991, 251:640-642.
74. Lyubchenko Y.L., Lindsay S.M., DeRose J.A., Thundat T. J. Vac. Sci. Technol. B 1991, 9:1288-1290.
75. Klinov D., Dwir B., Kapon E., Borovok N., Molotsky T., Kotlyar A. Nanotechnology 2007, 18:225102.
76. Adamcik J., Tobenas S., Di Santo G., Klinov D., Dietler G. Langmuir 2009, 25:3159-3162.
77. Zhong Q., Inniss D., Kjoller K., Elings V.B. Surf. Sci. Lett. 1993, 290:L688-L692.
78. Guo P. Nat Nanotechnol 2010, 5:833-842.
79. Oussatcheva E.A., Shlyakhtenko L.S., Glass R., Sinden R.R., Lyubchenko Y.L., Potaman V.N. J. Mol. Biol. 1999, 292:75-86.
80. Shlyakhtenko L.S., Potaman V.N., Sinden R.R., Gall A.A., Lyubchenko Y.L. Nucleic Acids Res. 2000, 28:3472-3477.
81. Shlyakhtenko L.S., Rekesh D., Lindsay S.M., Kutyavin I., Appella E., Harrington R.E., Lyubchenko Y.L. J. Biomol. Struct. Dyn. 1994, 11:1175-1189.
82. Shlyakhtenko L.S., Appella E., Harrington R.E., Kutyavin I., Lyubchenko Y.L. J. Biomol. Struct. Dyn. 1994, 12:131-143.
83. Holliday R. Genetics Res. 1964, 5:282-304.
84. Lilley D.M. Q. Rev. Biophys. 2008, 41:1-39.
85. Lushnikov A.Y., Bogdanov A., Lyubchenko Y.L. J. Biol. Chem. 2003, 278:43130-43134.
86. Seeman N.C. Trends Biochem. Sci. 2005, 30:119-125.
87. Hansma H.G., Oroudjev E., Baudrey S., Jaeger L. J. Microsc. 2003, 212:273-279.
88. Chworos A., Severcan I., Koyfman A.Y., Weinkam P., Oroudjev E., Hansma H.G., Jaeger L. Science 2004, 306:2068-2072.
89. Guo P., Zhang C., Chen C., Garver K., Trottier M. Mol. Cell 1998, 2:149-155.
90. Shu D., Moll W.-D., Deng Z., Mao C., Guo P. Nano Lett. 2004, 4:1717-1723.
91. Sheng S., Shao Z. Methods Cell Biol. 2002, 68:243-256.
92. Zhang Y., Sheng S., Shao Z. Biophys. J. 1996, 71:2168-2176.
93. Zhang Y., Shao Z., Somlyo A.P., Somlyo A.V. Biophys. J. 1997, 72:1308-1318.
94. Manalis S.R., Minne S.C., Quate A.C.F. Appl. Phys. Lett. 1996, 68:871-873.
95. Walters D.A., Cleveland J.P., Thomson N.H., Hansma P.K., Wendman M.A., Gurley G., Elings V. Rev. Sci. Instrum. 1996, 67:3583-3590.
96. Ando T., Kodera N., Takai E., Maruyama D., Saito K., Toda A. Proc. Natl. Acad. Sci. USA 2001, 98:12468-12472.
97. Ando T., Uchihashi T., Kodera N., Yamamoto D., Taniguchi M., Miyagi A., Yamashita H. J. Mol. Recognit. 2007, 20:448-458.
98. Ando T., Uchihashi T., Fukuma T. Prog. Surf. Sci. 2008, 83:337-437.
99. Zou Q., Leang K., Sadoun E., Reed M., Devasia S. Asian J. Control 2004, 6:164-178.
100. 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.
101. Kobayashi M., Sumitomo K., Torimitsu K. Ultramicroscopy 2007, 107:184-190.
102. Gilmore J.L., Suzuki Y., Tamulaitis G., Siksnys V., Takeyasu K., Lyubchenko Y.L. Biochemistry 2009, 48:10492-10498.
103. Suzuki Y., Higuchi Y., Hizume K., Yokokawa M., Yoshimura S.H., Yoshikawa K., Takeyasu K. Ultramicroscopy 2010, 110:682-688.
104. Schaffer T.E., Cleveland J.P., Ohnesorge F., Walters D.A., Hansma P.K. J. Appl. Phys. 1996, 80:3622-3627.
105. Schaffer T.E., Hansma P.K. J. Appl. Phys. 1998, 84:4661-4666.
106. Kitazawa M., Shiotani K., Toda A. Jpn. J. Appl. Phys. 2003, 42:4844-4847.
107. Ando T., Kodera N., Maruyama D., Takai E., Saito K., Toda A. Jpn. J. Appl. Phys. 2002, 41:4851.
108. Shibata M., Yamashita H., Uchihashi T., Kandori H., Ando T. Nat. Nanotechnol. 2010, 5:208-212.
109. Kodera N., Yamamoto D., Ishikawa R., Ando T. Nature 2010, 468:72-76.