Atomic force microscopy imaging and probing of DNA, proteins, and protein-DNA complexes: Silatrane surface chemistry

Methods in Molecular Biology

Volumn 543, Issue , 2009, Pages 337-351

  Lyubchenko, Yuri L ^a   Shlyakhtenko, Luda S ^a   Gall, Alexander A ^a  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

Author keywords

Atomic force microscopy (AFM); DNA local structures; Force spectroscopy; Mica functionalization; Protein DNA complexes; Silanes; Silatranes; Surface chemistry

Indexed keywords

ALPHA SYNUCLEIN; DNA; FUSED HETEROCYCLIC RINGS; MACROGOL DERIVATIVE; ORGANOSILICON DERIVATIVE; PROTEIN; SILATRANE; WATER;

AIR; ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMISTRY; DNA SUPERCOILING; METABOLISM; METHODOLOGY; SOLUTION AND SOLUBILITY; SPECTROSCOPY; SURFACE PROPERTY; SYNTHESIS; TIME; ULTRASTRUCTURE;

AIR; ALPHA-SYNUCLEIN; BICYCLO COMPOUNDS, HETEROCYCLIC; DNA; DNA, SUPERHELICAL; MICROSCOPY, ATOMIC FORCE; ORGANOSILICON COMPOUNDS; POLYETHYLENE GLYCOLS; PROTEINS; SOLUTIONS; SPECTRUM ANALYSIS; SURFACE PROPERTIES; TIME FACTORS; WATER;

EID: 67649099651     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-015-1_21     Document Type: Article

References (58)

1. Binnig, G., Rohrer, H., Gerber, C., and Weibel, E. (1982). Surface Studies by Scanning Tunneling Microscopy, Phys Rev Lett 49, 57-60.
2. Binnig, G., Quate, C. F., and Gerber, C. (1986). Atomic force microscope, Phys Rev Lett 56, 930-933.
3. Clemmer, C. R., and Beebe, T. P., Jr. (1991). Graphite: a mimic for DNA and other biomol-ecules in scanning tunneling microscope studies, Science 251, 640-642. (Pubitemid 21916884)
4. Heckl, W. M., and Binnig, G. (1992). Domain walls on graphite mimic DNA, Ultramicros-copy 42-44 (Pt B), 1073-1078.
5. Bustamante, C., Vesenka, J., Tang, C. L., Rees, W., Guthold, M., and Keller, R. (1992). Circular DNA molecules imaged in air by scanning force microscopy, Biochemistry 31, 22-26.
6. Yang, J., Takeyasu, K., and Shao, Z. (1992). Atomic force microscopy of DNA molecules, FEBS Lett 301, 173-176.
7. Vesenka, J., Guthold, M., Tang, C. L., Keller, D., Delaine, E., and Bustamante, C. (1992). Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope, Ultramicroscopy 42-44 (Pt B), 1243-1249.
8. Lyubchenko, Y. L., Gall, A. A., Shlyakhtenko, L. S., Harrington, R. E., Jacobs, B. L., Oden, P. I., and Lindsay, S. M. (1992). Atomic force microscopy imaging of double stranded DNA and RNA, J Biomol Struct Dyn 10, 589-606. (Pubitemid 23027540)
9. Allen, M. J., Dong, X. F., O'Neill, T. E., Yau, P., Kowalczykowski, S. C., Gatewood, J., Bal-horn, R., and Bradbury, E. M. (1993). Atomic force microscope measurements of nucleo-some cores assembled along defined DNA sequences, Biochemistry 32, 8390-8396. (Pubitemid 23270418)
10. Hegner, M., Wagner, P., and Semenza, G. (1993). Immobilizing DNA on gold via thiol modification for atomic force microscopy imaging in buffer solutions, FEBS Lett 336, 452-456. (Pubitemid 24036997)
11. Mou, J., Czajkowsky, D. M., Zhang, Y., and Shao, Z. (1995). High-resolution atomic-force microscopy of DNA: the pitch of the double helix, FEBS Lett 371, 279-282.
12. Bustamante, C., Erie, D., and Keller, D. (1994). Biochemical and structural applications of scanning force microscopy, Curr Opin Struct Biol 4, 750-760. (Pubitemid 24325296)
13. Bustamante, C., Rivetti, C., and Keller, D. J. (1997). Scanning force microscopy under aqueous solutions, Curr Opin Struct Biol 7, 709-716. (Pubitemid 27472592)
14. Lyubchenko, Y. L., Gall, A. A., and Shlyakhtenko, L. S. (2001). Atomic force microscopy of DNA and protein-DNA complexes using functionalized mica substrates, Methods Mol Biol 148, 569-578.
15. Lyubchenko, Y., Shlyakhtenko, L., Harrington, R., Oden, P., and Lindsay, S. (1993) Atomic force microscopy of long DNA: imaging in air and under water, Proc Natl Acad Sci U S A 90, 2137-2140. (Pubitemid 23078580)
16. Lyubchenko, Y. L., Jacobs, B. L., Lindsay, S. M., and Stasiak, A. (1995). Atomic force microscopy of nucleoprotein complexes, Scanning Microsc 9, 705-724; discussion 724-707.
17. Lyubchenko, Y. L., Blankenship, R. E., Gall, A. A., Lindsay, S. M., Thiemann, O., Simpson, L., and Shlyakhtenko, L. S. (1996). Atomic force microscopy of DNA, nucleoproteins and cellular complexes: the use of function-alized substrates, Scanning Microsc Suppl 10, 97-107; discussion 107-109.
18. Lyubchenko, Y. L., and Shlyakhtenko, L. S. (1997). Visualization of supercoiled DNA with atomic force microscopy in situ, Proc Natl Acad Sci U S A 94, 496-501. (Pubitemid 27053662)
19. Shlyakhtenko, L. S., Potaman, V. N., Sinden, R. R., Gall, A. A., and Lyubchenko, Y. L. (2000). Structure and dynamics of three-way DNA junctions: atomic force microscopy studies, Nucleic Acids Res 28, 3472-3477.
20. Lyubchenko, Y. L., Shlyakhtenko, L. S., Potaman, V. P. and Sinden, R. R. (2002). Global and local DNA structure and dynamics. Single molecule studies with AFM, Microsc Microanal 8, 170-171.
21. Yodh, J. G., Woodbury, N., Shlyakhtenko, L. S., Lyubchenko, Y. L., and Lohr, D. (2002). Mapping nucleosome locations on the 208-12 by AFM provides clear evidence for coopera-tivity in array occupation, Biochemistry 41, 3565-3574. (Pubitemid 34224668)
22. Kato, M., Hokabe, S., Itakura, S., Minoshima, S., Lyubchenko, Y. L., Gurkov, T. D., Okawara, H., Nagayama, K., and Shimizu, N. (2003). Interarm interaction of DNA cruciform forming at a short inverted repeat sequence, Biophys J 85, 402-408. (Pubitemid 36753643)
23. Potaman, V. N., Bissler, J. J., Hashem, V. I., Oussatcheva, E. A., Lu, L., Shlyakhtenko, L. S., Lyubchenko, Y. L., Matsuura, T., Ashizawa, T., Leffak, M., Benham, C. J., and Sinden, R. R. (2003). Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats, J Mol Biol 326, 1095-1111.
24. Shlyakhtenko, L. S., Gall, A. A., Filonov, A., Cerovac, Z., Lushnikov, A., and Lyubchenko, Y. L. (2003). Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials, Ultramicroscopy 97, 279-287. (Pubitemid 36686737)
25. Lushnikov, A. Y., Brown, B. A., 2nd, Oussatcheva, E. A., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (2004). Interaction of the Zalpha domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy, Nucleic Acids Res 32, 4704-4712. (Pubitemid 39317747)
26. Lyubchenko, Y. L. (2004). DNA structure and dynamics: an atomic force microscopy study, Cell Biochem Biophys 41, 75-98. (Pubitemid 41282435)
27. Tiner, W. J., Sr., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (2001). The structure of intramolecular triplex DNA: atomic force microscopy study, J Mol Biol 314, 353-357. (Pubitemid 33131839)
28. Kato, M., McAllister, C. J., Hokabe, S., Shimizu, N., and Lyubchenko, Y. L. (2002). Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy, Eur J Biochem 269, 3632-3636. (Pubitemid 34989111)
29. Dahlgren, P. R., Karymov, M. A., Bankston, J., Holden, T., Thumfort, P., Ingram, V. M., and Lyubchenko, Y. L. (2005). Atomic force microscopy analysis of the Huntington protein nanofibril formation, Dis Mon 51, 374-385.
30. Lonskaya, I., Potaman, V. N., Shlyakhtenko, L. S., Oussatcheva, E. A., Lyubchenko, Y. L., and Soldatenkov, V. A. (2005). Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding, J Biol Chem 280, 17076-17083. (Pubitemid 41389171)
31. Lushnikov, A. Y., Potaman, V. N., and Lyubchenko, Y. L. (2006). Site-specific labeling of supercoiled DNA, Nucleic Acids Res 34, 111-117.
32. Lushnikov, A. Y., Potaman, V. N., Oussatcheva, E. A., Sinden, R. R., and Lyubchenko, Y. L. (2006). DNA strand arrangement within the SfiI-DNA complex: Atomic force microscopy analysis, Biochemistry 45, 152-158. (Pubitemid 43054092)
33. McAllister, C., Karymov, M. A., Kawano, Y., Lushnikov, A. Y., Mikheikin, A., Uversky, V. N., and Lyubchenko, Y. L. (2005). Protein interactions and misfolding analyzed by AFM force spectroscopy, J Mol Biol 354, 1028-1042. (Pubitemid 41698913)
34. Kransnoslobodtsev, A. V., Shlyakhtenko, L. S., Ukraintsev, E., Zaikova, T. O., Keana, J. F., and Lyubchenko, Y. L. (2005). Nanomed-icine and protein misfolding diseases, Nanom-edicine 1, 300-305.
35. Lyubchenko, Y. L., Sherman, S., Shlyakhtenko, L. S., and Uversky, V. N. (2006). Nanoimaging for protein misfolding and related diseases, J Cell Biochem 99, 53-70 [Figure featured on journal cover]. (Pubitemid 44297949)
36. Krasnoslobodtsev, A. V., Shlyakhtenko, L. S., and Lyubchenko, Y. L. (2007). Probing Interactions within the synaptic DNA-SfiI complex by AFM force spectroscopy, J Mol Biol 365, 1407-1418.
37. Shlyakhtenko, L. S., Yuan, B., Emadi, S., Lyubchenko, Y. L., and Sierks, M. R. (2007). Single-molecule selection and recovery of structure-specific antibodies using atomic force microscopy, Nanomedicine 3, 192-197. (Pubitemid 47332341)
38. Lushnikov, A. Y., Bogdanov, A., and Lyubchenko, Y. L. (2003). DNA recombination: Holliday junctions dynamics and branch migration, J Biol Chem 278, 43130-43134 [Figure featured on journal cover]. (Pubitemid 37345931)
39. Mikheikin, A. L., Lushnikov, A. Y., and Lyubchenko, Y. L. (2006). Effect of DNA supercoiling on the geometry of Holliday junctions, Biochemistry 45, 12998-13006. (Pubitemid 44763422)
40. Liu, R., McAllister, C., Lyubchenko, Y., and Sierks, M. R. (2004). Residues 17-20 and 30-35 of beta-amyloid play critical roles in aggregation, J Neurosci Res 75, 162-171. (Pubitemid 38049387)
41. Liu, R., McAllister, C., Lyubchenko, Y., and Sierks, M. R. (2004). Proteolytic antibody light chains alter beta-amyloid aggregation and prevent cytotoxicity, Biochemistry 43, 9999-10007. (Pubitemid 39030890)
42. Liu, R., Yuan, B., Emadi, S., Zameer, A., Schulz, P., McAllister, C., Lyubchenko, Y., Goud, G., and Sierks, M. R. (2004). Single chain variable fragments against beta-amyloid (Abeta) can inhibit Abeta aggregation and prevent abeta-induced neurotoxicity, Biochemistry 43, 6959-6967. (Pubitemid 38720514)
43. Emadi, S., Liu, R., Yuan, B., Schulz, P., McAllister, C., Lyubchenko, Y., Messer, A., and Sierks, M. R. (2004). Inhibiting aggregation of alpha-synuclein with human single chain antibody fragments, Biochemistry 43, 2871-2878. (Pubitemid 38327818)
44. Yamin, G., Munishkina, L. A., Karymov, M. A., Lyubchenko, Y. L., Uversky, V. N., and Fink, A. L. (2005). Forcing nonamyloidog-enic beta-synuclein to fibrillate, Biochemistry 44, 9096-9107.
45. Watson, D., Castano, E., Kokjohn, T. A., Kuo, Y. M., Lyubchenko, Y., Pinsky, D., Connolly, E. S., Jr., Esh, C., Luehrs, D. C., Stine, W. B., Rowse, L. M., Emmerling, M. R., and Roher, A. E. (2005). Physicochemical characteristics of soluble oligomeric Abeta and their pathologic role in Alzheimer's disease, Neurol Res 27, 869-881. (Pubitemid 41790274)
46. Uversky, V. N., Yamin, G., Munishkina, L. A., Karymov, M. A., Millett, I. S., Doniach, S., Lyubchenko, Y. L., and Fink, A. L. (2005). Effects of nitration on the structure and aggregation of alpha-synuclein, Brain Res Mol Brain Res 134, 84-102. (Pubitemid 40403641)
47. Uversky, V. N., Kabanov, A. V., and Lyubchenko, Y. L. (2006). Nanotools for megaproblems: probing protein misfolding diseases using nanomedicine modus operandi, J Proteome Res 5, 2505-2522. (Pubitemid 44595152)
48. Dahlgren, P. R., Bankston, J., Holden, T., Kar ymov, M. A., Thumfor t, P., Ingram, V. M., and Lyubchenko, Y. L. (2005). Atomic force microscopy analysis of the Huntington protein nanofibril formation, Nanomedicine 1, 52-57. (Pubitemid 43963606)
49. Riener, C. K., Stroh, C. M., Ebner, A., Gall, A. A., Klampfl, C., Romanin, C., Lyubchenko, Y. L., Hinterdorfer, P., and Gruber, H. J. (2003). A simple test system for single molecule recognition force microscopy, Anal Chim Acta 479, 59-75. US Patent 3,118,921. (Pubitemid 36173935)
50. Hansma, H. G., and Hoh, J. H. (1994). Biomolecular imaging with the atomic force microscope, Annu Rev Biophys Biomol Struct 23, 115-139. (Pubitemid 24217364)
51. Lyubchenko, Y. L., Oden, P. I., Lampner, D., Lindsay, S. M., and Dunker, K. A. (1993). Atomic force microscopy of DNA and bac-teriophage in air, water and propanol: the role of adhesion forces, Nucleic Acids Res 21, 1117-1123. (Pubitemid 23155605)
52. Potaman, V. N., Lushnikov, A. Y., Sinden, R. R., and Lyubchenko, Y. L. (2002). Site-specific labeling of supercoiled DNA at the A + T rich sequences, Biochemistry 41, 13198-13206. (Pubitemid 35244709)
53. Shlyakhtenko, L. S., Potaman, V. N., Sinden, R. R., and Lyubchenko, Y. L. (1998). Structure and dynamics of supercoil-stabilized DNA cruciforms, J Mol Biol 280, 61-72. (Pubitemid 28312806)
54. Bezanilla, M., Manne, S., Laney, D. E., Lyubchenko, Y. L., and Hansma, H. G. (1995). Adsorption of DNA to mica, silylated mica, and minerals: characterization by atomic force microscopy, Langmuir 11, 655-659.
55. Bezanilla, M., Drake, B., Nudler, E., Kashlev, M., Hansma, P. K., and Hansma, H. G. (1994). Motion and enzymatic degradation of DNA in the atomic force microscope, Biophys J 67, 2454-2459. (Pubitemid 24369669)
56. Crampton, N., Yokokawa, M., Dryden, D. T., Edwardson, J. M., Rao, D. N., Takeyasu, K., Yoshimura, S. H., and Henderson, R. M. (2007). Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping, Proc Natl Acad Sci U S A 104, 12755-12760. (Pubitemid 47255227)
57. Hansma, H. G., and Laney, D. E. (1996). DNA binding to mica correlates with cationic radius: assay by atomic force microscopy, Bio-phys J 70, 1933-1939. (Pubitemid 26103965)
58. Kasas, S., Thomson, N. H., Smith, B. L., Hansma, H. G., Zhu, X., Guthold, M., Bustamante, C., Kool, E. T., Kashlev, M., and Hansma, P. K. (1997). Escherichia coli RNA polymerase activity observed using atomic force microscopy, Biochemistry 36, 461-468. (Pubitemid 27056993)