Mica functionalization for imaging of dna and protein-dna complexes with atomic force microscopy

Methods in Molecular Biology

Volumn 931, Issue , 2012, Pages 295-312

  Luda, Shlyakhtenko ^a   Alexander, A Gall ^b   Yuri, Lyubchenko ^a  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

^b Cepheid   (United States)

Author keywords

AFM; Atomic force microscopy; DNA structure and dynamics; Mica functionalization; Protein DNA complexes; Silanes; Silatranes; Surface chemistry

Indexed keywords

DNA; MICA; PROTEIN; SILANE DERIVATIVE; ALUMINUM SILICATE; AMINO PROPYL TRIETHOXYSILANE; AMINO-PROPYL-TRIETHOXYSILANE; DNA BINDING PROTEIN; FUSED HETEROCYCLIC RINGS; ORGANOSILICON DERIVATIVE; SILATRANE;

ARTICLE; ATOMIC FORCE MICROSCOPY; DNA DETERMINATION; DNA PROTEIN COMPLEX; IONIC STRENGTH; PRIORITY JOURNAL; PROTEIN ANALYSIS; RELIABILITY; REPRODUCIBILITY; SYNTHESIS; CHEMISTRY; METHODOLOGY; NUCLEOSOME; PLASMID; SURFACE PROPERTY; TIME LAPSE IMAGING; ULTRASTRUCTURE;

ALUMINUM SILICATES; BICYCLO COMPOUNDS, HETEROCYCLIC; DNA-BINDING PROTEINS; MICROSCOPY, ATOMIC FORCE; NUCLEOSOMES; ORGANOSILICON COMPOUNDS; PLASMIDS; SILANES; SURFACE PROPERTIES; TIME-LAPSE IMAGING;

EID: 84873514030     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-56-4_14     Document Type: Article

References (50)

1. Bustamante C, Vesenka J, Tang CL, Rees W, Guthold M, Keller R (1992) Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry 31:22-26
2. Brack C (1981) DNA electron microscopy. CRC Crit Rev Biochem 10:113-169
3. Thundat T, Allison DP, Warmack RJ, Brown GM, Jacobson KB, Schrick JJ, Ferrell TL (1992) Atomic force microscopy of DNA on mica and chemically modi fi ed mica. Scanning Microsc 6:911-918
4. Hansma HG, Vesenka J, Siegerist C, Kelderman G, Morrett H, Sinsheimer RL, Elings V, Bustamante C, Hansma PK (1992) Reproducible imaging and dissection of plasmid DNA under liquid with the atomic force microscope. Science 256:1180-1184
5. Bezanilla M, Manne S, Laney DE, Lyubchenko YL, Hansma HG (1995) Adsorption of DNA to mica, silylated mica, and minerals: characterization by atomic force microscopy. Langmuir 11:655-659
6. Bustamante C, Rivetti C (1996) Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope. Annu Rev Biophys Biomol Struct 25:395-429
7. Bustamante C, Rivetti C, Keller DJ (1997) Scanning force microscopy under aqueous solutions. Curr Opin Struct Biol 7:709-716
8. Yang J, Takeyasu K, Shao Z (1992) Atomic force microscopy of DNA molecules. FEBS Lett 301:173-176
9. Yang J, Tamm LK, Tillack TW, Shao Z (1993) New approach for atomic force microscopy of membrane proteins. The imaging of cholera toxin. J Mol Biol 229:286-290
10. Mou J, Czajkowsky DM, Zhang Y, Shao Z (1995) High-resolution atomic-force microscopy of DNA: the pitch of the double helix. FEBS Lett 371:279-282
11. Hegner M, Wagner P, Semenza G (1993) Immobilizing DNA on gold via thiol modi fi cation for atomic force microscopy imaging in buffer solutions. FEBS Lett 336:452-456
12. Allen MJ, Dong XF, O'Neill TE, Yau P, Kowalczykowski SC, Gatewood J, Balhorn R, Bradbury EM (1993) Atomic force microscope measurements of nucleosome cores assembled along de fi ned DNA sequences. Biochemistry 32:8390-8396
13. Lyubchenko YL, Gall AA, Shlyakhtenko LS, Harrington RE, Jacobs BL, Oden PI, Lindsay SM (1992) Atomic force microscopy imaging of double stranded DNA and RNA. J Biomol Struct Dyn 10:589-606
14. Lyubchenko Y, Shlyakhtenko L, Harrington R, Oden P, 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
15. Lyubchenko YL, Jacobs BL, Lindsay SM, Stasiak A (1995) Atomic force microscopy of nucleoprotein complexes. Scanning Microsc 9:705-724; discussion 724-707
16. Lyubchenko YL, Blankenship RE, Gall AA, Lindsay SM, Thiemann O, Simpson L, Shlyakhtenko LS (1996) Atomic force microscopy of DNA, nucleoproteins and cellular complexes: the use of functionalized substrates. Scanning Microsc Suppl 10:97-107; discussion 107-109
17. Lyubchenko YL, Shlyakhtenko LS (1997) Visualization of supercoiled DNA with atomic force microscopy in situ. Proc Natl Acad Sci U S A 94:496-501
18. Lyubchenko YL, Gall AA, Shlyakhtenko LS (2001) Atomic force microscopy of DNA and protein-DNA complexes using functionalized mica substrates. Methods Mol Biol 148:569-578
19. Shlyakhtenko LS, Potaman VN, Sinden RR, Gall AA, Lyubchenko YL (2000) Structure and dynamics of three-way DNA junctions: atomic force microscopy studies. Nucleic Acids Res 28:3472-3477
20. Lyubchenko YL, Shlyakhtenko LS, Potaman VP, Sinden RR (2002) Global and Local DNA Structure and Dynamics. Single molecule studies with AFM. Microsc Microanal 8:170-171
21. Yodh JG, Woodbury N, Shlyakhtenko LS, Lyubchenko YL, Lohr D (2002) Mapping nucleosome locations on the 208-12 by AFM provides clear evidence for cooperativity in array occupation. Biochemistry 41:3565-3574
22. Kato M, Hokabe S, Itakura S, Minoshima S, Lyubchenko YL, Gurkov TD, Okawara H, Nagayama K, Shimizu N (2003) Interarm interaction of DNA cruciform forming at a short inverted repeat sequence. Biophys J 85:402-408
23. Potaman VN, Bissler JJ, Hashem VI, Oussatcheva EA, Lu L, Shlyakhtenko LS, Lyubchenko YL, Matsuura T, Ashizawa T, Leffak M, Benham CJ, Sinden RR (2003) Unpaired structures in SCA10 (ATTCT)n. (AGAAT)n repeats. J Mol Biol 326:1095-1111
24. Shlyakhtenko LS, Gall AA, Filonov A, Cerovac Z, Lushnikov A, Lyubchenko YL (2003) Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials. Ultramicroscopy 97:279-287
25. Lushnikov AY, Brown BA 2nd, Oussatcheva EA, Potaman VN, Sinden RR, Lyubchenko YL (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
26. Lyubchenko YL (2004) DNA structure and dynamics: an atomic force microscopy study. Cell Biochem Biophys 41:75-98
27. Tiner WJ Sr, Potaman VN, Sinden RR, Lyubchenko YL (2001) The structure of intramolecular triplex DNA: atomic force microscopy study. J Mol Biol 314:353-357
28. Kato M, McAllister CJ, Hokabe S, Shimizu N, Lyubchenko YL (2002) Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy. Eur J Biochem 269:3632-3636
29. Dahlgren PR, Karymov MA, Bankston J, Holden T, Thumfort P, Ingram VM, Lyubchenko YL (2005) Atomic force microscopy analysis of the Huntington protein nano fi bril formation. Dis Mon 51:374-385
30. Lonskaya I, Potaman VN, Shlyakhtenko LS, Oussatcheva EA, Lyubchenko YL, Soldatenkov VA (2005) Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-speci fi c binding. J Biol Chem 280:17076-17083
31. Lushnikov AY, Potaman VN, Lyubchenko YL (2006) Site-speci fi c labeling of supercoiled DNA. Nucleic Acids Res 34: e111; (111-117)
32. Lushnikov AY, Potaman VN, Oussatcheva EA, Sinden RR, Lyubchenko YL (2006) DNA Strand Arrangement within the S fi I-DNA complex: atomic force microscopy analysis. Biochemistry 45:152-158
33. McAllister C, Karymov MA, Kawano Y, Lushnikov AY, Mikheikin A, Uversky VN, Lyubchenko YL (2005) Protein interactions and misfolding analyzed by AFM force spectroscopy. J Mol Biol 354:1028-1042
34. Kransnoslobodtsev AV, Shlyakhtenko LS, Ukraintsev E, Zaikova TO, Keana JF, Lyubchenko YL (2005) Nanomedicine and protein misfolding diseases. Nanomedicine 1:300-305
35. Lyubchenko YL, Sherman S, Shlyakhtenko LS, Uversky VN (2006) Nanoimaging for protein misfolding and related diseases. J Cell Biochem 99:53-70
36. Krasnoslobodtsev AV, Shlyakhtenko LS, Lyubchenko YL (2007) Probing interactions within the synaptic DNA-SFII complex by AFM force spectroscopy. J Mol Biol 365:1407-1418
37. Shlyakhtenko LS, Yuan B, Emadi S, Lyubchenko YL, Sierks MR (2007) Single-molecule selection and recovery of structure-speci fi c antibodies using atomic force microscopy. Nanomedicine 3:192-197
38. Lyubchenko YL, Shlyakhtenko LS, Gall AA (2009) Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: silatrane surface chemistry. Methods Mol Biol 543:337-351
39. Shlyakhtenko LS, Lushnikov AY, Li M, Lackey L, Harris RS, Lyubchenko YL (2011) Atomic force microscopy studies provide direct evidence for dimerization of the HIV restriction factor APOBEC3G. J Biol Chem 286:3387-3395
40. Lyubchenko YL, Shlyakhtenko LS (2009) AFM for analysis of structure and dynamics of DNA and protein-DNA complexes. Methods 47:206-213
41. Lyubchenko YL (2011) Preparation of DNA and nucleoprotein samples for AFM imaging. Micron 42:196-206
42. Lyubchenko YL, Shlyakhtenko LS (2011) and Ando, T. Imaging of nucleic acids with atomic force microscopy, Methods 54:274-283
43. Yamamoto D, Uchihashi T, Kodera N, Yamashita H, Nishikori S, Ogura T, Shibata M, Ando T (2010) High-speed atomic force microscopy techniques for observing dynamic biomolecular processes. Methods Enzymol 475:541-564
44. Ando T, Uchihashi T, Kodera N, Yamamoto D, Miyagi A, Taniguchi M, Yamashita H (2008) High-speed AFM and nano-visualization of biomolecular processes. P flugers Arch 456: 211-225
45. Ando T, Uchihashi T, Kodera N, Yamamoto D, Taniguchi M, Miyagi A, Yamashita H (2007) High-speed atomic force microscopy for observing dynamic biomolecular processes. J Mol Recognit 20:448-458
46. Shlyakhtenko LS, Potaman VN, Sinden RR, Lyubchenko YL (1998) Structure and dynamics of supercoil-stabilized DNA cruciforms. J Mol Biol 280:61-72
47. Lushnikov AY, Bogdanov A, Lyubchenko YL (2003) DNA recombination: holliday junctions dynamics and branch migration. J Biol Chem 278:43130-43134
48. Shlyakhtenko LS, Lushnikov AY, Lyubchenko YL (2009) Dynamics of nucleosomes revealed by time-lapse atomic force microscopy. Biochemistry 48:7842-7848
49. Shlyakhtenko LS, Gilmore J, Kriatchko AN, Kumar S, Swanson PC, Lyubchenko YL (2009) Molecular mechanism underlying RAG1/ RAG2 synaptic complex formation. J Biol Chem 284:20956-20965
50. Vesenka J, Guthold M, Tang CL, Keller D, Delaine E, Bustamante C (1992) Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope. Ultramicroscopy 42-44(Pt B): 1243-1249