Using DNA as a fiducial marker to study SMC complex interactions with the atomic force microscope

Biophysical Journal

Volumn 102, Issue 4, 2012, Pages 839-848

  Fuentes Perez, M E ^a   Gwynn, E J ^b   Dillingham, M S ^b   Moreno Herrero, F ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^b UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CELL CYCLE PROTEIN; DNA; SCPA PROTEIN, BACILLUS SUBTILIS; SMC PROTEIN, BACTERIA;

ADSORPTION; ARTICLE; ATOMIC FORCE MICROSCOPY; CHEMISTRY; METABOLISM; MOLECULAR PROBE; MOLECULAR WEIGHT; PROTEIN MULTIMERIZATION; PROTEIN QUATERNARY STRUCTURE;

ADSORPTION; BACTERIAL PROTEINS; CELL CYCLE PROTEINS; DNA; MICROSCOPY, ATOMIC FORCE; MOLECULAR PROBES; MOLECULAR WEIGHT; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, QUATERNARY;

EID: 84857334794     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.01.022     Document Type: Article

References (46)

1. G. Binnig, C.F. Quate, and C. Gerber Atomic force microscope Phys. Rev. Lett. 56 1986 930 933
2. C. Bustamante, and D. Keller Scanning force microscopy in biology Phys. Today 48 1995 32 38
3. C. Stroh, and H. Wang P. Hinterdorfer Single-molecule recognition imaging microscopy Proc. Natl. Acad. Sci. USA 101 2004 12503 12507
4. J. van Noort, and S. Verbrugge R.T. Dame Dual architectural roles of HU: formation of flexible hinges and rigid filaments Proc. Natl. Acad. Sci. USA 101 2004 6969 6974
5. G. Lia, and M. Indrieri D. Dunlap ATP-dependent looping of DNA by ISWI J. Biophoton 1 2008 280 286
6. F. Eghiaian, and I.A. Schaap Structural and dynamic characterization of biochemical processes by atomic force microscopy Methods Mol. Biol. 778 2011 71 95
7. + channel protein using atomic force microscopy Proc. Natl. Acad. Sci. USA 93 1996 8756 8760
8. C. Wyman, and I. Rombel S. Kustu Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein Science 275 1997 1658 1661
9. S.W. Schneider, and J. Lärmer H. Oberleithner Molecular weights of individual proteins correlate with molecular volumes measured by atomic force microscopy Pflugers Arch. 435 1998 362 367
10. N. Beerens, and J.H. Hoeijmakers C. Wyman The CSB protein actively wraps DNA J. Biol. Chem. 280 2005 4722 4729
11. L.S. Shlyakhtenko, and J. Gilmore Y.L. Lyubchenko Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy Biochemistry 46 2007 11128 11136
12. K.J. Neaves, and L.P. Cooper R.M. Henderson Atomic force microscopy of the EcoKI Type I DNA restriction enzyme bound to DNA shows enzyme dimerization and DNA looping Nucleic Acids Res. 37 2009 2053 2063
13. P.N. Minh, and N. Devroede D. Charlier Insights into the architecture and stoichiometry of Escherichia coli PepADNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy Nucleic Acids Res. 37 2009 1463 1476
14. E. van der Linden, and H. Sanchez C. Wyman RAD50 and NBS1 form a stable complex functional in DNA binding and tethering Nucleic Acids Res. 37 2009 1580 1588
15. L.S. Shlyakhtenko, and A.Y. Lushnikov Y.L. Lyubchenko Atomic force microscopy studies provide direct evidence for dimerization of the HIV restriction factor APOBEC3G J. Biol. Chem. 286 2011 3387 3395
16. G.C. Ratcliff, and D.A. Erie A novel single-molecule study to determine protein-protein association constants J. Am. Chem. Soc. 123 2001 5632 5635
17. E.E. Verhoeven, and C. Wyman N. Goosen The presence of two UvrB subunits in the UvrAB complex ensures damage detection in both DNA strands EMBO J. 21 2002 4196 4205
18. R.A. Britton, D.C. Lin, and A.D. Grossman Characterization of a prokaryotic SMC protein involved in chromosome partitioning Genes Dev. 12 1998 1254 1259
19. J. Mascarenhas, and J. Soppa P.L. Graumann Cell cycle-dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein EMBO J. 21 2002 3108 3118
20. M. Hirano, and T. Hirano Positive and negative regulation of SMC-DNA interactions by ATP and accessory proteins EMBO J. 23 2004 2664 2673
21. J. Soppa, and K. Kobayashi S. Moriya Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB Mol. Microbiol. 45 2002 59 71
22. T.E. Melby, and C.N. Ciampaglio H.P. Erickson The symmetrical structure of structural maintenance of chromosomes (SMC) and MukB proteins: long, antiparallel coiled coils, folded at a flexible hinge J. Cell Biol. 142 1998 1595 1604
23. C.H. Haering, and J. Löwe K. Nasmyth Molecular architecture of SMC proteins and the yeast cohesin complex Mol. Cell 9 2002 773 788
24. M. Hirano, and T. Hirano Hinge-mediated dimerization of SMC protein is essential for its dynamic interaction with DNA EMBO J. 21 2002 5733 5744
25. C.H. Haering, and D. Schoffnegger J. Löwe Structure and stability of cohesin's SMC1-kleisin interaction Mol. Cell 15 2004 951 964
26. J.S. Kim, and D.H. Shin S.H. Kim Crystal structure of ScpB from Chlorobium tepidum, a protein involved in chromosome partitioning Proteins 62 2006 322 328
27. T. Hirano At the heart of the chromosome: SMC proteins in action Nat. Rev. Mol. Cell Biol. 7 2006 311 322
28. P.L. Graumann, and T. Knust Dynamics of the bacterial SMC complex and SMC-like proteins involved in DNA repair Chromosome Res. 17 2009 265 275
29. J.T. Yeeles, and M.S. Dillingham A dual-nuclease mechanism for DNA break processing by AddAB-type helicase-nucleases J. Mol. Biol. 371 2007 66 78
30. J.T. Yeeles, and K. van Aelst F. Moreno-Herrero Recombination hotspots and single-stranded DNA binding proteins couple DNA translocation to DNA unwinding by the AddAB helicase-nuclease Mol. Cell 42 2011 806 816
31. I. Horcas, and R. Fernández A.M. Baro WSXM: a software for scanning probe microscopy and a tool for nanotechnology Rev. Sci. Instrum. 78 2007 013705
32. M. Lysetska, and A. Knoll G. Krausch UV light-damaged DNA and its interaction with human replication protein A: an atomic force microscopy study Nucleic Acids Res. 30 2002 2686 2691
33. B. Baumgarth, and F.W. Bartels R. Ros Detailed studies of the binding mechanism of the Sinorhizobium meliloti transcriptional activator ExpG to DNA Microbiology 151 2005 259 268
34. Y. Lyubchenko, and L. Shlyakhtenko S. Lindsay Atomic force microscopy of long DNA: imaging in air and under water Proc. Natl. Acad. Sci. USA 90 1993 2137 2140
35. C. Rivetti, M. Guthold, and C. Bustamante Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis J. Mol. Biol. 264 1996 919 932
36. Y.L. Lyubchenko, and L.S. Shlyakhtenko AFM for analysis of structure and dynamics of DNA and protein-DNA complexes Methods 47 2009 206 213
37. F. Moreno-Herrero, J. Colchero, and A.M. Baró DNA height in scanning force microscopy Ultramicroscopy 96 2003 167 174
38. A. Volkov, and J. Mascarenhas P.L. Graumann A prokaryotic condensin/cohesin-like complex can actively compact chromosomes from a single position on the nucleoid and binds to DNA as a ring-like structure Mol. Cell. Biol. 23 2003 5638 5650
39. J. Mascarenhas, and A.V. Volkov P.L. Graumann Dynamic assembly, localization and proteolysis of the Bacillus subtilis SMC complex BMC Cell Biol. 6 2005 28
40. G. Witte, R. Fedorov, and U. Curth Biophysical analysis of Thermus aquaticus single-stranded DNA binding protein Biophys. J. 94 2008 2269 2279
41. A. San Paulo, and R. García High-resolution imaging of antibodies by tapping-mode atomic force microscopy: attractive and repulsive tip-sample interaction regimes Biophys. J. 78 2000 1599 1605
42. J.S. Woo, and J.H. Lim B.H. Oh Structural studies of a bacterial condensin complex reveal ATP-dependent disruption of intersubunit interactions Cell 136 2009 85 96
43. K. Matoba, and M. Yamazoe S. Hiraga Comparison of MukB homodimer versus MukBEF complex molecular architectures by electron microscopy reveals a higher-order multimerization Biochem. Biophys. Res. Commun. 333 2005 694 702
44. M. Gloyd, R. Ghirlando, and A. Guarné The role of MukE in assembling a functional MukBEF complex J. Mol. Biol. 412 2011 578 590
45. I. Onn, and J.M. Heidinger-Pauli D.E. Koshland Sister chromatid cohesion: a simple concept with a complex reality Annu. Rev. Cell Dev. Biol. 24 2008 105 129
46. C.R. Cantor, and P.R. Schimmel Biophysical Chemistry. Part II: Techniques for the Study of Biological Structure and Function 1980 W.H. Freeman New York