Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin labeling and PELDOR

Nucleic Acids Research

Volumn 41, Issue 1, 2013, Pages

  Reginsson, Gunnar W ^a,b   Shelke, Sandip A ^b   Rouillon, Christophe ^a   White, Malcolm F ^a   Sigurdsson, Snorri Th ^b   Schiemann, Olav ^a,c  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b UNIVERSITY OF ICELAND   (Iceland)

^c UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; DOUBLE STRANDED DNA; LAC REPRESSOR; OLIGONUCLEOTIDE;

ARTICLE; BINDING KINETICS; COVALENT BOND; DNA BINDING; DNA CONFORMATION; DNA HYBRIDIZATION; DNA STRUCTURE; ELECTRON SPIN RESONANCE; GEL MOBILITY SHIFT ASSAY; MOLECULAR DYNAMICS; NONCOVALENT SITE DIRECTED SPIN LABELING; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PULSED ELECTRON ELECTRON DOUBLE RESONANCE; SPIN LABELING;

DNA; ELECTRON SPIN RESONANCE SPECTROSCOPY; LAC REPRESSORS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OPERATOR REGIONS, GENETIC; SPIN LABELS;

EID: 84871772025     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks817     Document Type: Article

References (42)

1. Milov, A.D., Salikhov, K.M. and Shirov, M.D. (1981) Application of the double resonance method to electron spin echo in a study of the spatial distribution of paramagnetic centers in solids. Soviet Phys Solid State, 23, 565-569.
2. Martin, R., Pannier, M., Diederich, F., Gramlich, V., Hubrich, M. and Spiess, H. (1998) Determination of end-to-end distances in a series of TEMPO diradicals of up to 2.8 nm length with a new four-pulse double electron electron resonance experiment. Angew. Chem. Int. Ed., 37, 2833-2837.
3. Zhang, X., Cekan, P., Sigurdsson, S.T. and Qin, P. (2009) Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy. Methods Enzymol., 469, 303-328.
4. Klare, J.P. and Steinhoff, H.-J. (2009) Spin labeling EPR. Photosynth. Res. 102, 377-390.
5. Shelke, S.A. and Sigurdsson, S.T. (2012) Site-directed spin labelling of nucleic acids. Eur. J. Org. Chem., 2012, 2291-2301.
6. Schiemann, O. and Prisner, T.F. (2007) Long-range distance determinations in biomacromolecules by EPR spectroscopy. Q. Rev. Biophys., 40, 1-53.
7. Griffith, O.H. and Waggoner, A.S. (1969) Nitroxide free radicals: spin labels for probing biomolecular structure. Acc. Chem. Res., 2, 17-24.
8. Miller, T.R., Alley, S.C., Reese, A.W., Solomon, M.S., McCallister, W.V., Mailer, C., Robinson, B.H. and Hopkins, P.B. (1995) A probe for sequence-dependent nucleic acid dynamics. J. Am. Chem. Soc, 117, 9377-9378.
9. Schiemann, O., Cekan, P., Margraf, D., Prisner, T.F. and Sigurdsson, S.T. (2009) Relative orientation of rigid nitroxides by PELDOR: beyond distance measurements in nucleic acids. Angew. Chem. Int. Ed., 48, 3292-3295.
10. Barhate, N., Cekan, P., Massey, A. and Sigurdsson, S. (2007) A nucleoside that contains a rigid nitroxide spin label: a fluorophore in disguise. Angew. Chem. Int. Ed., 46, 2655-2658.
11. Cekan, P., Smith, A.L., Barhate, N., Robinson, B.H. and Sigurdsson, S.T. (2008) Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation. Nucleic Acids Res., 36, 5946-5954.
12. Smith, A.L., Cekan, P., Brewood, G.P., Okonogi, T.M., Alemayehu, S., Hustedt, E.J., Benight, A.S., Sigurdsson, S.T. and Robinson, B.H. (2009) Conformational equilibria of bulged sites in duplex DNA studied by EPR spectroscopy. J. Phys. Chem. B, 113, 2664-2675.
13. Cekan, P., Jonsson, E.O. and Sigurdsson, S.T. (2009) Folding of the cocaine aptamer studied by EPR and fluorescence spectroscopies using the bifunctional spectroscopic probe C. Nucleic Acids Res., 37, 3990-3995.
14. Marko, A., Denysenkov, V., Margraf, D., Cekan, P., Schiemann, O., Sigurdsson, S.T. and Prisner, T.F. (2011) Conformational flexibility of DNA. J. Am. Chem. Soc., 133, 13375-13379.
15. Shelke, S.A. and Sigurdsson, S.T. (2010) Noncovalent and site-directed spin labeling of nucleic acids. Angew. Chem. Int. Ed., 49, 7984-7986.
16. Jeschke, G., Chechik, V., Ionita, P., Godt, A., Zimmermann, H., Banham, J., Timmel, C.R., Hilger, D. and Jung, H. (2006) DeerAnalysis2006-a comprehensive software package for analyzing pulsed ELDOR data. Appl. Magn. Reson., 30, 473-498.
17. Reginsson, G.W., Hunter, R.I., Cruickshank, P.A.S., Bolton, D.R., Sigurdsson, S.T., Smith, G.M. and Schiemann, O. (2012) W-band PELDOR with 1kW microwave power: molecular geometry, flexibility and exchange coupling. J. Magn. Reson., 216, 175-182.
18. Galas, D.J. and Schmitz, A. (1978) DNAase footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res., 5, 3157-3170.
19. Welsh, J. and Cantor, C.R. (1984) Protein-DNA cross-linking. Trends Biochem. Sci., 9, 505-508.
20. Lohman, T.M. and Bujalowski, W. (1991) Thermodynamic methods for model-independent determination of equilibrium binding isotherms for protein-DNA interactions: spectroscopic approaches to monitor binding. Methods Enzymol., 208, 258-290.
21. Rhodes, D., Schwabe, J.W.R., Chapman, L. and Fairall, L. (1996) Towards an understanding of protein-DNA recognition. Philos. Trans. Roy Soc. B: Biol. Sci., 351, 501-509.
22. Luscombe, N.M., Austin, S.E., Berman, H.M. and Thornton, J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol., 1, 001.1-001.10.
23. Frederick, C.A., Grable, J., Melia, M., Samudzi, C., Jen-Jacobson, L., Wang, B.-C., Greene, P., Boyer, H.W. and Rosenberg, J.M. (1984) Kinked DNA in crystalline complex with EcoRI endonuclease. Nature, 309, 327-331.
24. Prestegard, J.H., Al-Hashimi, H.M. and Tolman, J.R. (2000) NMR structures of biomolecules using field oriented media and residual dipolar couplings. Q. Rev. Biophys., 33, 371-424.
25. Renault, M., Cukkemane, A. and Baldus, M. (2010) Solid-state NMR spectroscopy on complex biomolecules. Angew. Chem. Int. Ed., 49, 8346-8357.
26. Langowski, J., Benight, A.S., Fujimoto, B.S., Schurr, J.M. and Schomburg, U. (1985) Change of conformation and internal dynamics of supercoiled DNA upon binding of Escherichia coli single-strand binding protein. Biochemistry, 24, 4022-4028.
27. Hillisch, A., Lorenz, M. and Diekmann, S. (2001) Recent advances in FRET: distance determination in protein-DNA complexes. Curr. Opin. Struct. Biol., 11, 201-207.
28. Steinhoff, H. (2004) Inter-and intra-molecular distances determined by EPR spectroscopy and site-directed spin labeling reveal protein-protein and protein-oligonucleotide interaction. Biol. Chem., 385, 913-920.
29. Slichter, C.P. (1990) Principles of Magnetic Resonance, 3rd edn. Springer, Heidelberg, Germany.
30. Bode, B.E., Margraf, D., Plackmeyer, J., Durner, G., Prisner, T.F. and Schiemann, O. (2008) Counting the monomers in nanometer-sized oligomers by pulsed electron-electron double resonance. J. Am. Chem. Soc, 129, 6736-6745.
31. Shelke, SA. and Sigurdsson, S.T. (2011) Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label c. Nucleic Acids Res., 40, 3732-3740.
32. Jeschke, G. and Polyhach, Y. (2007) Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance. Phys. Chem. Chem. Phys., 9, 1895-1910.
33. Godt, A., Schulte, M., Zimmermann, H. and Jeschke, G (2006) How flexible are poly (paraphenyleneethynylene)s? Angew. Chem. Int. Ed., 45, 7560-7564.
34. Gore, J., Bryant, Z., Nollmann, M., Le, M.U., Cozzarelli, N.R. and Bustamante, C. (2006) DNA overwinds when stretched. Nature, 442, 836-839.
35. Marko, J. (1997) Stretching must twist DNA. Europhys. Lett., 38, 183-188.
36. Lewis, M., Chang, G., Horton, N.C., Kercher, M.A., Pace, H.C., Schumacher, M.A., Brennan, R.G. and Lu, P. (1996) Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science, 271, 1247-1254.
37. Bahl, C.P., Wu, R., Stawinsky, J. and Narang, S.A. (1977) Minimal length of the lactose operator sequence for the specific recognition by the lactose repressor. Proc. Natl Acad. Sci. USA, 74, 966-970.
38. Bell, C. and Lewis, M. (2000) A closer view of the conformation of the Lac repressor bound to operator. Nat. Struct. Mol. Biol., 7, 209-214.
39. Lewis, M. (2005) The lac repressor. C. R. Biol., 328, 521-548.
40. Riggs, A.D., Suzuki, H. and Bourgeois, S. (1970) lac repressor-operator interaction. J. Mol. Biol., 48, 67-83.
41. Kuznetsov, N.A., Milov, A.D., Koval, V.V., Samoilova, R.I., Grishin, Y.A., Knorre, D.G., Tsvetkov, Y.D., Fedorova, O.S. and Dzuba, S. (2009) PELDOR study of conformations of double-spinlabeled single-and double-stranded DNA with non-nucleotide inserts. Phys. Chem. Chem. Phys., 11, 6826-6832.
42. Jeschke, G. (2012) Interpretation of dipolar EPR data in terms of protein structure. In: Structure and Bonding, Springer-Verlag Berlin Heidelberg, Germany. pp.1-38.