A novel secondary DNA binding site in human topoisomerase i unravelled by using a 2D DNA origami platform

ACS Nano

Volumn 4, Issue 10, 2010, Pages 5969-5977

  Subramani, Ramesh ^a   Juul, Sissel ^a   Rotaru, Alexandru ^a   Andersen, Felicie F ^a   Gothelf, Kurt V ^a   Mamdouh, Wael ^a   Besenbacher, Flemming ^a   Dong, Mingdong ^a   Knudsen, Birgitta R ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

atomic force microscopy (AFM); functionalized 2D origami; human topoisomerase I; secondary binding site; supercoil recognition

Indexed keywords

ATOMIC FORCE; COVALENTLY BOUND; DETECTION SCHEME; DNA BINDING SITE; DNA FRAGMENT; DNA INTERACTION; FUNCTIONALIZED; HUMAN TOPOISOMERASE; NUCLEAR ENZYME; SECONDARY BINDING SITE; SINGLE MOLECULE; SUPERCOIL RECOGNITION; SUPERCOILED DNA;

ATOMIC FORCE MICROSCOPY; ATOMS; BINDING ENERGY; BINDING SITES; ENZYMES;

DNA;

CIRCULAR DNA; DNA; DNA TOPOISOMERASE; DODECYL SULFATE SODIUM; RECOMBINANT PROTEIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; BINDING SITE; CHEMISTRY; CONFORMATION; ESCHERICHIA COLI; GEL; HUMAN; METABOLISM; METHODOLOGY; NANOTECHNOLOGY; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; DNA TOPOISOMERASES, TYPE I; DNA, CIRCULAR; ESCHERICHIA COLI; GELS; HUMANS; MICROSCOPY, ATOMIC FORCE; MOLECULAR CONFORMATION; NANOTECHNOLOGY; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; SODIUM DODECYL SULFATE;

EID: 78049323681     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn101662a     Document Type: Article

References (33)

1. Champoux, J. J. DNA Topoisomerases: Structure, Function, and Mechanism Annu. Rev. Biochem. 2001, 70, 369-413
2. Jaxel, C.; Kohn, K. W.; Pommier, Y. Topoisomerase I Interaction with SV40 DNA in the Presence and Absence of Camptothecin Nucleic Acids Res. 1988, 16, 11157-11170
3. Shen, C. C.; Shen, C. K. Specificity and Flexibility of the Recognition of DNA Helical Structure by Eukaryotic Topoisomerase I J. Mol. Biol. 1990, 212, 67-78
4. Parker, L. H.; Champoux, J. J. Analysis of the Biased Distribution of Topoisomerase I Break Sites on Replicating Simian Virus 40 DNA J. Mol. Biol. 1993, 231, 6-18
5. Madden, K. R.; Stewart, L.; Champoux, J. J. Preferential Binding of Human Topoisomerase I to Superhelical DNA EMBO J. 1995, 14, 5399-5409
6. Müller, M. T. Quantitation of Eukaryotic Topoisomerase I Reactivity with DNA. Preferential Cleavage of Supercoiled DNA Biochim. Biophys. Acta 1985, 824, 263-267
7. Camilloni, G.; Martino, E. D.; Caserta, M.; Mauro, E. D. Eukaryotic DNA Topoisomerase I Reaction is Topology Dependent Nucleic Acids Res. 1988, 16, 7071-7085
8. Caserta, M.; Amadei, A.; Camilloni, G.; Mauro, E. D. Regulation of the Function of Eukaryotic DNA Topoisomerase I: Analysis of the Binding Step and of the Catalytic Constants of Topoisomerization as a Function of DNA Topology Biochemistry 1990, 29, 8152-8157
9. Zechiedrich, E. L.; Osheroff, N. Eukaryotic Topoisomerases Recognize Nucleic Acid Topology by Preferentially Interacting with DNA Crossovers EMBO J. 1990, 9, 4555-4562
10. Yang, Z.; Carey, J. F.; Champoux, J. J. Mutational Analysis of the Preferential Binding of Human Topoisomerase I to Supercoiled DNA FEBS J. 2009, 276, 5906-5919
11. Staker, B. L.; Hjerrild, K.; Feese, M. D.; Behnke, C. A.; Burgin, A. B., Jr.; Stewart, L. The Mechanism of Topoisomerase I Poisoning by a Camptothecin Analog Proc Natl Acad Sci U.S.A. 2002, 99, 15387-15392
12. Shuman, S.; Bear, D. G.; Sekiguchi, J. Intramolecular Synapsis of Duplex DNA by Vaccinia Topoisomerase EMBO J. 1997, 3, 6584-6589
13. Moreno-Herrero, F.; Holtzer, L.; Koster, D. A.; Shuman, S.; Dekker, C.; Dekker, N. H. Atomic Force Microscopy Shows that Vaccinia Topoisomerase IB Generates Filaments on DNA in a Cooperative Fashion Nucleic Acids Res. 2005, 33, 5945-5953
14. Patel, A.; Yakovleva, L.; Shuman, S.; Mondragón, A. Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site Structure 2010, 18, 725-733
15. Shuman, S. Vaccinia Virus DNA Topoisomerase: a Model Eukaryotic Type IB Enzyme Biochim. Biophys. Acta 1998, 1400, 321-337
16. Grainge, I.; Jayaram, M. The Integrase Family of Recombinase: Organization and Function of the Active Site Mol. Microbiol. 1999, 33, 449-456
17. Chen, Y.; Narendra, U.; Iype, L. E.; Cox, M. M.; Rice, P. A. Crystal Structure of a Flp Recombinase-Holliday Junction Complex: Assembly of an Active Oligomer by Helix Swapping Mol. Cell 2000, 6, 885-897
18. Guo, F.; Gopaul, D. N.; van Duyne, G. D. Structure of Cre Recombinase Complexed with DNA in a Site-Specific Recombination Synapse Nature 1997, 389, 40-46
19. Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns Nature 2006, 440, 297-302
20. Maune, H. T.; Han, S. P.; Barish., R. D.; Bockrath, M.; Lii, W. A. G.; Rothemund, P. W. K.; Winfree, E. Self-assembly of Carbon Nanotubes into Two-Dimensional Geometries Using DNA Origami Templates Nat. Nanotechnol. 2010, 5, 61-66
21. Sharma, J.; Chhabra, R.; Andersen, C. S.; Gothelf, K. V.; Yan, H.; Liu, Y. Toward Reliable Gold Nanoparticle Patterning on Self-assembled DNA Nanoscaffold J. Am. Chem. Soc. 2008, 130, 7820-7821
22. Hung, A.; Micheel, C. M.; Bozano, L. D.; Osterbur, L. W.; Wallraff, G. M.; Cha, J. N. Large-Area Spatially Ordered Arrays of Gold Nanoparticles Directed by Lithographically Confined DNA Origami Nat. Nanotechnol. 2009, 5, 121-126
23. Kuzyk, A.; Laitinen, K. T.; Törmä, P. DNA Origami as a Nanoscale Template for Protein Assembly Nanotechnology 2009, 20, 235305
24. Kuzuya, A.; Kimura, M.; Numajiri, K.; Koshi, N.; Ohnishi, T.; Okada, F.; Komiyama, M. Precisely Programmed and Robust 2D Streptavidin Nanoarrays by Using Periodical Nanometer-Scale Wells Embedded in DNA Origami Assembly ChemBioChem 2009, 10, 1811-1815
25. Stephanopoulos, N.; Liu, M.; Tong, G. J.; Li, Z.; Liu, Y.; Yan, H.; Francis, M. B. Immobilization and One-Dimensional Arrangement of Virus Capsids with Nanoscale Precision Using DNA Origami Nano Lett. 2010, 10, 2714-2720
26. Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H. Regulation of DNA Methylation Using Different Tensions of Double Strands Constructed in a Defined DNA Nanostructure J. Am. Chem. Soc. 2010, 132, 1592-1597
27. Voigt, N. V.; Torring, T.; Rotaru, A.; Jacobsen, M. F.; Ravnsbaek, J. B.; Subramani, R.; Mamdouh, W.; Kjems, J.; Mokhir, A.; Besenbacher, F. Single-Molecule Chemical Reactions on DNA Origami Nat. Nanotechnol. 2010, 5, 200-203
28. Lisby, M.; Krogh, B. O.; Boege, F.; Westergaard, O.; Knudsen, B. R. Camptothecins Inhibit the Utilization of Hydrogen Peroxide in the Ligation Step of Topoisomerase I Catalysis Biochemistry 1998, 37, 10815-10827
29. Redinbo, M. R.; Stewart, L.; Kuhn, P.; Champoux, J. J.; Hol, W. G. Crystal Structures of Human Topoisomerase I in Covalent and Noncovalent Complexes with DNA Science 1998, 279, 1504-1513
30. Stevnsner, T.; Mortensen, U. H.; Westergaard, O.; Bonven, B. J. Interactions Between Eukaryotic DNA Topoisomerase I and a Specific Binding Sequence J. Biol. Chem. 1989, 264, 10110-10113
31. Bendixen, C.; Thomsen, B.; Alsner, J.; Westergaard, O. Camptothecin-stabilized Topoisomerase I-DNA Adducts Cause Premature Termination of Transcription Biochemistry 1990, 29, 5613-5619
32. Andersen, F. F.; Andersen, K. E.; Kusk, M.; Frøhlich, R. F.; Westergaard, O.; Andersen, A. H.; Knudsen, B. R. Recombinogenic Flap Ligation Mediated by Human Topoisomerase I J. Mol. Biol. 2003, 330, 235-246
33. Lisby, M.; Olesen, J. R.; Skouboe, C.; Krogh, B. O.; Straub, T.; Boege, F.; Velmurugan, S.; Martensen, P. M.; Andersen, A. H.; Jayaram, M. Residues Within the N-terminal Domain of Human Topoisomerase I Play a Direct Role in Relaxation J. Biol. Chem. 2001, 276, 20220-20227