A clamp-like biohybrid catalyst for DNA oxidation

Nature Chemistry

Volumn 5, Issue 11, 2013, Pages 945-951

  Van Dongen, Stijn F M ^a   Clerx, Joost ^a   Nørgaard, Kasper ^a   Bloemberg, Tom G ^a   Cornelissen, Jeroen J L M ^a   Trakselis, Michael A ^b   Nelson, Scott W ^c   Benkovic, Stephen J ^d   Rowan, Alan E ^a   Nolte, Roeland J M ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^b 801 Chevron Science Center ^*  (United States)

^c IOWA STATE UNIVERSITY   (United States)

^d PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COORDINATION COMPOUND; DNA; OLIGOPEPTIDE;

ATOMIC FORCE MICROSCOPY; CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; DNA DAMAGE; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; ARTICLE;

BASE SEQUENCE; CATALYSIS; COORDINATION COMPLEXES; DNA; DNA DAMAGE; MICROSCOPY, ATOMIC FORCE; MODELS, MOLECULAR; OLIGOPEPTIDES; OXIDATION-REDUCTION;

EID: 84887798690     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.1752     Document Type: Article

References (30)

1. Breyer, W. A. & Matthews, B. W. A structural basis for processivity. Protein Sci. 10, 1699-1711 (2001).
2. Stillman, B. Smart machines at the DNA-replication fork. Cell 78, 725-728 (1994).
3. Kovall, R. & Matthews, B. W. Toroidal structure of l-exonuclease. Science 277, 1824-1827 (1997).
4. Benkovic, S. J., Valentine, A. M., & Salinas, F. Replisome-mediated DNA replication. Annu. Rev. Biochem. 70, 181-208 (2001).
5. Champoux, J. J. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70, 369-413 (2001).
6. López de Saro, F. J., Georgescu, R. E. & O'Donnell, M. A peptide switch regulates DNA polymerase processivity. Proc. Natl Acad. Sci. USA 100, 14689-14694 (2003).
7. Índiani, C., McÍnerney, P., Georgescu, R., Goodman, M. F & O'Donnell, M. A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously. Mol. Cell 19, 805-815 (2005).
8. Trakselis, M. A., Alley, S. C., Abel-Santos, E. & Benkovic, S. J. Creating a dynamic picture of the sliding clamp during T4 DNA polymerase holoenzyme assembly by using fluorescence resonance energy transfer. Proc. Natl Acad. Sci. USA 98, 8368-8375 (2001).
9. Yang, J., Zhuang, Z., Roccasecca, R. M., Trakselis, M. A. & Benkovic, S. J. The dynamic processivity of the T4 DNA polymerase during replication. Proc. Natl Acad. Sci. USA 101, 8289-8294 (2004).
10. Breslow, R. Artificial enzymes. Science 218, 532-537 (1982).
11. Murakami, Y., Kikuchi, J., Hisaeda, Y. & Hayashida, O. Artificial enzymes. Chem. Rev. 96, 721-758 (1996).
12. Nanda, V. & Koder, R. L. Designing artificial enzymes by intuition and computation. Nature Chem. 2, 15-24 (2010).
13. Takashima, Y., Osaki, M., Íshimaru, Y., Yamaguchi, H. & Harada, A. Artificial molecular clamp: a novel device for synthetic polymerases. Angew. Chem. Ínt. Ed. 50, 7524-7528 (2011).
14. Thordarson, P., Bijsterveld, E. J., Rowan, A. E. & Nolte, R. J. Epoxidation of polybutadiene by a topologically linked catalyst. Nature 424, 915-918 (2003).
15. Coumans, R. G. E., Elemans, J., Nolte, R. J. M. & Rowan, A. E. Processive enzyme mimic: kinetics and thermodynamics of the threading and sliding process. Proc. Natl Acad. Sci. USA 103, 19647-19651 (2006).
16. Monnereau, C. et al. Porphyrin macrocyclic catalysts for the processive oxidation of polymer substrates. J. Am. Chem. Soc. 132, 1529-1531 (2010).
17. Meunier, B. Metalloporphyrins as versatile catalysts for oxidation reactions and oxidative DNA cleavage. Chem. Rev. 92, 1411-1456 (1992).
18. Pratviel, G., Bernadou, J. & Meunier, B. DNA and RNA cleavage by metal complexes. Adv. Ínorg. Chem. 45, 251-312 (1998).
19. Bernadou, J. & Meunier, B. Biomimetic chemical catalysts in the oxidative activation of drugs. Adv. Synth. Catal. 346, 171-184 (2004).
20. Berdis, A., Soumillion, P. & Benkovic, S. The carboxyl terminus of the bacteriophage T4 DNA polymerase is required for holoenzyme complex formation. Proc. Natl Acad. Sci. USA 93, 12822-12827 (1996).
21. Zhuang, Z. H., Berdis, A. J. & Benkovic, S. J. An alternative clamp loading pathway via the T4 clamp loader gp44/62-DNA complex. Biochemistry 45, 7976-7989 (2006).
22. Smiley, R. D., Zhuang, Z. H., Benkovic, S. J. & Hammes, G. G. Single-molecule investigation of the T4 bacteriophage DNA polymerase holoenzyme: multiple pathways of holoenzyme formation. 45, 7990-7997 (2006).
23. Vologodskii, A. V., Lukashin, A. V., Anshelevich, V. V. & Frank- Kamenetskii, M. D. Fluctuations in superhelical DNA. Nucleic Acids Res. 6, 967-982 (1979).
24. Freifeld, D. & Trumbo, B. Matching of single-strand breaks to form doublestrand breaks in DNA. Biopolymers 7, 681-693 (1969).
25. Pratviel, G., Duarte, V., Bernadou, J. & Meunier, B. Nonenzymic cleavage and ligation of DNA at a three A+T base pair site. A two-step pseudohydrolysis of DNA. J. Am. Chem. Soc. 115, 7939-7943 (1993).
26. Neish, C. S., Martin, Í. L., Henderson, R. M. & Edwardson, J. M. Direct visualization of ligand-protein interactions using atomic force microscopy. Br. J. Pharmacol. 135, 1943-1950 (2002).
27. Alley, S. C., Abel-Santos, E. & Benkovic, S. J. Tracking sliding clamp opening and closing during bacteriophage T4 DNA polymerase holoenzyme assembly. Biochemistry 39, 3076-3090 (2000).
28. Jarvis, T. C., Paul, L. S., Hockensmith, J. W. & Von Hippel, P. H. Structural and enzymatic studies of the T4 DNA replication system. ÍÍ. ATPase properties of the polymerase accessory protein complex. J. Biol. Chem. 264, 12717-12729 (1989).
29. Heiter, D. F., Lunnen, K. D. & Wilson, G. G. Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCÍ. J. Mol. Biol. 348, 631-640 (2005).
30. Nakamura, J. et al. Highly sensitive apurinic/apyrimidinic site assay can detect spontaneous and chemically induced depurination under physiological conditions. Cancer Res. 58, 222-225 (1998).