DNA translocation by human uracil DNA glycosylase: The case of single-stranded DNA and clustered uracils

Biochemistry

Volumn 52, Issue 15, 2013, Pages 2536-2544

  Schonhoft, Joseph D ^a   Stivers, James T ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BASE PAIRS; DNA REPAIR; DNA TRANSLOCATION; DOUBLE-STRANDED DNA (DS-DNA); LOCAL SEARCH; SEARCH MECHANISM; SINGLE-STRANDED DNA; URACIL-DNA GLYCOSYLASE;

AROMATIC COMPOUNDS; REPAIR;

DNA;

DOUBLE STRANDED DNA; SINGLE STRANDED DNA; URACIL DNA GLYCOSIDASE;

ARTICLE; GENE INSERTION; GENE TRANSLOCATION; HUMAN; PRIORITY JOURNAL;

DNA, SINGLE-STRANDED; HUMANS; NUCLEIC ACID HETERODUPLEXES; URACIL; URACIL-DNA GLYCOSIDASE;

EID: 84876234449     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi301562n     Document Type: Article

References (32)

1. Stivers, J. T. (2008) Extrahelical damaged base recognition by DNA glycosylase enzymes Chemistry 14, 786-793
2. Longley, D. B., Harkin, D. P., and Johnston, P. G. (2003) 5-Fluorouracil: Mechanisms of action and clinical strategies Nat. Rev. Cancer 3, 330-338
3. Van Triest, B., Pinedo, H. M., Giaccone, G., and Peters, G. J. (2000) Downstream molecular determinants of response to 5-fluorouracil and antifolate thymidylate synthase inhibitors Ann. Oncol. 11, 385-391
4. Di Noia, J. M. and Neuberger, M. S. (2007) Molecular mechanisms of antibody somatic hypermutation Annu. Rev. Biochem. 76, 1-22
5. Stavnezer, J., Guikema, J. E. J., and Schrader, C. E. (2008) Mechanism and regulation of class switch recombination Annu. Rev. Immunol. 26, 261-292
6. Li, Z., Woo, C. J., Iglesias-Ussel, M. D., Ronai, D., and Scharff, M. D. (2004) The generation of antibody diversity through somatic hypermutation and class switch recombination Genes Dev. 18, 1-11
7. Porecha, R. H. and Stivers, J. T. (2008) Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils Proc. Natl. Acad. Sci. U.S.A. 105, 10791-10796
8. Schonhoft, J. D. and Stivers, J. T. (2012) Timing facilitated site transfer of an enzyme on DNA Nat. Chem. Biol. 8, 205-210
9. Halford, S. E. and Marko, J. F. (2004) How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32, 3040-3052
10. Berg, H. C. (1993) Random walks in biology, Princeton University Press, Princeton, NJ.
11. Stanford, N. P., Szczelkun, M. D., Marko, J. F., and Halford, S. E. (2000) One- and three-dimensional pathways for proteins to reach specific DNA sites EMBO J. 19, 6546-6557
12. Berg, O. G., Winter, R. B., and von Hippel, P. H. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory Biochemistry 20, 6929-6948
13. Murphy, M. C., Rasnik, I., Cheng, W., Lohman, T. M., and Ha, T. (2004) Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy Biophys. J. 86, 2530-2537
14. Chen, H., Meisburger, S. P., Pabit, S. A., Sutton, J. L., Webb, W. W., and Pollack, L. (2012) Ionic strength-dependent persistence lengths of single-stranded RNA and DNA Proc. Natl. Acad. Sci. U.S.A. 109, 799-804
15. Maul, R. W. and Gearhart, P. J. (2010) AID and Somatic Hypermutation Adv. Immunol. 105, 159-191
16. Bransteitter, R., Pham, P., Calabrese, P., and Goodman, M. F. (2004) Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase J. Biol. Chem. 279, 51612-51621
17. Pham, P., Chelico, L., and Goodman, M. F. (2007) DNA deaminases AID and APOBEC3G act processively on single-stranded DNA DNA Repair 6, 689-692, 693-694 (author reply)
18. Pham, P., Bransteitter, R., Petruska, J., and Goodman, M. F. (2003) Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation Nature 424, 103-107
19. Friedman, J. I., Majumdar, A., and Stivers, J. T. (2009) Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage Nucleic Acids Res. 37, 3493-3500
20. Parker, J. B., Bianchet, M. A., Krosky, D. J., Friedman, J. I., Amzel, L. M., and Stivers, J. T. (2007) Enzymatic capture of an extrahelical thymine in the search for uracil in DNA Nature 449, 433-437
21. Parker, J. B. and Stivers, J. T. (2008) Uracil DNA glycosylase: Revisiting substrate-assisted catalysis by DNA phosphate anions Biochemistry 47, 8614-8622
22. Jiang, Y. L., Ichikawa, Y., Song, F., and Stivers, J. T. (2003) Powering DNA Repair through Substrate Electrostatic Interactions Biochemistry 42, 1922-1929
23. Xiao, G., Tordova, M., Jagadeesh, J., Drohat, A. C., Stivers, J. T., and Gilliland, G. L. (1999) Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: Structure and glycosylase mechanism revisited Proteins 35, 13-24
24. Schurr, J. M. (1979) The one-dimensional diffusion coefficient of proteins absorbed on DNA: Hydrodynamic considerations Biophys. Chem. 9, 413-414
25. Bagchi, B., Blainey, P. C., and Xie, X. S. (2008) Diffusion Constant of a Nonspecifically Bound Protein Undergoing Curvilinear Motion along DNA J. Phys. Chem. B 112, 6282-6284
26. Chelico, L., Pham, P., Calabrese, P., and Goodman, M. F. (2006) APOBEC3G DNA deaminase acts processively 3′ → 5′ on single-stranded DNA Nat. Struct. Mol. Biol. 13, 392-399
27. Senavirathne, G., Jaszczur, M., Auerbach, P. A., Upton, T. G., Chelico, L., Goodman, M. F., and Rueda, D. (2012) Single-stranded DNA scanning and deamination by APOBEC3G cytidine deaminase at single molecule resolution J. Biol. Chem. 287, 15826-15835
28. Roberts, V. A., Pique, M. E., Hsu, S., Li, S., Slupphaug, G., Rambo, R. P., Jamison, J. W., Liu, T., Lee, J. H., Tainer, J. A., Ten Eyck, L. F., and Woods, V. L. (2012) Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase Nucleic Acids Res. 40, 6070-6081
29. Krosky, D. J., Schwarz, F. P., and Stivers, J. T. (2004) Linear Free Energy Correlations for Enzymatic Base Flipping: How Do Damaged Base Pairs Facilitate Specific Recognition? Biochemistry 43, 4188-4195
30. Krosky, D. J., Song, F., and Stivers, J. T. (2005) The Origins of High-Affinity Enzyme Binding to an Extrahelical DNA Base Biochemistry 44, 5949-5959
31. Pérez-Durán, P., Belver, L., de Yébenes, V. G., Delgado, P., Pisano, D. G., and Ramiro, A. R. (2012) UNG shapes the specificity of AID-induced somatic hypermutation J. Exp. Med. 209, 1379-1389
32. Mazur, A. K. (2006) Evaluation of elastic properties of atomistic DNA models Biophys. J. 91, 4507-4518