Specificity of binding of single-stranded DNA-binding protein to its target

Biochemistry

Volumn 51, Issue 7, 2012, Pages 1500-1509

  Shlyakhtenko, Luda S ^a   Lushnikov, Alexander Y ^a   Miyagi, Atsushi ^a   Lyubchenko, Yuri L ^a  

^a UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DUPLEXES; DNA SUBSTRATES; DOUBLE STRANDED DNA; GENETIC PROCESS; HIGH IONIC STRENGTH; HYBRID SUBSTRATES; SINGLE-STRANDED DNA (SS-DNA); SINGLE-STRANDED DNA-BINDING PROTEINS; SPECIFIC RECOGNITION;

ATOMIC FORCE MICROSCOPY; ESCHERICHIA COLI; IONIC STRENGTH; POSITIVE IONS;

DNA;

DNA BINDING PROTEIN; DNA HYBRID; MAGNESIUM ION; SINGLE STRANDED DNA; SODIUM CHLORIDE;

ARTICLE; ATOMIC FORCE MICROSCOPY; BINDING KINETICS; COMPLEX FORMATION; DNA PROTEIN COMPLEX; ESCHERICHIA COLI; IONIC STRENGTH; MOLECULAR RECOGNITION; MORPHOLOGY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION;

BIOCHEMISTRY; CATIONS; DNA; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MAGNESIUM; MICROSCOPY, ATOMIC FORCE; PROTEIN BINDING; SALTS;

EID: 84857407275     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201863z     Document Type: Article

References (28)

1. Kur, J., Olszewski, M., Dlugolecka, A., and Filipkowski, P. (2005) Single-stranded DNA-binding proteins (SSBs): Sources and applications in molecular biology Acta Biochim. Pol. 52, 569-574
2. Krauss, G., Sindermann, H., Schomburg, U., and Maass, G. (1981) Escherichia coli single-strand deoxyribonucleic acid binding protein: Stability, specificity, and kinetics of complexes with oligonucleotides and deoxyribonucleic acid Biochemistry 20, 5346-5352
3. Dillingham, M. S., Tibbles, K. L., Hunter, J. L., Bell, J. C., Kowalczykowski, S. C., and Webb, M. R. (2008) Fluorescent single-stranded DNA binding protein as a probe for sensitive, real-time assays of helicase activity Biophys. J. 95, 3330-3339
4. McEntee, K., Weinstock, G. M., and Lehman, I. R. (1980) recA protein-catalyzed strand assimilation: Stimulation by Escherichia coli single-stranded DNA-binding protein Proc. Natl. Acad. Sci. U.S.A. 77, 857-861
5. Bochkarev, A. and Bochkareva, E. (2004) From RPA to BRCA2: Lessons from single-stranded DNA binding by the OB-fold Curr. Opin. Struct. Biol. 14, 36-42
6. Shereda, R. D., Kozlov, A. G., Lohman, T. M., Cox, M. M., and Keck, J. L. (2008) SSB as an organizer/mobilizer of genome maintenance complexes Crit. Rev. Biochem. Mol. Biol. 43, 289-318
7. Lohman, T. M. and Ferrari, M. E. (1994) Escherichia coli single-stranded DNA-binding protein: Multiple DNA-binding modes and cooperativities Annu. Rev. Biochem. 63, 527-570
8. Ryzhikov, M., Koroleva, O., Postnov, D., Tran, A., and Korolev, S. (2011) Mechanism of RecO recruitment to DNA by single-stranded DNA binding protein Nucleic Acids Res. 39, 6305-6314
9. Overman, L. B. and Lohman, T. M. (1994) Linkage of pH, anion and cation effects in protein-nucleic acid equilibria. Escherichia coli SSB protein-single stranded nucleic acid interactions J. Mol. Biol. 236, 165-178
10. Raghunathan, S., Kozlov, A. G., Lohman, T. M., and Waksman, G. (2000) Structure of the DNA binding domain of E. coli SSB bound to ssDNA Nat. Struct. Biol. 7, 648-652
11. Chrysogelos, S. and Griffith, J. (1982) Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like units Proc. Natl. Acad. Sci. U.S.A. 79, 5803-5807
12. Schneider, R. J. and Wetmur, J. G. (1982) Kinetics of transfer of Escherichia coli single strand deoxyribonucleic acid binding protein between single-stranded deoxyribonucleic acid molecules Biochemistry 21, 608-615
13. Lyubchenko, Y. L. (2004) DNA structure and dynamics: An atomic force microscopy study Cell Biochem. Biophys. 41, 75-98
14. Lyubchenko, Y. L. and Shlyakhtenko, L. S. (2009) AFM for analysis of structure and dynamics of DNA and protein-DNA complexes Methods 47, 206-213
15. Lyubchenko, Y. L., Shlyakhtenko, L. S., and Ando, T. (2011) Imaging of nucleic acids with atomic force microscopy Methods 54, 274-283
16. Lyubchenko, Y. L. (2011) Preparation of DNA and nucleoprotein samples for AFM imaging Micron 42, 196-206
17. Miyagi, A., Ando, T., and Lyubchenko, Y. L. (2011) Dynamics of nucleosomes assessed with time-lapse high-speed atomic force microscopy Biochemistry 50, 7901-7908
18. Hamon, L., Pastre, D., Dupaigne, P., Le Breton, C., Le Cam, E., and Pietrement, O. (2007) High-resolution AFM imaging of single-stranded DNA-binding (SSB) protein-DNA complexes Nucleic Acids Res. 35, e58
19. Shlyakhtenko, L. S., Lushnikov, A. Y., Li, M., Lackey, L., Harris, R. S., and Lyubchenko, Y. L. (2011) Atomic force microscopy studies provide direct evidence for dimerization of the HIV restriction factor APOBEC3G J. Biol. Chem. 286, 3387-3395
20. Shlyakhtenko, L. S., Gilmore, J., Kriatchko, A. N., Kumar, S., Swanson, P. C., and Lyubchenko, Y. L. (2009) Molecular mechanism underlying RAG1/RAG2 synaptic complex formation J. Biol. Chem. 284, 20956-20965
21. Uchihashi, T. and Ando, T. (2011) High-speed atomic force microscopy and biomolecular processes Methods Mol. Biol. 736, 285-300
22. Lohman, T. M., Overman, L. B., and Datta, S. (1986) Salt-dependent changes in the DNA binding co-operativity of Escherichia coli single strand binding protein J. Mol. Biol. 187, 603-615
23. Shlyakhtenko, L. S., Lushnikov, A. Y., and Lyubchenko, Y. L. (2009) Dynamics of nucleosomes revealed by time-lapse atomic force microscopy Biochemistry 48, 7842-7848
24. Bujalowski, W., Overman, L. B., and Lohman, T. M. (1988) Binding mode transitions of Escherichia coli single strand binding protein-single-stranded DNA complexes. Cation, anion, pH, and binding density effects J. Biol. Chem. 263, 4629-4640
25. Roy, R., Kozlov, A. G., Lohman, T. M., and Ha, T. (2007) Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein J. Mol. Biol. 369, 1244-1257
26. Delagoutte, E., Heneman-Masurel, A., and Baldacci, G. (2011) Single-stranded DNA binding proteins unwind the newly synthesized double-stranded DNA of model miniforks Biochemistry 50, 932-944
27. Kuznetsov, S. V., Kozlov, A. G., Lohman, T. M., and Ansari, A. (2006) Microsecond dynamics of protein-DNA interactions: Direct observation of the wrapping/unwrapping kinetics of single-stranded DNA around the E. coli SSB tetramer J. Mol. Biol. 359, 55-65
28. Pham, P., Calabrese, P., Park, S. J., and Goodman, M. F. (2011) Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity J. Biol. Chem. 286, 24931-24942