Probing the structure of RecA-DNA filaments. Advantages of a fluorescent guanine analog

Tetrahedron

Volumn 63, Issue 17, 2007, Pages 3553-3566

  Singleton, Scott F ^a   Roca, Alberto I ^b   Lee, Andrew M ^c   Xiao, Jie ^d  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

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

Author keywords

DNA repair; Fluorescence; Pteridine nucleoside; Recombination

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA; FLUORESCEIN; FLUORESCENT DYE; GUANINE DERIVATIVE; ISOXANTHOPTERIN; NUCLEOSIDE; OLIGONUCLEOTIDE; PTERIN DERIVATIVE; RECA PROTEIN;

ARTICLE; BACTERIAL VIRULENCE; DNA PROBE; DNA RECOMBINATION; DNA REPAIR; DNA STRUCTURE; ESCHERICHIA COLI; GENE INTERACTION; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; RECA GENE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 33947192465     PISSN: 00404020     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tet.2006.10.092     Document Type: Article

References (98)

1. Matic I., Taddei F., and Radman M. Res. Microbiol. 155 (2004) 337-341
2. Friedberg E.C., Walker G.C., and Siede W. DNA Repair and Mutagenesis (1995), ASM, Washington, DC 407-464
3. Sassanfar M., and Roberts J.W. J. Mol. Biol. 212 (1990) 79-96
4. Goodman M.F. Trends Biochem. Sci. 25 (2000) 189-195
5. Courcelle J., Ganesan A.K., and Hanawalt P.C. BioEssays 23 (2001) 463-470
6. Roca A.I., and Cox M.M. Prog. Nucleic Acid Res. Mol. Biol. 56 (1997) 129-223
7. Casjens S. Mol. Microbiol. 49 (2003) 277-300
8. Kline K.A., Sechman E.V., Skaar E.P., and Seifert H.S. Mol. Microbiol. 50 (2003) 3-13
9. Bisognano C., Kelley W.L., Estoppey T., Francois P., Schrenzel J., Li D., Lew D.P., Hooper D.C., Cheung A.L., and Vaudaux P. J. Biol. Chem. 279 (2004) 9064-9071
10. Miller C., Thomsen L.E., Gaggero C., Mosseri R., Ingmer H., and Cohen S.N. Science 305 (2004) 1629-1631
11. Hersh M.N., Ponder R.G., Hastings P.J., and Rosenberg S.M. Res. Microbiol. 155 (2004) 352-359
12. Foster P.L. Mutat. Res. 569 (2005) 3-11
13. Beaber J.W., Hochhut B., and Waldor M.K. Nature 427 (2004) 72-74
14. Hastings P.J., Rosenberg S.M., and Slack A. Trends Microbiol. 12 (2004) 401-404
15. Lee A.M., and Singleton S.F. J. Inorg. Biochem. 98 (2004) 1981-1986
16. Lee A.M., Ross C.T., Zeng B.B., and Singleton S.F. J. Med. Chem. 48 (2005) 5408-5411
17. Kowalczykowski S.C., and Eggleston A.K. Annu. Rev. Biochem. 63 (1994) 991-1043
18. Egelman E.H., and Stasiak A. Micron 24 (1993) 309-324
19. Bell C.E. Mol. Microbiol. 58 (2005) 358-366
20. McGrew D.A., and Knight K.L. Crit. Rev. Biochem. Mol. Biol. 38 (2003) 385-432
21. Yu X., VanLoock M.S., Yang S., Reese J.T., and Egelman E.H. Curr. Protein Pept. Sci. 5 (2004) 73-79
22. Egelman E.H., and Stasiak A. J. Mol. Biol. 200 (1988) 329-349
23. Lee A.M., and Singleton S.F. Biochemistry 45 (2006) 4514-4529
24. Xiao J., Lee A.M., and Singleton S.F. Chembiochem 7 (2006) 1265-1278
25. Yu X., and Egelman E.H. J. Mol. Biol. 225 (1992) 193-216
26. Cox J.M., Tsodikov O.V., and Cox M.M. PLoS Biol. 3 (2005) e52
27. Zlotnick A., Mitchell R.S., Steed R.K., and Brenner S.L. J. Biol. Chem. 268 (1993) 22525-22530
28. Honigberg S.M., Gonda D.K., Flory J., and Radding C.M. J. Biol. Chem. 260 (1985) 11845-11851
29. Menetski J.P., Bear D.G., and Kowalczykowski S.C. Proc. Natl. Acad. Sci. U.S.A. 87 (1990) 21-25
30. Daniels M., and Hauswirth W. Science 171 (1971) 675-677
31. Dombroski D.F., Scraba D.G., Bradley R.D., and Morgan A.R. Nucleic Acids Res. 11 (1983) 7487-7504
32. Eriksson S., Nordén B., and Takahashi M. J. Biol. Chem. 268 (1993) 1805-1810
33. Morrical S.W., Lee J., and Cox M.M. Biochemistry 25 (1986) 1482-1494
34. Wittung P., Ellouze C., Maraboeuf F., Takahashi M., and Norden B. Eur. J. Biochem. 245 (1997) 715-719
35. Sjöback R., Nygren J., and Kubista M. Biopolymers 46 (1998) 445-453
36. Ellouze C., Selmane T., Kim H.K., Tuite E., Norden B., Mortensen K., and Takahashi M. Eur. J. Biochem. 262 (1999) 88-94
37. Bar-Ziv R., and Libchaber A. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 9068-9073
38. Gourves A.S., Defais M., and Johnson N.P. J. Biol. Chem. 276 (2001) 9613-9619
39. Norman D.G., Grainger R.J., Uhrin D., and Lilley D.M. Biochemistry 39 (2000) 6317-6324
40. Volodin A.A., Smirnova H.A., and Bocharova T.N. FEBS Lett. 349 (1994) 65-68
41. Silver M.S., and Fersht A.R. Biochemistry 21 (1982) 6066-6072
42. Kouchakdjian M., Eisenberg M., Yarema K., Basu A., Essigmann J., and Patel D.J. Biochemistry 30 (1991) 1820-1828
43. Hawkins M.E. In: Lakowicz J.R. (Ed). Topics in Fluorescence Spectroscopy: DNA Technology (2003), Plenum, New York, NY 151-176
44. Bujalowski W., and Jezewska M.J. J. Mol. Biol. 295 (2000) 831-852
45. Cazenave C., Toulmé J.J., and Hélène C. EMBO J. 2 (1983) 2247-2251
46. Menetski J.P., and Kowalczykowski S.C. J. Mol. Biol. 181 (1985) 281-295
47. Raney K.D., Sowers L.C., Millar D.P., and Benkovic S.J. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 6644-6648
48. Bjornson K.P., Moore K.J.M., and Lohman T.M. Biochemistry 35 (1996) 2268-2282
49. Gupta R.C., Folta-Stogniew E., O'Malley S., Takahashi M., and Radding C.M. Mol. Cells 4 (1999) 705-714
50. Sen S., Krishnamoorthy G., and Rao B.J. FEBS Lett. 491 (2001) 289-298
51. Singleton S.F., Shan F., Kanan M.W., McIntosh C.M., Stearman C.J., Helm J.S., and Webb K.J. Org. Lett. 3 (2001) 3919-3922
52. Lehrach H., and Scheit K.H. Biochim. Biophys. Acta 308 (1973) 28-34
53. Bloom L.B., Otto M.R., Beechem J.M., and Goodman M.F. Biochemistry 32 (1993) 11247-11258
54. Wu P., Nordlund T.M., Gildea B., and McLaughlin L.W. Biochemistry 29 (1990) 6508-6514
55. Hawkins M.E., Pfleiderer W., Balis F.M., Porter D., and Knutson J.R. Anal. Biochem. 244 (1997) 86-95
56. Bianco P.R., and Weinstock G.M. Nucleic Acids Res. 24 (1996) 4933-4939
57. Leahy M.C., and Radding C.M. J. Biol. Chem. 261 (1986) 6954-6960
58. Podyminogin M.A., Meyer R.B., and Gamper H.B. Biochemistry 34 (1995) 13098-13108
59. Lee A.M., Xiao J., and Singleton S.F. J. Mol. Biol. 360 (2006) 343-359
60. Xiao J., Lee A.M., and Singleton S.F. Biopolymers 81 (2006) 473-496
61. Brenner S.L., Mitchell R.S., Morrical S.W., Neuendorf S.K., Schutte B.C., and Cox M.M. J. Biol. Chem. 262 (1987) 4011-4016
62. Kelley S.O., and Barton J.K. Science 283 (1999) 375-381
63. O'Neill M.A., Dohno C., and Barton J.K. J. Am. Chem. Soc. 126 (2004) 1316-1317
64. Wan C., Fiebig T., Schiemann O., Barton J.K., and Zewail A.H. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 14052-14055
65. Kowalczykowski S.C. Biochemistry 25 (1986) 5872-5881
66. Mikawa T., Masui R., and Kuramitsu S. J. Biochem. (Tokyo) 123 (1998) 450-457
67. Howard-Flanders P., West S.C., and Stasiak A. Nature 309 (1984) 215-219
68. Mazin A.V., and Kowalczykowski S.C. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 10673-10678
69. Wittung P., Bazemore L.R., Takahashi M., Norden B., and Radding C. Biochemistry 35 (1996) 15349-15355
70. Roca A.I., and Singleton S.F. J. Am. Chem. Soc. 125 (2003) 15366-15375
71. Xiao J., and Singleton S.F. J. Mol. Biol. 320 (2002) 529-558
72. Singleton S.F., and Xiao J. Biopolymers 61 (2001) 145-158
73. Ramreddy T., Sen S., Rao B.J., and Krishnamoorthy G. Biochemistry 42 (2003) 12085-12094
74. Gumbs O.H., and Shaner S.L. Biochemistry 37 (1998) 11692-11706
75. Folta-Stogniew E., O'Malley S., Gupta R., Anderson K.S., and Radding C.M. Mol. Cells 15 (2004) 965-975
76. Fujimoto J., Nuesca Z., Mazurek M., and Sowers L.C. Nucleic Acids Res. 24 (1996) 754-759
77. Xu D.G., and Nordlund T.M. Biophys. J. 78 (2000) 1042-1058
78. Fiebig T., Wan C., and Zewail A.H. Chemphyschem 3 (2002) 781-788
79. Nordlund T.M., Wu P., Andersson S., Nilsson L., Rigler R., Gräslund A., McLaughlin L.W., and Gildea B. Proc. SPIE 1204 (1990) 344-353
80. Bazemore L.R., Folta-Stogniew E., Takahashi M., and Radding C.M. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 11863-11868
81. Bazemore L.R., Takahashi M., and Radding C.M. J. Biol. Chem. 272 (1997) 14672-14682
82. Wigle T.J., Lee A.M., and Singleton S.F. Biochemistry 45 (2006) 4502-4513
83. Fulconis R., Mine J., Bancaud A., Dutreix M., and Viovy J.L. EMBO J. (2006)
84. Joo C., McKinney S.A., Nakamura M., Rasnik I., Myong S., and Ha T. Cell 126 (2006) 515-527
85. Li B.S., Sattin B.D., and Goh M.C. Nano Lett. 6 (2006) 1474-1478
86. Shivashankar G.V., Feingold M., Krichevsky O., and Libchaber A. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 7916-7921
87. Singleton S.F., Simonette R.A., Sharma N.C., and Roca A.I. Protein Expr. Purif. 26 (2002) 476-488
88. Craig N.L., and Roberts J.W. J. Biol. Chem. 256 (1981) 8039-8044
89. Ts'o P.O.P., Rapaport S.A., and Bollum F.J. Biochemistry 5 (1966) 4153-4170
90. Bock R.M., Ling N.-S., Morell S.A., and Lipton S.H. Arch. Biochem. Biophys. 62 (1956) 253-264
91. Borer P.N. Handbook of Biochemistry and Molecular Biology, Nucleic Acids. 3rd ed. Vol. I (1975), CRC, Cleveland, OH
92. Hawkins M.E., Pfleiderer W., Mazumder A., Pommier Y.G., and Balis F.M. Nucleic Acids Res. 23 (1995) 2872-2880
93. Fox J.J., Wempen I., Hampton A., and Doerr I.L. J. Am. Chem. Soc. 80 (1958) 1669-1675
94. Kato R., and Kuramitsu S. Eur. J. Biochem. 259 (1999) 592-601
95. Ladokhin A.S., Jayasinghe S., and White S.H. Anal. Biochem. 285 (2000) 235-245
96. Silver M.S., and Fersht A.R. Biochemistry 22 (1983) 2860-2866
97. Takahashi M., Strazielle C., Pouyet J., and Daune M. J. Mol. Biol. 189 (1986) 711-714
98. Stewart J.E., and Gallaway W.S. Appl. Opt. 1 (1962) 421-429