A positively charged residue bound in the minor groove does not alter the bending of a DNA duplex

Journal of the American Chemical Society

Volumn 118, Issue 51, 1996, Pages 13073-13074

  Glasfeld, Arthur ^a,b   Schumacher, Maria A ^a   Choi, Kang Yell ^c   Zalkin, Howard ^c   Brennan, Richard G ^a  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b REED COLLEGE   (United States)

^c PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA HELIX; DNA STRUCTURE; IN VITRO STUDY; NUCLEOTIDE SEQUENCE;

EID: 0030447808     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja962416b     Document Type: Article

References (19)

1. Schumacher, M. A.; Choi, K. Y.; Zalkin, H.; Brennan, R. G. Science 1994, 266, 763-770.
2. Werner, M. H.; Gronenborn, A. M.; Clore, G. M. Science 1996, 271, 778-784.
3. Travers, A. A. Nat. Struct. Biol. 1995, 2, 615-618.
4. Elcock, A. H.; McCammon, J. A. J. Am. Chem. Soc. 1996, 118, 3787-3788.
5. Choi, K. Y.; Zalkin, H. J. Bacteriol. 1994, 176, 1767-1772.
6. The 5′-fluoresceinated duplex was prepared from two complementary 24mers, one of which contained the fluorescent label, by the method of Ebright (Ebright, R. Meth. Enzymol. 1996. In press). The sequence of the labeled oligonucleotide is 5′-F-GAAAAAGAAAACGTTTGCGTAGGG. The anisotropy measurements were carried out at room temperature in 1 mL of binding buffer (250 mM potassium glutamate, 150 mM NaCl, 10 mM magnesium acetate, 1 mM EDTA, 5% w/v glycerol, 100 mM HEPES, pH 7.5) containing 1 μg of poly dI-dC, 100 μM hypoxanthine, and 2 nM of the labeled duplex. The repressor was titrated into this mixture, and readings were taken after each addition using a Beacon Fluorescence Polarization instrument.
7. The sequence of the duplex containing the palindromic sequence is 5′-TACGCAAACGTTTGCGT-3′. The numbering of the sequence is 1-2-3-4-5-6-7-8-9-9′-8′-7′-6′-5′-4′-3′ -2′, respectively.
8. Crystals were grown as described by Schumacher et al. (Schumacher, M. A.; Choi, K. Y.; Zalkin, H.; Brennan, R. G. J. Mol. Biol. 1994, 242, 302-305.) Refinement was performed using the TNT package (Tronrud, D. E.; Ten Eyck, L. J.; Matthews, B. W. Acta Crystallogr. 1987, A43, 489-501.) The WT structure was solved to 3.0 Å resolution with an R-factor of 15.7% (bond lengths showed 0.013 Å rms deviation from ideality, bond angles 1.63°). The Lys55Ala structure was solved to 2.7 Å resolution with an Ä-factor of 16.8% (bond lengths showed 0.017 Å rms deviation from ideality, bond angles 1.90°). Coordinates for the structures have been deposited in the Brookhaven Protein Data Bank and have PDB ID codes 1BDH and 1BDI for the Lys55Ala-hypoxanthine-palF and WT-hypoxanthine-palF complexes, respectively.
9. Crystals were grown as described by Schumacher et al. (Schumacher, M. A.; Choi, K. Y.; Zalkin, H.; Brennan, R. G. J. Mol. Biol. 1994, 242, 302-305.) Refinement was performed using the TNT package (Tronrud, D. E.; Ten Eyck, L. J.; Matthews, B. W. Acta Crystallogr. 1987, A43, 489-501.) The WT structure was solved to 3.0 Å resolution with an R-factor of 15.7% (bond lengths showed 0.013 Å rms deviation from ideality, bond angles 1.63°). The Lys55Ala structure was solved to 2.7 Å resolution with an Ä-factor of 16.8% (bond lengths showed 0.017 Å rms deviation from ideality, bond angles 1.90°). Coordinates for the structures have been deposited in the Brookhaven Protein Data Bank and have PDB ID codes 1BDH and 1BDI for the Lys55Ala-hypoxanthine-palF and WT-hypoxanthine-palF complexes, respectively.
10. Calculated using MidasPlus. Ferrin, T. E.; Huang, C. C.; Jarvis, L. E.; Langridge, R. J. Mol. Graphics 1988, 6, 13-37.
11. Honig, B.; Nicholls, A. Science 1995, 268, 1144-1149.
12. Lavery, R.; Sklenar, H. J. Biomol. Struct. Dynam. 1990, 6, 215-235. Global parameters were calculated from base pair C3/G3′ to G3/C3′ due to the poorer electron density about the first and last base pairs.
13. Kissinger, C. R.; Liu, B.; Martin-Blanco, E.; Kornberg, T. B.; Pabo, C. O. Cell 1990, 63, 579-590.
14. Wolberger, C.; Vershon, A. K.; Lieu, B.; Johnson, A. D.; Pabo, C. O. Cell 1991, 67, 517-528.
15. Lewis, M.; Chang, G.; Horton, N. C.; Kercher, M. A.; Pace, H. C.; Schumacher, M. A.; Brennan, R. G.; Lu, P. Science 1996, 271, 1247-1254.
16. Strauss, J. K.; Maher, L. J. Science 1994, 266, 1829-1834.
17. (a) Lefebvre, A.; Mauffret, O.; Hartmann, B.; Lescot, E.; Fermandjian, S. Biochemistry 1995, 34, 12019-12028.
18. (b) Dickerson, R. E.; Goodsell, D.; Kopka, M. L. J. Mol. Biol. 1996, 256, 108-125.
19. (c) Young, M. A.; Ravishanker, G.; Beveridge, D. L.; Berman, H. M. Biophys. J. 1995, 68, 2454-2468.