H. Mackay et al. / Bioorg. Med. Chem. 16 (2008) 9145–9153
9153
4
.8. Solvent accessible surface areas (SASA)
1993, 115, 9892; (c) Mrksich, M.; Dervan, P. B. J. Am. Chem. Soc. 1994, 116, 3663;
d) Olenyuk, B.; Jitianu, C.; Dervan, P. B. J. Am. Chem. Soc. 2003, 125, 4741.
(a) Lacy, E. R.; Le, N. M.; Price, C. A.; Lee, M.; Wilson, W. D. J. Am. Chem. Soc.
002, 124, 2153; (b) Buchmueller, K. L.; Staples, A. M.; Howard, C. M.; Horick, S.
M.; Uthe, P. B.; Le, N. M.; Cox, K. K.; Nguyen, B.; Pacheco, K. A. O.; Wilson, W. D.;
Lee, M. J. Am. Chem. Soc. 2005, 127, 742; (c) Buchmueller, K. L.; Staples, A. M.;
Uthe, P. B.; Howard, C. M.; Pacheco, K. A. O.; Cox, K. K.; Henry, J. A.; Bailey, S. L.;
Horick, S. M.; Nguyen, B.; Wilson, W. D.; Lee, M. Nucleic Acids Res/ 2005, 33, 912;
(d) Buchmueller, K. L.; Bailey, S. L.; Matthews, D. A.; Taherbhai, Z. T.; Register, J.
K.; Davis, Z. S.; Bruce, C. D.; O’Hare, C. C.; Hartley, J. A.; Lee, M. Biochemistry
(
7
.
The SASA calculation procedures have been previously descri-
2
bed.7
c,20
In brief, ions were removed and carbon, carbon-bound
hydrogen, and phosphorus atoms were assigned as non-polar and
the rest polar. The PyImPyIm/CGCG complex (a total of 780 atoms:
6
30 from DNA, 150 from ligands) consists of 284 polar (p) atoms
(
(
244 from DNA, 40 from ligands) and 496 non-polar (np) atoms
386 from DNA, 110 from ligands). The solvent accessible surface
2006, 45, 13551.
8
.
(a) Verma, R.; Patapoutian, A.; Gordon, C. B.; Campbell, J. L. Proc. Natl. Acad. Sci.
U.S.A. 1991, 88, 7155; (b) Wu, X.; Lee, H. Oncogene 2002, 21, 7786; (c) Yamada,
M.; Sato, N.; Taniyama, C.; Ohtani, K.; Arai, K.; Masai, H. J. Biol. Chem. 2002, 277,
27668; (d) Hess, G. F.; Drong, R. F.; Weiland, K. L.; Slightom, J. L.; Sclafani, R. A.;
Hollingsworth, R. E. Gene 1998, 28, 133.
21
area (SASA) was calculated with GRASP using a probe radius of
1
.7683 Å and Cornell et al. radii.22
The heat capacity change (cal mol
ꢁ1
ꢁ1
K ) arisen from the polar/
non-polar area change was calculated with three different models
9. O’Hare, C. C.; Uthe, P. B.; Mackay, H.; Blackmon, K. N.; Jones, J.; Brown, T.;
Eq. 2,2 Eq. 3, Eq. 4.
3
24
25
Nguyen, B.; Wilson, W. D.; Lee, M.; Hartley, J. A. Biochemistry 2007, 46,
11661.
D
A ¼ Acomplex ꢁ ðAfree dna þ Aligand
1
þ Aligand
2
Þ
10. Brown, T.; Mackay, H.; Turlington, M.; Sutterfield, A.; Smith, T.; Sielaff, A.;
Westrate, L.; Bruce, C.; Kluza, J.; O’Hare, C.; Hartley, J. A.; Nguyen, B.; Wilson,
W. D.; Lee, M. Bioorg. Med. Chem. 2008, 16, 5266.
D
D
C
C
p-sasa ¼ ð0:32 ꢃ 0:04Þ
p-sasa ¼ ð0:45 ꢃ 0:02Þ
D
AÞnp ꢁ ð0:14 ꢃ 0:04Þ
D
A
p
ð2Þ
11.
Mulder, K.; Brown, T.; Nolan, P.; Smith, T.; Lee, M. Heterocycl. Commun. 2008,
4, 137.
1
DA
np ꢁ ð0:26 ꢃ 0:03Þ
DA
p
12. (a) Lyng, R.; Rodger, A.; Norden, B. Biopolymers 1992, 32, 1201; (b) Lyng, R.;
þ ð0:17 ꢃ 0:07Þ
D
A
OH
ð3Þ
ð4Þ
Rodger, A.; Norden, B. Biopolymers 1991, 31, 1709.
1
1
3. Lah, J.; Vesnaver, G. J. Mol. Biol. 2004, 3, 73.
D
C
p-sasa ¼ ð0:382 ꢃ 0:026Þ
D
A
np ꢁ ð0:121 ꢃ 0:077Þ
DA
p
4. (a) Paal, K.; Baeuerle, P. A.; Schmitz, M. L. Nucleic Acids Res. 1997, 25, 1050; (b)
Ptashne, M.; Gann, A. Genes and Signals, first ed.; Cold Spring Harbor
Laboratory: NY, 2001.
Acknowledgments
15. Jencks, W. P. Proc. Natl. Acad. Sci. U.S.A. 1981, 78, 4046.
6. (a) Nickols, N. G.; Jacobs, C. S.; Farkas, M. E.; Dervan, P. B. ACS Chem. Biol.
007, 2, 561; (b) Nickols, N. G.; Jacobs, C. S.; Farkas, M. E.; Dervan, P. B.
1
2
Support from the National Science Foundation (CHE-0550992),
the National Institutes of Health, (GM61587 to WDW), Glaxo-
smithkline summer undergraduate research fellowship (J.P.L.),
Cancer Research UK (C2259/A3083), and Hope College is gratefully
acknowledged.
Nucleic Acids Res. 2007, 35, 363; (c) Edelson, B. S.; Best, T. P.; Olenyuk, B.;
Nickols, N. G.; Doss, R. M.; Foister, S.; Heckel, A.; Dervan, P. B. Nucleic Acids
Res. 2004, 20, 2802; (d) Best, T. P.; Edelson, B. S.; Nickols, N. G.; Dervan, P.
B. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12063; (e) Belitsky, J. M.; Leslie, S.
J.; Arora, P. S.; Beerman, T. A.; Dervan, P. B. Bioorg. Med. Chem. 2002, 10,
3313; (f) Anthony, N. G.; Fox, K. R.; Johnston, B. F.; Khalaf, A. I.; Mackay, S.
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