218d: Difference between revisions

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==Overview==

The structure of the synthetic dodecamer (d[CGTGAATTC(O6Me)GCG])2 has been, determined to a resolution of 2.25 A and refined to a final R factor of, 16.7%. The volume of the unit cell is significantly smaller by 16% than, the original Drew and Dickerson parent dodecamer [Drew, H. R., Wing, R., M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E., (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7318-7322]. The double helix is, in a different position in the unit cell, rotated by -85.9 degrees, and, translated by 9.9 A around the helical axis with respect to the parent, structure. The intermolecular arrangement of helices, characterized by, double hydrogen bonded guanine-guanine minor groove interactions, remains, conserved. The molecular geometry exhibits several significant changes, that are related to the changed position of the helix and the presence of, two mismatched base pairs with O6-methylguanine. Both mispairs are found, in a symmetrical T(anti).(O6Me)G(anti) conformation, and the methyl groups, are in proximal orientation. The hydration pattern of the structure is, different and can be related to changes in the minor groove geometry. An, incorrect model that was isomorphous to the parent dodecamer could be, refined to a low R factor. Characteristics of the refinement and of the, geometry that are indicative of incorrect structures have been analyzed.

The structure of the synthetic dodecamer (d[CGTGAATTC(O6Me)GCG])2 has been determined to a resolution of 2.25 A and refined to a final R factor of 16.7%. The volume of the unit cell is significantly smaller by 16% than the original Drew and Dickerson parent dodecamer [Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7318-7322]. The double helix is in a different position in the unit cell, rotated by -85.9 degrees, and translated by 9.9 A around the helical axis with respect to the parent structure. The intermolecular arrangement of helices, characterized by double hydrogen bonded guanine-guanine minor groove interactions, remains conserved. The molecular geometry exhibits several significant changes that are related to the changed position of the helix and the presence of two mismatched base pairs with O6-methylguanine. Both mispairs are found in a symmetrical T(anti).(O6Me)G(anti) conformation, and the methyl groups are in proximal orientation. The hydration pattern of the structure is different and can be related to changes in the minor groove geometry. An incorrect model that was isomorphous to the parent dodecamer could be refined to a low R factor. Characteristics of the refinement and of the geometry that are indicative of incorrect structures have been analyzed.

==About this Structure==

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Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs., Vojtechovsky J, Eaton MD, Gaffney B, Jones R, Berman HM, Biochemistry. 1995 Dec 26;34(51):16632-40. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8527436 8527436]

[[Category: Protein complex]]

[[Category: Berman, H.M.]]

[[Category: Berman, H M.]]

[[Category: Eaton, M.D.]]

[[Category: Eaton, M D.]]

[[Category: Gaffney, B.]]

[[Category: Jones, R.]]

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[[Category: modified]]

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@@ Line 4: / Line 4: @@
 ==Overview==
-The structure of the synthetic dodecamer (d[CGTGAATTC(O6Me)GCG])2 has been, determined to a resolution of 2.25 A and refined to a final R factor of, 16.7%. The volume of the unit cell is significantly smaller by 16% than, the original Drew and Dickerson parent dodecamer [Drew, H. R., Wing, R., M., Takano, T., Broka, C., Tanaka, S., Itakura, K., &amp; Dickerson, R. E., (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7318-7322]. The double helix is, in a different position in the unit cell, rotated by -85.9 degrees, and, translated by 9.9 A around the helical axis with respect to the parent, structure. The intermolecular arrangement of helices, characterized by, double hydrogen bonded guanine-guanine minor groove interactions, remains, conserved. The molecular geometry exhibits several significant changes, that are related to the changed position of the helix and the presence of, two mismatched base pairs with O6-methylguanine. Both mispairs are found, in a symmetrical T(anti).(O6Me)G(anti) conformation, and the methyl groups, are in proximal orientation. The hydration pattern of the structure is, different and can be related to changes in the minor groove geometry. An, incorrect model that was isomorphous to the parent dodecamer could be, refined to a low R factor. Characteristics of the refinement and of the, geometry that are indicative of incorrect structures have been analyzed.
+The structure of the synthetic dodecamer (d[CGTGAATTC(O6Me)GCG])2 has been determined to a resolution of 2.25 A and refined to a final R factor of 16.7%. The volume of the unit cell is significantly smaller by 16% than the original Drew and Dickerson parent dodecamer [Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., &amp; Dickerson, R. E. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7318-7322]. The double helix is in a different position in the unit cell, rotated by -85.9 degrees, and translated by 9.9 A around the helical axis with respect to the parent structure. The intermolecular arrangement of helices, characterized by double hydrogen bonded guanine-guanine minor groove interactions, remains conserved. The molecular geometry exhibits several significant changes that are related to the changed position of the helix and the presence of two mismatched base pairs with O6-methylguanine. Both mispairs are found in a symmetrical T(anti).(O6Me)G(anti) conformation, and the methyl groups are in proximal orientation. The hydration pattern of the structure is different and can be related to changes in the minor groove geometry. An incorrect model that was isomorphous to the parent dodecamer could be refined to a low R factor. Characteristics of the refinement and of the geometry that are indicative of incorrect structures have been analyzed.
 ==About this Structure==
@@ Line 12: / Line 12: @@
 Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs., Vojtechovsky J, Eaton MD, Gaffney B, Jones R, Berman HM, Biochemistry. 1995 Dec 26;34(51):16632-40. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8527436 8527436]
 [[Category: Protein complex]]
-[[Category: Berman, H.M.]]
+[[Category: Berman, H M.]]
-[[Category: Eaton, M.D.]]
+[[Category: Eaton, M D.]]
 [[Category: Gaffney, B.]]
 [[Category: Jones, R.]]
@@ Line 22: / Line 22: @@
 [[Category: modified]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:47:33 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:21:06 2008''