Structure of a new crystal form of a DNA dodecamer containing T.cntdot.(O6Me)G base pairs

Abstract

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.

Transcription elongation past O6-methylguanine by human RNA polymerase II and bacteriophage T7 RNA polymerase

“…Our results show that for O 6 -meG, the possible variation in the torsion angle κ, which governs the rotation about the O 6 –C6 bond, and hence the placement of the bulky methyl group in the polymerase active site is key. Both distal and proximal conformations have been explicitly observed by NMR (29–32) and X-ray crystallography (33,35,36). The conformation of the methyl group is the determinant for whether bypass or blockage occurs.…”

Crystal structures of nucleic acids and their drug complexes

“…The structures of two dodecanucleotide duplexes containing this mismatch have been reported. 55,56 The base pairing in both is analogous to the normal Watson-Crick arrangement (Fig. 3), whereas NMR solution studies 57 have suggested that the N1G• • •N3T hydrogen bond is absent or very weak.…”

MGMT: A personal perspective

“…Our results showing increased turnover of C or T during replication of the m 6 G -containing template supports this conclusion. Subsequent NMR spectroscopy and X-ray crystallography studies of m 6 G -containing oligonucleotides provided direct evidence for the m 6 G•T pair (19,20).…”