title: Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.
abstract: The crystal structures of two alternating octamers d(Gm(5)CGm(5)CGCGC) and d(GCGCGm(5)CGm(5)C) have been determined at 1.7 and 1.9 A resolution with R(work)/R(free) of 16.9/19.6% and 17.9/19.8%, respectively. The two octamers crystallized in the same tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 43.0, c = 24.9 A and a = b = 43.1, c = 24.7 A, respectively. Both structures adopt the A-type double helix and the abutting crystal packing. Despite the different positions of the methylated cytosine in the sequence, the two octamers display essentially the same conformation. The close similarity of the two structures indicates that methylation at different positions in a DNA sequence does not affect the helical conformation of the alternating DNA octamer. Investigation of other related crystal structures implies that methylation of cytosine stabilizes the A-type conformation for alternating DNA sequences beginning with a 5'-purine but is beneficial to the Z-type conformation for alternating DNA sequences beginning with a 5'-pyrimidine.
authors.affiliation: Departments of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Laboratory, 176 West 19th Avenue, Columbus, OH 43210, USA.
authors.forename: Ke
authors.initials: K
authors.lastname: Shi
authors.forename: Baocheng
authors.initials: B
authors.lastname: Pan
authors.forename: Douglas
authors.initials: D
authors.lastname: Tippin
authors.forename: Muttaiya
authors.initials: M
authors.lastname: Sundaralingam
mesh_terms: D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D019175:DNA Methylation; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; D004247:DNA