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Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):61-5. Epub 2003 Dec 18.

Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.

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Departments of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Laboratory, 176 West 19th Avenue, Columbus, OH 43210, USA.


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.

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