1R41

Crystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effects of methylation on alternating DNA octamers

Summary for 1R41

• Entry DOI: 10.2210/pdb1r41/pdb
• Related: 1R3Z
• Descriptor: 5'-D(*GP*CP*GP*CP*GP*(5CM)P*GP*(5CM))-3' (2 entities in total)
• Functional Keywords: dna
• Total number of polymer chains: 1
• Total formula weight: 2456.65

Authors

Shi, K.,Pan, B.,Tippin, D.,Sundaralingam, M. (deposition date: 2003-10-03, release date: 2003-12-23, Last modification date: 2024-02-14)

Primary citation

Shi, K.,Pan, B.,Tippin, D.,Sundaralingam, M.
Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.
Acta Crystallogr.,Sect.D, 60:61-65, 2004

PubMed 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.

PubMed: 14684893
DOI: 10.1107/S0907444903021899

Experimental method

X-RAY DIFFRACTION (1.9 Å)