Structures of d(Gm5CGm5CGCGC) and d(GCGCGm 5CGm5C): Effects of methylation on alternating DNA octamers

Ke Shi, Baocheng Pan, Douglas Tippin, Muttaiya Sundaralingam

Research output: Contribution to journalArticlepeer-review

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Abstract

The crystal structures of two alternating octamers d(Gm5CGm 5CGCGC) and d(GCGCGm5CGm5C) have been determined at 1.7 and 1.9 Å resolution with Rwork/R free of 16.9/19.6% and 17.9/19.8%, respectively. The two octamers crystallized in the same tetragonal space group P43212, with unit-cell parameters a = b = 43.0, c = 24.9 Å and a = b = 43.1, c = 24.7 Å, 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.

Original languageEnglish (US)
Pages (from-to)61-65
Number of pages5
JournalActa Crystallographica Section D: Biological Crystallography
Volume60
Issue number1
DOIs
StatePublished - Jan 1 2004

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