327D

CRYSTAL STRUCTURES OF D(GM5CGM5CGCGCGC)

Summary for 327D

• Entry DOI: 10.2210/pdb327d/pdb
• Descriptor: DNA (5'-D(*GP*(5CM)P*GP*(5CM)P*GP*CP*GP*CP*GP*C)-3') (2 entities in total)
• Functional Keywords: a-dna, double helix, modified, dna
• Total number of polymer chains: 1
• Total formula weight: 3075.03

Authors

Tippin, D.B.,Ramakrishnan, B.,Sundaralingam, M. (deposition date: 1997-03-17, release date: 1997-05-22, Last modification date: 2024-02-21)

Primary citation

Tippin, D.B.,Ramakrishnan, B.,Sundaralingam, M.
Methylation of the Z-DNA decamer d(GC)5 potentiates the formation of A-DNA: crystal structure of d(Gm5CGm5CGCGCGC).
J.Mol.Biol., 270:247-258, 1997

PubMed Abstract: It is well known that methylation of alternating Py x Pu sequences potentiates the formation of Z-DNA. However, we have now observed that methylation of the alternating Z-DNA oligomer d(GCGCGCGCGC), which starts with a 5'-purine, unexpectedly stabilizes the A-DNA conformation. The double methyl derivative d(Gm5CGm5CGCGCGC), which crystallizes as duplex A-DNA in the hexagonal space group P6(1)22, a = b = 39.33 A and c = 77.93 A with one strand per asymmetric unit and six duplexes in the unit cell, refined to an R factor of 19.1 for 204 DNA atoms and 43 solvent molecules. This is the first report of a DNA sequence crystallized in both right and left-handed conformations, allowing structural comparisons not previously possible and, more importantly, this is the first time that methylation has been shown to potentiate the formation of A-DNA from a sequence known to crystallize as Z-DNA. From this study, ten base-pairs appear to be the critical length in determining the handedness of d(GC)n-type sequences in the crystalline state. Because methylation of nuclear DNA is linked to a number of cellular processes, including transcriptional inactivation, this study has important implications for the role of A-DNA in methylated regions of genomic DNA and, thus, in the regulation of gene expression. In this context, the structure of d(Gm5Cm5CGCGCGC) will be compared with that of the alternating A-DNA decamer d(GCACGCGTGC) and the alternating Z-DNA decamer d(GCGCGCGCGC) and discussed in terms of the forces that govern the handedness of duplex DNA oligomers.

PubMed: 9236126
DOI: 10.1006/jmbi.1997.1102

Experimental method

X-RAY DIFFRACTION (1.94 Å)