AT base pairs are less stable than GC base pairs in Z-DNA: The crystal structure of d(m5CGTAm5CG)

Andrew H.J. Wang, Toshio Hakoshima, Gijs van der Marel, Jacques H. van Boom, Alexander Rich

Research output: Contribution to journalArticlepeer-review

159 Citations (Scopus)


Two hexanucleoside pentaphosphates, 5-methyl and 5-bromo cytosine derivatives of d(CpGpTp-ApCpG) have been synthesized, crystallized, and their three-dimensional structure solved. They both form left-handed Z-DNA and the methylated derivative has been refined to 1.2 Å resolution. These are the first crystal Z-DNA structures that contain AT base pairs. The overall form of the molecule is very similar to that of the unmethylated or the fully methylated (dC-dG)3 hexamer although there are slight changes in base stacking. However, significant differences are found in the hydration of the helical groove. When GC base pairs are present, the helical groove is systematically filled with two water molecules per base pair hydrogen bonded to the bases. Both of these water molecules are not seen in the electron density map in the segments of the helix containing AT base pairs, probably because of solvent disorder. This could be one of the features that makes AT base pairs form Z-DNA less readily than GC base pairs.

Original languageEnglish
Pages (from-to)321-331
Number of pages11
Issue number1
Publication statusPublished - May 1984
Externally publishedYes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)


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