Recombination-like structure of d(CCGCGG)

Lucy Malinina, Lourdes Urpí, Xavier Salas, Tam Huynh-Dinh, Juan A. Subirana

Research output: Contribution to journalArticlepeer-review

26 Scopus citations


We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C2221 with a = 34.33 Å, b = 44.04 Å and c = 38 27 Å. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F ≥ 2σ (F) in the resolution region 8.0 to 1.92 Å. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.

Original languageEnglish (US)
Pages (from-to)484-493
Number of pages10
JournalJournal of Molecular Biology
Issue number3
StatePublished - Oct 27 1994
Externally publishedYes


  • B/Z junction
  • DNA
  • Oligonucleotide conformation
  • Recombination
  • X-ray diffraction


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