Structure of the d(CGCCCGCGGGCG) dodecamer: A kinked A-DNA molecule showing some B-DNA features

Lucy Malinina, Luzimar G. Fernandez, Tam Huynh-Dinh, Juan A. Subirana

Research output: Contribution to journalArticle

24 Scopus citations

Abstract

We have determined the structure of the dodecamer duplex d(CGCCCGCGGGCG)2. A careful use of the molecular replacement programme AMoRe has been essential in order to solve the structure. This dodecamer shows a unique conformation, quite different from all the previously studied oligonucleotide duplexes: the central octamer has an A conformation, but with a sharp 65°kink in the centre; the terminal base-steps have a B-like conformation; the major groove is completely closed in the centre, a hollow molecule is thus found. The results obtained confirm the high degree of variability of DNA structure. A new type of kink and an intermediate A/B double-helical conformation have been found. Such intermediate conformation differs from those described in DNA polymerase complexes.

Original languageEnglish (US)
Pages (from-to)1679-1690
Number of pages12
JournalJournal of Molecular Biology
Volume285
Issue number4
DOIs
StatePublished - Jan 29 1999

Keywords

  • AMoRe
  • DNA kink
  • DNA polymerase
  • DNA structure
  • Oligonucleotides

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