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 journalArticlepeer-review

26 Scopus citations


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
Issue number4
StatePublished - Jan 29 1999
Externally publishedYes

Bibliographical note

Funding Information:
We are thankful to Dr V. Ivanov for valuable suggestions, to Dr. N. Verdaguer and Dr J. L. Campos for their help in many stages of this work and to Dr R. Dickerson for providing NEWHELIX93. This work has been supported by grants INTAS-93-2755 and DGICYT PB93-1067. Support from the Comissionat de Recerca de la Generalitat de Catalunya is also acknowledged. Part of this work was carried out while L.M. was a visiting professor at the UPC. L.G.F. was a recipient of a fellowship from the Instituto de Cooperación Iberoamericano.


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


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