399D

STRUCTURE OF D(CGCCCGCGGGCG)

Summary for 399D

• Entry DOI: 10.2210/pdb399d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*G)-3') (2 entities in total)
• Functional Keywords: double helix, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 7330.74

Authors

Malinina, L.,Fernandez, L.G.,Subirana, J.A. (deposition date: 1998-05-11, release date: 1999-01-18, Last modification date: 2024-02-21)

Primary citation

Malinina, L.,Fernandez, L.G.,Huynh-Dinh, T.,Subirana, J.A.
Structure of the d(CGCCCGCGGGCG) dodecamer: a kinked A-DNA molecule showing some B-DNA features.
J.Mol.Biol., 285:1679-1690, 1999

PubMed 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 degrees 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.

PubMed: 9917405
DOI: 10.1006/jmbi.1998.2424

Experimental method

X-RAY DIFFRACTION (1.9 Å)