Recombination-like structure of d(CCGCGG).
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 C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. 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 > or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.
Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain.
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Malinina
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Urpí
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Salas
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Huynh-Dinh
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Subirana
D003460:Crystallization; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D015226:Dinucleoside Phosphates / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D011995:Recombination, Genetic
D015226:Dinucleoside Phosphates; D009838:Oligodeoxyribonucleotides; C015101:cytidylyl-(3'-5')-cytidine; C018309:guanylyl-(3'-5')-guanosine; D004247:DNA