Crystal structure analysis of the B-DNA dodecamer CGTGAATTCACG.
The crystal structure of the DNA dodecamer C-G-T-G-A-A-T-T-C-A-C-G has been determined at a resolution of 2.5 A, with a final R factor of 15.8% for 1475 nonzero reflections measured at 0 degrees C. The structure is isomorphous with that of the Drew dodecamer, with the space group P2(1)2(1)2(1) and cell dimensions of a = 24.94 A, b = 40.78 A, and c = 66.13 A. The asymmetric unit contains all 12 base pairs of the B-DNA double helix and 36 water molecules. The structure of C-G-T-G-A-A-T-T-C-A-C-G is very similar to that of C-G-C-G-A-A-T-T-C-G-C-G, with no major alterations in helix parameters. Water peaks in the refined structure appear to represent a selection of peaks that were observed in the Drew dodecamer. The minor-groove spine of hydration at 2.5 A is fragmentary, but as Narendra et al. (1991) [Biochemistry (following paper in this issue)] have observed, lowering the temperature leads to a more complete representation of the spine.
Larsen
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Department of Chemistry and Biochemistry, University of California, Los Angeles 90024-1570.
Kopka
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Dickerson
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D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D005583:Fourier Analysis; D008969:Molecular Sequence Data; D009429:Netropsin / Q000031:analogs & derivatives / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000235:genetics; D013237:Stereoisomerism; D014867:Water / Q000737:chemistry; D014961:X-Ray Diffraction
D009841:Oligonucleotides; D014867:Water; C053654:lexitropsin; D009429:Netropsin; D004247:DNA