The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG).poly(dC).

Journal article

The structure of the DNA oligomer d(G-G-G-G-C-C-C-C) has been determined at a resolution of 2.5 A by single-crystal X-ray methods. There are two strands in the asymmetric unit, and these coil about each other to form a right-handed double-helix of the A-type with Watson-Crick hydrogen bonds between base-pairs. The helix has a shallow minor groove and a deep, water-filled major groove; almost all exposed functional groups on the DNA are hydrated, and 106 ordered solvent molecules have been found. The two d(G-G-G-G).d(C-C-C-C) segments in the octamer exhibit similar and uniform structures, but there is a slight discontinuity at the GpC step between them. A recurring feature of the structure is the overlap of adjacent guanine bases in each GpG step, with the five-membered ring of one guanine stacking on the six-membered ring of its neighbour. There is little or no overlap between adjacent cytosine rings. Conformational parameters for these GpG steps are compared with those from other single-crystal X-ray analyses. In general, GpG steps exhibit high slide, low roll and variable twist. Models for poly(dG).poly(dC) were generated by applying a simple rotation and translation to each of the unmodified d(G-G-G-G).d(C-C-C-C) units. Detailed features of these models are shown to be compatible with various assays of poly(dG).poly(dC) in solution, and are useful in understanding the polymorphic behaviour of this sequence under a variety of experimental conditions.

Authors: McCall, M; Brown, T; Kennard, O

• Publication status: Published
• Journal: Journal of molecular biology
• Volume: 183
• Issue: 3
• Pages: 385-396
• Publication date: 1985-06-01
• DOI: 10.1016/0022-2836(85)90009-9
• EISSN: 1089-8638
• ISSN: 0022-2836
• Language: English
• Keywords: Oligodeoxyribonucleotides; Chemistry; Models, Molecular; X-Ray Diffraction; Oligonucleotides; Macromolecular Substances; Chemical Phenomena; Polydeoxyribonucleotides