Structure of a B-DNA dodecamer: conformation and dynamics

H. R. Drew, R. M. Wing, T. Takano, C. Broka, S. Tanaka, K. Itakura, R. E. Dickerson
1981 Proceedings of the National Academy of Sciences of the United States of America  
The crystal structure of the synthetic DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error ofR = 17.8% at 1.9-A resolution (two-o'data). The molecule forms slightly more than one complete turn of righthanded double-stranded B helix. The two ends of the helix overlap and interlock minor grooves with neighboring molecules up and down a 21 screw axis, producing a 190 bend in helix axis over the 11-base-pair steps ofthe dodecamer. In the center ofthe molecule, where
more » ... ation is least, the helix has a mean rotation of 36.9°p er step, or 9.8 base pairs per turn. The mean propeller twist (total dihedral angle between base planes) between APT base pairs in the center of the molecule is 17.30, and that between COG pairs on the two ends averages 11.50. Individual deoxyribose ring conformations as measured by the C5'-C4'-C3'-03' torsion angle 8, exhibit an approximately Gaussian distribution centered around the Cl'exo position with 8., = 1230 and a range of 790 to 157. Purine sugars cluster at hig; 8 values, and pyrimidine sugars cluster at lower 8. A tendency toward 2-fold symmetry in sugar conformation about the center of the molecule is detectable in spite of the destruction of ideal 2-fold symmetry by the molecular bending. More strikingly, sugar conformations of paired bases appear to follow a "principle of anticorrelation," with 8 values lying approximately the same distance to either side of the center value, 6 = 1230. This same anticorrelation is also observed in other DNA and DNARNA structures. In the 28 years since a double helix model for B-DNA was proposed by Watson and Crick (2), direct evidence for its structure has been based on refinement of models having standard bond parameters against x-ray diffraction data from oriented fibers (3-6). This has had two disadvantages: loss of information because of rotational disorder about the fiber axis, and lack of information about the effect ofspecific base sequences, aside from a limited number of experiments on homopolymers and alternating copolymers. Recent advances in triester methods of DNA synthesis have made possible the preparation of molecules ofpredetermined base sequence, in quantities and purities suitable for single-crystal x-ray analysis. This paper presents the results ofa structure analysis and refinement ofa complete turn of right-handed B-DNA, with the sequence d(CpGpCpGpApApTpTpCpGpCpG). A preliminary report of the partially refined structure has appeared (7). the tendency of mixed-sequence DNA to adopt the Z conformation. In spite of favorable salt conditions, the central A-A-T-T segment apparently is sufficient to counteract the Z-forming tendencies ofthe tetrameric C-G-C-G ends, resulting in a classical Watson-Crick B helix throughout. Structure analysis and refinement The dodecamer crystallizes in space group P212121 with a = 24.87 A, b = 40.39 A, c = 66.20 A, and two single strands or one double helix per asymmetric unit. Two isomorphous heavy atom derivatives were obtained by de novo triester synthesis with 5-bromodeoxycytidine at the third position along each strand and by diffusion of the anticancer agent cisplatin [cisdichlorodiamminoplatinum(II)] into pregrown crystals. Phases from this analysis were used to obtain a starting model for restrained least-squares refinement (10). Initial energy parameters for DNA as obtained from Michael Levitt were modified so that conformational energy would restrain the molecule to a sterically acceptable structure but would allow the x-ray data to determine this structure. Internal sugar ring bond angles were set to the average oftheir C2'-endo and C3'-endo values but were left flexible enough that other conformations could be obtained (11). The residual error or R factor for 2725. two-oa data between 8.0 and 1.9 A was reduced from 42% to 18.1% by 50 cycles of position and temperature factor refinement. During this process, 10 superimposed Fourier/difference Fourier maps were inspected in order to make manual corrections and introduce solvent molecules. At the end ofthe 50 cycles, all 5534 zero-o-data between 8.0 and 1.9 A were included in refinement. (Data out to 2.2-A resolution were measured at least twice on different crystals.) After 62 cycles, the final R factor for 486 DNA atoms and 80 ordered solvent molecules is 23.9% for the complete zero-a data or 17.8% for the two-oa data (calculated with the same parameter set). The worst bond length in the structure deviates by 0.03 A from its ideal value, and the worst bond angle deviates by 4.40. Both intensity data and final coordinates have been deposited with the Brookhaven Protein Data Bank. Nonuniform motion in the helix The refined dodecamer structure is shown in Fig. 1 . It is a righthanded, Watson-Crick B double helix with an average of 10.1 base pairs per turn over the entire helix. Two striking depar-* This is paper no. 1 of a series; paper no. 2 is ref. 1.
doi:10.1073/pnas.78.4.2179 pmid:6941276 pmcid:PMC319307 fatcat:543qte6gkrhh7gnpi22xu63tzm