Helix geometry and hydration in an A-DNA tetramer: IC-C-G-G.

The DNA oligomer of sequence IC-C-G-G has been synthesized, and its X-ray crystal structure solved at a resolution of 2.0 A, using anomalous scattering from iodines in phase analysis: 48 cycles of Jack-Levitt restrained least-squares refinement resulted in a residual error of 19.9% over all data, or 16.5% for two-sigma data. Two double-helical tetramers stack in the crystal to form a continuous octamer, except for the two missing phosphate connections across the center. The octamer has a mean helix rotation of 33.7 degrees (10.7 base-pairs per turn), rise of 2.87 A, mean inclination angle of base-pairs of 14 degrees, and mean base-pair propeller twist of +16.3 degrees. Local variations in both helix rotation and base plane roll angles, including those across the center of the octamer, are as predicted from base sequence by sum functions sigma 1 and sigma 2. The three known DNA octamers: IC-C-G-G/IC-C-G-G, G-G-T-A-T-A-C-C and G-G-C-C-G-G-C-C, make up a graded series in this order, with monotonically changing structural parameters. An exhaustive comparison of torsion angle correlations among the known A helices confirms some structural expectations and reveals some new features. 86 water molecules have been located per double-helical IC-C-G-G tetramer (the asymmetric unit), of which 451/2 per tetramer lie within a first hydrogen-bonded shell of hydration. No ordered water structure is observed comparable to the minor groove spine of hydration in B-DNA.

The anatomy of A-, B-, and Z-DNA.

Recent advances in DNA synthesis methods have made it possible to carry out single-crystal x-ray analyses of double-stranded DNA molecules of predetermined sequence, with 4 to 12 base pairs. At least one example has been examined from each of the three known families of DNA helix: A, B, and Z. Each family has its own intrinsic restrictions on chain folding and structure. The observed solvent positions in these crystal structures have confirmed earlier fiber and solution measurements, and have led to proposals explaining the transitions from B to A and from B to Z helices. Prospects are improving for an understanding of the mode of bending of DNA in chromatin, and the way in which specific DNA sequences are recognized by drug molecules and repressor proteins.

The molecular structure of d(ICpCpGpG), a fragment of right-handed double helical A-DNA.

The DNA tetramer d(ICpCpGpG) or ICCGG crystallizes as a double-stranded 4-base pair (bp) segment of an A helix. Two such tetramer helices are packed together in the crystal with local helix axes nearly coincident, simulating an 8-bp helix, and four such octamers make up the tetragonal unit cell. Restrained energy and reciprocal space refinement has led to an R factor of 20.5% at 2.1 A resolution. The ICCGG helix has a twist corresponding to 10.7 bp per turn, a 19 degree base tilt and a 2.3 A rise per base pair along the helix axis. The mean propeller twist of 18 degree is comparable with, and has the same rotational sense as that observed in the B-DNA dodecamer CGCGAATTCGCG at similarly high alcohol concentration. Backbone phosphate groups in A-DNA are extensively hydrated, including a network across the opening of the major groove, whereas base edge N and O groups in major and minor grooves are less hydrated than in B-DNA. The minor groove spine of hydration observed in B-DNA is totally absent. These observations of relative hydration confirm and extend the model for the B- to A- helix transition proposed earlier on the basis of the B helix structure.

Synthesis an crystal structure of 3beta-p-bromobenzoyloxy-14alpha, 15alpha-epoxy-5alpha-cholest-7-ene.

The chemical synthesis of 3beta-bromobenzoyloxy-14alpha, 15alpha-epoxy-5alpha-cholest-7-ene is described. Single crystal structral analysis was employed to unambiguously determine the location and absolute configuration of the epoxide moiety in the 3beta-p-bromobenzoyloxy-14alpha, 15alpha-epoxy-5alpha-cholest-7-ene. The space group of the crystal was P1, with unit cell parameters: a=10.873 A, b=13.841 A, c=11.037 A, alpha=75.19 degrees, beta=78.79 degrees, gamma=101.57 degrees, and two molecules per unit cell. Intitial phases were derived from the two bromine atoms. Least squares refinements on all non-hydrogen atoms were carried out to a final unweighted R value of 0.10 and weighted R value of 0.04. The epoxide ring was located at the 14, 15 position and was found to extend to the alpha side of the molecule. Molecular measurements for asymmetry parameters of the sterol nuceus indicate that ring A has a symmetrical chair conformation and ring B has a half chair conformation due to the double bond at C(7). Ring C has a fairly distorted chair conformation due to the trigonal C(8) on one sie and the almost planar 5-membered ring on the other. Ring D has the 17alpha-envelope conformation.