The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove.

The crystal and molecular structure of 2'-O-Me(CGCGCG)(2) has been determined at 1.19 A resolution, at 100 K, using synchrotron radiation. The structure in space group P3(2)12 is a half-turn right-handed helix that includes two 2-methyl-2,4-pentanediol (MPD) molecules bound in the minor groove. The structure deviates from A-form RNA. The duplex is overwound with an average value of 9.7 bp per turn, characterised as having a C3'-endo sugar pucker, very low base pair rise and high helical twist and inclination angles. The structure includes 65 ordered water molecules. Only a single row of water molecules is observed in the minor groove due to the presence of hydrophobic 2'-O-methyl groups. As many as five magnesium ions are located in the structure. Two are in the major groove and interact with O(6) and N(7) of guanosine and N(4) of cytidine residues through their hydration spheres. This work provides the first example of molecular interactions of nucleic acids with MPD, which was used as a precipitant, cryo-solvent and resolution enhancing agent. The two MPD molecules intrude into the hydration network in the minor groove, each forming hydrogen bonds between their secondary hydroxyl group and exo-amino functions of guanosine residues. Comparison of the 2'-O-Me(CGCGCG)(2) structure in the P3(2)12 and P6(1)22 crystals delineates stability of the water network within the minor groove to dehydration by MPD and is of interest for evaluating factors governing small molecule binding to RNA. Intrusion of MPD into the minor groove of 2'-O-Me(CGCGCG)(2) is discussed with respect to RNA dehydration, a prerequisite of Z-RNA formation.

Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy.

The crystal structure of a left-handed Z-DNA hexamer duplex d(CGCGCG)(2) has been solved based on the anomalous diffraction signal of inherent P atoms using data collected at the single wavelength of 1.54 A. The anomalous signal of about 2% of the total diffracted intensity, constant for all nucleic acids, may be generally useful for solving crystal structures of DNA and RNA oligomers. The multiplicity of intensity measurements is shown to crucially affect the data quality and the ability to solve the phase problem. The anisotropic model refined to an R factor of 8.9% at 0.95 A resolution.

Studies on synthesis and structure of O-beta-D-ribofuranosyl(1"-->2')ribonucleosides and oligonucleotides.

Minor nucleosides found in several eukaryotic initiator tRNASiMet, O-beta-D-ribofuranosyl(1"-->2')adenosine and -guanosine (Ar and Gr), as well as their pyrimidine analogues, were obtained from N-protected 3',5'-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)ribonucle osides and 1-O-acetyl-2,3,5-tri-O-benzoyl-beta-D-ribofuranose in the presence of tin tetrachloride in 1,2-dichloroethane. A crystal structure has been solved for 2'-O-ribosyluridine. The 3'-phosphoramidites of protected 2'-O-ribosylribonucleosides were prepared as the reagents for 2'-O-ribofuranosyloligonucleotides synthesis. O-beta-D-Ribofuranosyl(1"-->2')adenylyl(3'-->5')guanosine (ArpG) was obtained and its structure was analysed by NMR spectroscopy.

Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA.

The molecular and crystal structure of 2'-O-Me (CGCGCG)2 has been determined using synchrotron radiation at near-atomic resolution (1.30 A), the highest resolution to date in the RNA field. The crystal structure is a half-turn A-type helix with some helical parameters deviating from canonical A-RNA, such as low base pair rise, elevated helical twist and inclination angles. In CG steps, inter-strand guanines are parallel while cytosines are not parallel. In steps GC this motif is reversed. This type of regularity is not seen in other RNA crystal structures. The structure includes 44 water molecules and two hydrated Mg2+ions one of which lies exactly on the crystallographic 2-fold axis. There are distinct patterns of hydration in the major and the minor grooves. The major groove is stabilised by water clusters consisting of fused five- and six-membered rings. Minor groove contains only a single row of water molecules; each water bridges either two self-parallel cytosines or two self-parallel guanines by a pair of hydrogen bonds. The structure provides the first view of the hydration scheme of 2'-O-methylated RNA duplex.

The X-ray structure and absolute configuration of the anticancer drug (+)-4-ketocyclophosphamide.

4-Ketocyclophosphamide (4-keto CP), C7H12Cl2N2O3P, monoclinic, P2(1), a = 11.909 (2), b = 10.254 (1), c = 9.873 (1) A, beta = 91.08 (1) degrees, V = 1205.45 (3) A3 Z = 4, Dc = 1.51 Mg-m-3, Cu K alpha, lambda = 1.54178 A, alpha 25 = +53.8 degrees (c = 3.0, MeOH), m.p. 107 degrees C, mu = 61.8 cm-1, F (000) = 564, R = 0.064 for 2961 observed reflexions with I greater than 1.96 sigma(I). Dextrarotatory enantiomer of 4-keto CP has S configuration at the stereogenic center. One of the two crystallographically independent molecules is disordered both in a six-membered ring and in --N(CH2CH2Cl)2 moiety. With the exception of a less populated conformer of a disordered molecule, 4-keto CP molecules adopt a conformation in which 1,3,2-oxazophosphorinane ring is in the sofa form with C(6) deviating from the plane through the remaining five ring atoms while an exocyclic N atom with its three substituents is nearly coplanar with the phosphoryl oxygen atom O(8). In a less populated conformer, the six membered ring takes the form of sofa with C(5) as a flap while an exocyclic N atom and its substituents are oriented toward the P--N(3) bond.

X-ray-diffraction study and determination of absolute configuration of the anticancer drug S(--)cyclophosphamide (Endoxan, Cytoxan, NSC-26271).

(--)Cyclophosphamide(1) crystallized from tetrachloromethane in the triclinic space group P1 with cell dimensions a = 10.500 (4) A, b = 10.490 (4) A, c = 10.761 (4) A, alpha = 110.0 (2) degrees, beta = 110.0 (2) degrees, gamma = 108.9 (2) degrees. Three molecules are contained in the unit cell. The X-ray analysis was based on diffractometer measurement of 2635 independent reflections and the structure was solved by Patterson and direct methods. The final R and Rw factors after full-matrix least-squares refinement are 0.0717 and 0.0677, respectively. The absolute configuration is S based on Hamilton's R-factor ratio test. The oxazaphosphorinane ring exists in a chair form with the bis-beta chloroethyl-amino group in equatorial position and about perpendicular to and bisecting the O--P--N plane. The structure is similar to that found in racemic 1 except a different conformation about one ethyl-amino N--C bond.

X-ray analysis of glucagon and its relationship to receptor binding.

X-ray analysis of the pancreatic hormone glucagon shows that in crystals the polypeptide adopts a mainly helical conformation, which is stabilised by hydrophobic interactions between molecules related by threefold symmetry. A model is presented in which the glucagon molecule exists in dilute solutions as an equilibrium population of conformers with little retention of conformers with little retention of structure, and in which the helical conformation is stablised by hydrophobic interactions either as an oligomer or as a complex with the receptor.