Locating monovalent cations in the grooves of B-DNA.

Here we demonstrate that monovalent cations can localize around B-DNA in geometrically regular, sequence-specific sites in oligonucleotide crystals. Positions of monovalent ions were determined from high-resolution X-ray diffraction of DNA crystals grown in the presence of thallium(I) cations (Tl(+)). Tl(+) has previously been shown to be a useful K(+) mimic. Tl(+) positions determined by refinement of model to data are consistent with positions determined using isomorphous F(Tl) - F(K) difference Fouriers and anomalous difference Fouriers. None of the observed Tl(+) sites surrounding CGCGAATTCGCG are fully occupied by Tl(+) ions. The most highly occupied sites, located within the G-tract major groove, have estimated occupancies ranging from 20% to 35%. The occupancies of the minor groove sites are estimated to be around 10%. The Tl(+) positions in general are not in direct proximity to phosphate groups. The A-tract major groove appears devoid of localized cations. The majority of the observed Tl(+) ions interact with a single duplex and so are not engaged in lattice interactions or crystal packing. The locations of the cation sites are dictated by coordination geometry, electronegative potential, avoidance of electropositive amino groups, and cation-pi interactions. It appears that partially dehydrated monovalent cations, hydrated divalent cations, and polyamines compete for a common binding region on the floor of the G-tract major groove.

A Supramolecular Tetra-Keggin Polyoxometalate

Giant polyoxometalates with catalytic, magnetic, and antiviral properties, which are in part attributable to their structures, are currently of great interest. Herein is described the synthesis and characterization of 1, a structurally novel tetrameric complex from Keggin ions (see picture). This complex is stable under the physiological conditions of the stomach (pH 1-2), which is interesting since related keggin anions are among the least toxic and yet most potent antiviral agents of the more than 300 polyoxometalates investigated biologically and pharmacologically.

Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations.

The potassium form of d(CGCGAATTCGCG) solved by X-ray diffraction to 1.75 A resolution indicates that monovalent cations penetrate the primary and secondary layers of the "spine of hydration". Both the sodium [Shui, X., McFail-Isom, L., Hu, G. G., and Williams, L. D. (1998) Biochemistry 37, 8341-8355] and the potassium forms of the dodecamer at high resolution indicate that the original description of the spine, only two layers deep and with full occupancy by water molecules, requires substantive revision. The spine is merely the bottom two layers of a four layer solvent structure. The four layers combine to form a repeating motif of fused hexagons. The top two solvent layers were not apparent from previous medium-resolution diffraction data. We propose that the narrow minor groove and axial curvature of A-tract DNA arise from localization of cations within the minor groove. In general, the results described here support a model in which most or all forces that drive DNA away from canonical B-conformation are extrinsic and arise from interaction of DNA with its environment. Intrinsic forces, originating from direct base-base interactions such as stacking, hydrogen bonding, and steric repulsion among exocyclic groups appear to be insignificant. The time-averaged positions of the ubiquitous inorganic cations that surround DNA are influenced by DNA bases. The distribution of cations depends on sequence. Regions of high and low cation density are generated spontaneously in the solvent region by heterogeneous sequence or even within the grooves of homopolymers. The regions of high and low cation density deform DNA by electrostatic collapse. Thus, the effects of small inorganic cations on DNA structure are similar to the effects of proteins.

4-Chloro-7-(iodoacetyl)amino-3-methoxy-isocoumarin.

The crystal structure of the iodo analog of 7-(bromoacetyl)amino-4-chloro-3-methoxyisocoumarin, an inhibitor of human neutrophil elastase (HNE), C12H9ClINO4, has been determined. The isocoumarin ring system is highly planar, with the carbonyl group of the amide function being coplanar with the isocoumarin ring.

Water ring structure at DNA interfaces: hydration and dynamics of DNA-anthracycline complexes.

In crystallographic structures of biological macromolecules, one can observe many hydration rings that originate at one water molecule, pass via hydrogen bonds through several others, and return to the original water molecule. Five-membered water rings have been thought to occur with greater frequency than other ring sizes. We describe a quantitative assessment of relationships between water ring size and frequency of occurrence in the vicinity of nucleic acid interfaces. This report focuses on low-temperature X-ray crystallographic structures of two anthracyclines, adriamycin (ADRI) and daunomycin (DAUN), bound to d(CGATCG) and on several DNA structures published previously by others. We have obtained excellent low-temperature (-160 degrees C, LT) X-ray intensity data for d(CGATCG)-adriamycin and d(CGATCG)-daunomycin with a multiwire area detector. The LTX-ray data sets contain 20% (daunomycin, LT-DAUN) and 35% (adriamycin, LT-ADRI) more reflections than were used to derive the original room-temperature (15 degrees C) structures [Frederick, C.A., Williams, L.D., Ughetto, G., van der Marel, G. A., van Boom, J.H., Rich, A., & Wang, A.H.-J. (1990) Biochemistry 29, 2538-2549]. The results show that five-membered water rings are not preferred over other ring sizes. This assessment is consistent with our observation of broad dispersion W-W-W angles (sigma = 20 degrees). In addition, we report that the thermal mobility, distinct from the static disorder, of the amino sugar of daunomycin and adriamycin is significantly greater than that of the rest of the complex. This mobility implies that if the central AT base pair is switched to a CG base pair, there should be a low energy cost in avoiding the guanine amino group. The energy difference (for the sugar-binding preference) between d(CGTACG) and d(CGCGCG) could be considerably less than 20 kcal/mol, a value proposed previously from computation.

N-succinimidyl methoxyphenylacetic acid ester, an amine-directed chiral derivatizing reagent suitable for enzymatic scale resolutions.

A chiral derivatizing reagent, N-succinimidyl-2-(S)-methoxy-2-phenylacetic acid ester (SMPA), directed toward reaction with primary amine-containing compounds has been synthesized and characterized. This reagent is suitable for HPLC resolution from enzymatic-scale reactions where only microgram quantities of chiral products may be obtainable. SMPA derivatization was shown to be effective in the resolution of the enantiomers of a number of different racemic compounds. SMPA was used to resolve the diastereoisomeric derivatives of a previously unknown enzymatically oxygenated product, allowing determination of the stereochemical course of the enzymatic reaction. SMPA is easily prepared from an inexpensive, commercially available, and enantiomerically pure precursor with the formation of a shelf-stable crystalline product which is utilizable in water-containing solutions. In addition to its usefulness for micro-determinations, SMPA is useful for preparative-scale resolutions of enantiomers since the reagent is cleaved from the diastereoisomeric derivative by acid hydrolysis.

Structural identification of a heterocyclic compound implicated in the Spanish toxic oil syndrome.

The compound 1-phenyl-5-vinylimidazolidine-2-thione was previously reported to be the causative agent in the outbreak referred to as Spanish toxic oil syndrome. X-ray crystallography, together with nuclear magnetic resonance and infra-red spectroscopy, now show the correct structure of this compound to be N-(5-vinyl-1,3-thiazolidin-2-ylidene)phenylamine (5-VTPA). Data for the structural characterization of 5-VTPA and the closely related isomer N-(4-vinyl-1,3-thiazolidin-2-ylidene)phenylamine are reported.

Macrocyclic pyrrolizidine alkaloids from Senecio anonymus. Separation of a complex alkaloid extract using droplet counter-current chromatography.

Ten 12-membered macrocyclic pyrrolizidine alkaloids, all of them esters of the necines, retronecine or otonecine, have been isolated from Senecio anonymus. The separation, carried out by droplet counter-current chromatography, afforded senecionine [1], integerrimine [2], retrorsine [3], senkirkine [5], neosenkirkine [6], otosenine [10], hydroxysenkirkine [7], and a new alkaloid given the trivial name anonamine [9]. Traces of usaramine [4] and another new alkaloid, hydroxyneosenkirkine [8], were detected by 1H nmr. In addition, the previously unreported 3a beta-hydroxy-4-ethoxy-2,6-perhydroindoledione [11] was isolated. X-ray structures were obtained for neosenkirkine [6], hydroxysenkirkine [7], anonamine [9], and [11]. 1H-13C heteronuclear shift correlated nmr (HETCOR) provided unambiguous chemical shift assignments for 13C-nmr data. Antitumor activity was assayed using the A204-rhabdomyosarcoma cell line in soft agarose.