The DNA fragment d(CpGpCpGpCpG) crystallises as a left-handed double helical molecule with Watson-Crick base pairs and an antiparallel organisation of the sugar phosphate chains. The helix has two nucleotides in the asymmetric unit and contains twelve base pairs per turn. It differs significantly from right-handed B-DNA.

Four different crystals of d(CpGpCpGpCpG) have been solved by x-ray diffraction analysis and all form similar left-handed double helical Z-DNA molecules in the crystal lattice. Two different conformations are observed for the phosphates in the GpC sequences, as the phosphates are found either facing the helical groove or rotated away from it. The latter conformation is often found when hydrated magnesium ions are complexed to a phosphate oxygen atom. These different conformations may be used when right-handed B-DNA joins left-handed Z-DNA. Atomic coordinates and torsion angles are presented for both types of Z-DNA.

With the emergence of multidrug resistant (MDR) bacteria, it is imperative to develop new intervention strategies. Current antibiotics typically target pathogen rather than host-specific biochemical pathways. Here we have developed kinase inhibitors that prevent intracellular growth of unrelated pathogens such as Salmonella typhimurium and Mycobacterium tuberculosis. An RNA interference screen of the human kinome using automated microscopy revealed several host kinases capable of inhibiting intracellular growth of S. typhimurium. The kinases identified clustered in one network around AKT1 (also known as PKB). Inhibitors of AKT1 prevent intracellular growth of various bacteria including MDR-M. tuberculosis. AKT1 is activated by the S. typhimurium effector SopB, which promotes intracellular survival by controlling actin dynamics through PAK4, and phagosome-lysosome fusion through the AS160 (also known as TBC1D4)-RAB14 pathway. AKT1 inhibitors counteract the bacterial manipulation of host signalling processes, thus controlling intracellular growth of bacteria. By using a reciprocal chemical genetics approach, we identified kinase inhibitors with antibiotic properties and their host targets, and we determined host signalling networks that are activated by intracellular bacteria for survival.

The structure of the crystalline daunomycind(CpGpTpApCpG) complex has been solved by x-ray diffraction analysis. The DNA forms a six-base-pair right-handed double helix with two daunomycin molecules intercalated in the d(CpG) sequences. The daunomycin aglycone chromophore is oriented at right angles to the long dimension of the DNA base pairs and the cyclohexene ring rests in the minor groove. Substituents on this ring have hydrogen bonding interactions to the base pairs above and below the intercalation site. These appear to be specific for anthracycline antibiotics. The amino sugar lies in the minor groove of the double helix without bonding to the DNA. The DNA double helix is distorted in a novel manner in accommodating the drug.An important group of antibiotics are those that interact with DNA and have antitumor activity. Daunomycin, an anthracycline antibiotic, has been found to inhibit virus multiplication and shows considerable activity against tumors; it was the first antibiotic to show activity against acute leukemia in man. It has an aglycone chromophore containing four fused rings and an amino sugar (Fig. 1). The closely related antitumor agent adriamycin (14-hydroxydaunomycin) is widely used in treating various solid tumors. These compounds have been the subject of intensive chemical and biological research since their discovery 17 years ago. More than 500 compounds of this type have been synthesized or isolated from nature and tested for activity (1, 2). These agents are believed to act by binding to DNA and inhibiting both DNA replication and transcription. Several studies suggest that the unsaturated chromophore intercalates between DNA base pairs (1, 2). However, the complexity of the molecule makes its mode of interaction with DNA a matter of considerable interest.Here we report the crystal structure of daunomycin with a self-complementary DNA fragment, d(CpGpTpApCpG). The structure has been solved by x-ray diffraction methods. A sixbase-pair fragment of double-helical DNA was found with two molecules of daunomycin bound to it, plus 80 mM spermine, and 30 mM cacodylate buffer (pH 6.5) was equilibrated with 30% (vol/vol) 2-methyl-2,4-pentanediol. After 1 week, attractive bright red-orange, tetragonal, rod-like crystals appeared. Spectroscopic analysis of the dissolved crystal revealed a 1:1 ratio of hexanucleotide to daunomycin. X-ray diffraction studies indicated a tetragonal crystal system with space group P4 212 or P43212, a = b = 27.92 A, c = 52.89 A.The asymmetric unit contained one hexanucleotide and one daunomycin molecule. Intense meridional reflections at 3.3 A along the c axis strongly suggested that the bases were stacked perpendicular to that direction. Three-dimensional data were collected on a Nicolet x-ray diffractometer to a resolution of

The crystal structure of a complex containing deoxy CpG and a terpyridine platinum compound (TPH) shows a DNA double helical fragment with TPH intercalated between two Watson-Crick GC base pairs. The DNA unwinding angle is 23 degrees and the pucker of the deoxyribose rings differ at the 3' and 5' ends.

In this paper, a detailed description is presented of the aromatic part of the 500-MHZ 1H nuclear magnetic resonance (NMR) spectrum of the helix-destabilizing gene-5 protein (GVP) encoded by the coliphage M13. As a result of the resolution obtained at 500 MHZ, it was possible to perform selective decoupling and time-resolved selective Overhauser experiments. The magnitudes of the observed Overhauser effects compare favorably with magnitudes expected on the basis of theoretical calculations. These experiments in conjunction with selective decoupling experiments allowed a detailed interpretation of the aromatic part of the protein spectrum. The spectrum of the aromatic part of the GVP-d(A)8 complex could be interpreted in a similar fashion. The ring protons of one phenylalanyl residue and of two tyrosyl residues show rather large shifts upon complex formation. This indicates that these residues are involved in the interaction with the DNA molecule in accordance with earlier observations. Direct evidence for the proximity of these aromatic rings and the DNA fragment in the complex was obtained by additional Overhauser experiments. It turns out that the H3',H4', and/or the H5' sugar protons of the oligonucleotide are situated near the ring protons of (most likely) two or all three of the aromatic residues of which the resonances undergo large shifts upon complex formation.

No abstract

No abstract