Water and ions in a high resolution structure of B-DNA.

A detailed picture of hydration and counterion location in the B-DNA duplex d(GCGAATTCG) is presented. Detailed data have been obtained by single crystal x-ray diffraction at atomic resolution (0.89 A) in the presence of Mg(2+). The latter is the highest resolution ever obtained for a B-DNA oligonucleotide. Minor groove hydration is compared with that found in the Na(+) and Ca(2+) crystal forms of the related dodecamer d(CGCGAATTCGCG). High resolution data (1.45 A) of the Ca(2+) form obtained in our laboratory are used for that purpose. The central GAATTC has a very stable hydration spine identical in all cases, independent of duplex length and crystallization conditions (counterions, space group). However, the organization of the water molecules (tertiary and quaternary layers) associated with the central spine vary in each case.     

The complex of poly(dG).poly(dC) with arginine: stabilization of the B form and transition to multistranded structures

We have studied by X-ray diffraction fibers of complexes of poly(dG).poly(dC) with N-alpha-acetyl-L-arginine ethylamide. Although these polynucleotides favour the A form of DNA, in this complex it is never found, thus confirming that arginine prevents the appearance of this form of DNA. At high relative humidity the B form is present. Upon dehydration two new structures appear. One of them is a triple helix, most likely formed by poly(dC+).poly(dG).poly(dC). The other structure found also has features which indicate a multistranded conformation.     

The diameter of chromatin fibres depends on linker length

We have studied the diameter of chromatin fibres embedded in epoxy resins for three different materials: mouse thymus, chicken erythrocytes and sea cucumber spermatozoa. We confirm that the diameter of chromatin fibres increases with linker length, both values being influenced by the protein composition of chromatin.     

Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs.

The left-handed Z-DNA conformation has been observed in crystals made from the self-complementary DNA hexamer d(CACGTG). This is the first time that a non disordered Z form is found in the crystal structure of an alternating sequence containing AT base pairs without methylated or brominated cytosines. The structure has been determined and refined to an agreement factor R = 22.9% using 746 reflections in the resolution in the resolution shell 7 to 2.5 A. The overall shape of the molecule is very similar to the Z-structure of the related hexamer d(CG)3 confirming the rigidity of the Z form. No solvent molecules were detected in the minor groove of the helix near the A bases. The disruption of the spine of hydration in the AT step appears to be a general fact in the Z form in contrast with the B form. The biological relevance of the structure in relation to the CA genome repeats is discussed.     

Evolution of several cytoskeletal proteins of astrocytes in primary culture: Effect of prenatal alcohol exposure

In the present work we have analyzed, using immunoblotting and immunofluorescence techniques, the evolution of several cytoskeletal proteins during the development of astrocytes in primary culture. The effect of prenatal exposure to alcohol on these proteins was also evaluated. Microtubular protein -tubulin decreased approximately 47% from 4 to 7 days after which its content remained practically constant. Immunofluorescence studies showed also that the content of -tubulin was greater at day 4 of culture. This increase in fluorescence was coincident with the presence of globular particles which were found in interphase astrocytes and stained with both anti - and anti--tubulin. These structures appeared only in proliferating cells. Glial fibrillary acidic protein (GFAP) and vimentin were analyzed as intermediate filament (IF) proteins. GFAP, in cytoskeletal preparations, increased regularly for 14 days followed by a decrease to day 21. In contrast, vimentin showed a progressive increase throughout the entire culture period. Fluorescence studies revealed some differences between the IF distribution patterns of GFAP and vimentin.In astrocytes obtained from rats prenatally exposed to ethanol, decreases in the amounts of all the cytoskeletal proteins studied were found during the entire culture period. In these cells a striking disorganization of cytoskeleton was also observed. The alcohol-induced decrease of GFAP in cultured astrocytes was also found when this protein was studied in preparations from whole brain developed in vivo.Special issue dedicated to Dr. Santiago Grisolia     

Solid-state conformation of some basic sequential polypeptides

We have studied the structure of solid films obtained by x-ray diffraction, from several basic polypeptides with a defined sequence. The alterating polypeptides poly(Ala-Lys), poly(Leu-Lys), poly(Val-Lys), and poly(Arg-Leu) all show a cross-β-structure in which layers of hydrophilic side chains alternate with layers containing hydrophobic side chains. The other polypeptides studied are not in the β-conformation and appear to be in the α-helical conformation. The helices obtained from poly(Lys-Ala-Ala) and poly(Lys-Ala-Ala-Lys) appear to be packed in an unusual fashion, which favors interaction between alanine side chains. Such behavior is not found in poly(Lys-Leu-Ala).     

Comparison of the solution and crystal conformations of (G + C)-rich fragments of DNA.

DNA fragments crystallize in an unpredictable manner, and relationships between their crystal and solution conformations still are not known. We have studied, using circular dichroism spectroscopy, solution conformations of (G + C)-rich DNA fragments, the crystal structures of which were solved in the laboratory of one of the present authors. In aqueous trifluorethanol (TFE) solutions, all of the examined oligonucleotides adopted the same type of double helix as in the crystal. Specifically, the dodecamer d(CCCCCGCGGGGG) crystalized as A-DNA and isomerized into A-DNA at high TFE concentrations. On the other hand, the hexamer d(CCGCGG) crystallized in Z-form containing tilted base pairs, and high TFE concentrations cooperatively transformed it into the same Z-form as adopted by the RNA hexamer r(CGCGCG), although d(CCGCGG) could isomerize into Z-DNA in the NaCl + NiCl2) aqueous solution. The fragments crystallizing as B-DNA remained B-DNA, regardless of the solution conditions, unless they denatured or aggregated. Effects on the oligonucleotide conformation of 2-methyl-2,4-pentanediol and other crystallization agents were also studied. 2-Methyl-2,4-pentanediol induced the same conformational transitions as TFE but, in addition, caused an oligonucleotide condensation that was also promoted by the other crystallization agents. The present results indicate that the crystal double helices of DNA are stable in aqueous TFE rather than aqueous solution.     

Condensation of DNA by basic protiens does not depend on protien composition

We have studied by electron microscopy the size and morphology of the complexes obtained with different DNAs (between 500 and 5243 base pairs long) and four different proteins: sea urchin histone H1; sea cucumber histone ?₀, chicken erythrocyte histone H5, and clupeine. Surprisingly, the type of protein used has only a marginal influence on the complexes formed. The molecular weight and topology of DNA do not show any influence. The size of the complexes depends strongly on the ratio of positive to negative charges and also on the ionic conditions. Our studies have been mainly carried out at a ratio of 0.4. Under these conditions the average thickness of rods and toroids observed varies between 165 Å at 1.5 mM salt to 290 Å at 100 mM salt, with minor variations around these values depending on the type of DNA and protein used. We conclude that the formation of DNA condensates is mainly determined by a balance of electrostatic and intermolecular forces, the influence of specific interactions is only marginal. This conclusion seems to apply not only to the complexes described here, but also to chromatin fibers and to DNA condensed by low molecular weight counterions and other compounds (polyamines, inorganic ions, ethanol, etc.). © 1994 John Wiley & Sons, Inc.