Joan Aymamí

Crystal structure of a DNA Holliday junction

DNA recombination is a universal biological event responsible both for the generation of genetic diversity and for the maintenance of genome integrity. A four-way DNA junction, also termed Holliday junction, is the key intermediate in nearly all recombination processes. This junction is the substrate of recombination enzymes that promote branch migration or catalyze its resolution. We have determined the crystal structure of a four-way DNA junction by multiwavelength anomalous diffraction, and refined it to 2.16 Å resolution. The structure has two-fold symmetry, with pairwise stacking of the double-helical arms, which form two continuous B-DNA helices that run antiparallel, cross in a right-handed way, and contain two G-A mismatches. The exchanging backbones form a compact structure with strong van der Waals contacts and hydrogen bonds, implying that a conformational change must occur for the junction to branch-migrate or isomerize. At the branch point, two phosphate groups from one helix occupy the major groove of the other one, establishing sequence-specific hydrogen bonds. These interactions, together with different stacking energies and steric hindrances, explain the preference for a particular junction stacked conformer.

Molecular Structure of the Netropsin-d(CGCGATATCGCG) Complex: DNA Conformation in an Alternating AT Segment

The molecular structure of the complex between a minor groove binding drug (netropsin) and the DNA dodecamer d(CGCGATATCGCG) has been solved and refined by single-crystal X-ray diffraction analysis to a final R factor of 20.0% to 2.4-A resolution. The crystal is similar to that of the other related dodecamers with unit cell dimensions of a = 25.48 A, b = 41.26 A, and c = 66.88 A in the space group P2(1)2(1)2(1). In the complex, netropsin binds to the central ATAT tetranucleotide segment in the narrow minor groove of the dodecamer B-DNA double helix as expected. However, in the structural refinement the drug is found to fit the electron density in two orientations equally well, suggesting the disordered model. This agrees with the results from solution studies (chemical footprinting and NMR) of the interactions between minor groove binding drugs (e.g., netropsin and distamycin A) and DNA. The stabilizing forces between drug and DNA are provided by a combination of ionic, van der Waals, and hydrogen-bonding interactions. No bifurcated hydrogen bond is found between netropsin and DNA in this complex due to the unique dispositions of the hydrogen-bond acceptors (N3 of adenine and O2 of thymine) on the floor of the DNA minor groove. Two of the four AT base pairs in the ATAT stretch have low propeller twist angles, even though the DNA has a narrow minor groove. Alternating helical twist angles are observed in the ATAT stretch with lower twist in the ApT steps than in the TpA step.

The anticancer agent ellipticine unwinds DNA by intercalative binding in an orientation parallel to base pairs.

Ellipticine is a natural plant product that has been found to be a powerful anticancer drug. Although still unclear, its mechanism of action is considered to be mainly based on DNA intercalation and/or the inhibition of topoisomerase II. Many experimental data suggest an intercalation based on stacking interactions along the major base-pair axis, but alternative binding modes have been proposed, in particular for ellipticine derivatives. The 1.5 A resolution structure of ellipticine complexed to a 6 bp oligonucleotide unveils its mode of binding and enables a detailed analysis of the distorting effects of the drug on the DNA.

The inherent properties of DNA four-way junctions: Comparing the crystal structures of holliday junctions

Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. Much work has focused on the overall structure and properties of four-way junctions in solution, but we are just now beginning to understand these complexes at the atomic level. The crystal structures of two all-DNA Holliday junctions have been determined recently from the sequences d(CCGGGACCGG) and d(CCGGTACCGG). A detailed comparison of the two structures helps to distinguish distortions of the DNA conformation that are inherent to the cross-overs of the junctions in this crystal system from those that are consequences of the mismatched dG.dA base-pair in the d(CCGGGACCGG) structure. This analysis shows that the junction itself perturbs the sequence-dependent conformational features of the B-DNA duplexes and the associated patterns of hydration in the major and minor grooves only minimally. This supports the idea that a DNA four-way junction can be assembled at relatively low energetic cost. Both structures show a concerted rotation of the adjacent duplex arms relative to B-DNA, and this is discussed in terms of the conserved interactions between the duplexes at the junctions and further down the helical arms. The interactions distant from the strand cross-overs of the junction appear to be significant in defining its macroscopic properties, including the angle relating the stacked duplexes across the junction.

The layered organization of nucleosomes in 30 nm chromatin fibers

We have used electron microscopy and established methods of three-dimensional reconstruction to obtain structural information on the 30 nm chromatin fibers from sea cucumber sperm and chicken erythrocytes. The fibers show a longitudinal periodicity of 10–11 nm. We have interpreted this periodicity as due to a grouping of nucleosomes into disks, each disk containing about 5–6 nucleosomes. These disks are closely stacked to form the chromatin fiber. We have built a detailed model for four fibers and we have determined the approximate coordinates of all the nucleosomes in them. The average distance found between neighboring nucleosomes has a value close to 11 nm. They may be connected either as a regularly distorted helix or as a layered zigzag. The second model appears more appropriate, since in the constrictions of the fibers the nucleosomes can only be connected as a zigzag.

Molecular structure of a complete turn of A-DNA.

We have determined the crystal structure of the dodecamer d(CCCCCGCGGGGG), showing for the first time a complete turn of A-DNA. It has average structural parameters similar to those determined in fibres. Nevertheless it shows a considerable local variation in structure which is in part associated with the presence of a bound spermine molecule. We conclude that the local DNA conformation does not only depend on the base sequence, but may be strongly modified upon interaction with other molecules. In particular, the CpG sequence, which is found in hypersensitive regions of the genome, appears to be able to easily change its conformation under external influences.

Micro-molding with ultrasonic vibration energy: New method to disperse nanoclays in polymer matrices

Ultrasound technology was proved as an efficient processing technique to obtain micro-molded specimens of polylactide (PLA) and polybutylene succinate (PBS), which were selected as examples of biodegradable polyesters widely employed in commodity and specialty applications. Operational parameters such as amplitude, molding force and processing time were successfully optimized to prepare samples with a decrease in the number average molecular weight lower than 6%. Ultrasonic waves also seemed an ideal energy source to provide effective disaggregation of clay silicate layers, and therefore exfoliated nanocomposites. X-ray diffraction patterns of nanocomposites prepared by direct micro-molding of PLA or PBS powder mixtures with natural montmorillonite or different organo-modified clays showed the disappearance of the 001 silicate reflection for specimens having up to 6 wt.% clay content. All electron micrographs revealed relatively homogeneous dispersion and sheet nanostructures oriented in the direction of the melt flow. Incorporation of clay particles during processing had practically no influence on PLA characteristics but enhanced PBS degradation when an organo-modifier was employed. This was in agreement with thermal stability data deduced from thermogravimetric analysis. Cold crystallization experiments directly performed on micro-molded PLA specimens pointed to a complex influence of clay particles reflected by the increase or decrease of the overall non-isothermal crystallization rate when compared to the neat polymer. In all cases, the addition of clay led to a clear decrease in the Avrami exponent.

Preparation of micro-molded exfoliated clay nanocomposites by means of ultrasonic technology

Ultrasound micro-molding technology has been tested as a new method to get polymer/clay nanocomposites. Biodegradable polylactide (PLA) and poly (nona-methylene azelate) (PE99) have been used as polymer matrices, whereas different silicate clays have been assayed. The new technology is able to get specimens without evidences of degradation during processing. Only the use of organo-modified clays could give rise to a slight molecular weight decrease when the poly (alkylene dicarboxylate) sample was considered. Ultrasonic micro-molding has revealed effective to get directly nanocomposites with the final form required for a selected application, a homogeneous clay distribution up to a load of 6 wt-% and more interestingly exfoliated structures without being necessary the use of a compatibilizer agent between the organic polymer and the inorganic silicate clay. Transmission electron micrographs and X-ray diffraction profiles revealed exfoliated structure when N757, C20A, C25A, and N848 clays were employed.Crystallization behavior of exfoliated PLA nanocomposites was highly peculiar since clay particles had an antinucleating effect that decreased the overall crystallization rate respect to the neat polymer. In addition, the incorporation of layers into growing spherulites increased the crystal growth rate. A typical crystallization effect was on the contrary observed for nanocomposites derived from the poly (alkylene dicarboxylate) sample.

Intercalative DNA binding of the marine anticancer drug variolin B

Variolin B is a rare marine alkaloid that showed promising anti-cancer activity soon after its isolation. It acts as a cyclin-dependent kinase inhibitor, although the precise mechanism through which it exerts the cytotoxic effects is still unknown. The crystal structure of a variolin B bound to a DNA forming a pseudo-Holliday junction shows that this compound can also contribute, through intercalative binding, to either the formation or stabilization of multi-stranded DNA forms.