J. Lourdes Campos

Structure vs. properties — chirality, optics and shapes — in amphiphilic porphyrin J-aggregates

The structure of the meso-tetrakis(4-sulfonatophenyl)porphyrin (TPPS4) J-aggregates could be determined by X-ray and electron diffraction methods. A sheet-like architecture reveals the relationship between structure and chirality, optics and shapes of the J-aggregates of the meso 4-sulfonatophenyl- and phenyl-substituted porphyrins. The structure of the J-aggregates of H4TPPS4 belongs to the chiral space group P21 and includes four porphyrin molecules in its unit cell. The intermolecular stabilization of the zwitterionic units by hydrogen bonding and electrostatic interactions between the positively charged central NH groups and the periphery anionic sulfonato groups results in a structure of porphyrins sheets along the [01] plane direction. The structure of the sheet on the [01] plane is already chiral and its molecular architecture explains the simultaneous presence of H- and J-aggregate bands in their absorption spectra. This structure also accounts for the high similarity observed between the absorption spectra of different mesomorphs of the same substance and even between different members of the series of meso-4-sulfonatophenyl- and aryl-substituted diprotonated porphyrins. The possibility, or not, of the sheet-like structure on [01] to interact with other layers, either through ionic or hydrophobic interactions, depends on the substitution pattern at the meso-positions of the porphyrin ring. Thus, the different morphologies of the particles [mono- bi- and multilayered] of this series of J-aggregates are explained taking into account the role that the fourth meso-substituent plays in the interlayer stabilization. The results suggest that supramolecular helicity, previously detected in several J-aggregates, is not the explanation of their chirality but would be the expression of the intrinsic chirality of the packing between building blocks.

Crystal structure of a complex of DNA with one AT-hook of HMGA1.

We present here for the first time the crystal structure of an AT-hook domain. We show the structure of an AT-hook of the ubiquitous nuclear protein HMGA1, combined with the oligonucleotide d(CGAATTAATTCG)2, which has two potential AATT interacting groups. Interaction with only one of them is found. The structure presents analogies and significant differences with previous NMR studies: the AT-hook forms hydrogen bonds between main-chain NH groups and thymines in the minor groove, DNA is bent and the minor groove is widened.

Structure of the DNA duplex d(ATTAAT)(2) with Hoogsteen hydrogen bonds

The traditional Watson-Crick base pairs in DNA may occasionally adopt a Hoogsteen conformation, with a different organization of hydrogen bonds. Previous crystal structures have shown that the Hoogsteen conformation is favored in alternating AT sequences of DNA. Here we present new data for a different sequence, d(ATTAAT)2, which is also found in the Hoogsteen conformation. Thus we demonstrate that other all-AT sequences of DNA with a different sequence may be found in the Hoogsteen conformation. We conclude that any all-AT sequence might acquire this conformation under appropriate conditions. We also compare the detailed features of DNA in either the Hoogsteen or Watson-Crick conformations.

The interaction of manganese ions with DNA

We present the structure of the duplex formed by a fragment of auto-complementary DNA with the sequence d(CGTTAATTAACG). The structure was determined by X-ray crystallography. Up to date it is the first structure presenting the interaction between a DNA oligonucleotide and manganese ions. The presence of Mn2+ creates bonds among the N7 atom of guanines and phosphates. These bonds stabilize and determine the crystallographic network in a P3(2) space group, unusual in oligonucleotide crystals. The crystal structure observed is compared with those found in the presence of Mg2+, Ca2+ and Ni2+, which show different kinds of interactions. The double helices show end-to-end interactions, in a manner that the terminal guanines interact with the minor groove of the neighboring duplex, while the terminal cytosines are disordered. We have chosen this sequence since it contains a TTAA repeat. Such repeats are very rare in all genomes. We suggest that this sequence may be very susceptible to the formation of closely spaced thymine dimers.

A unique vertebrate histone H1-related protamine-like protein results in an unusual sperm chromatin organization

Protamine‐like proteins constitute a group of sperm nuclear basic proteins that have been shown to be related to somatic linker histones (histone H1 family). Like protamines, they usually replace the chromatin somatic histone complement during spermiogenesis; hence their name. Several of these proteins have been characterized to date in invertebrate organisms, but information about their occurrence and characterization in vertebrates is still lacking. In this sense, the genus Mullus is unique, as it is the only known vertebrate that has its sperm chromatin organized by virtually only protamine‐like proteins. We show that the sperm chromatin of this organism is organized by two type I protamine‐like proteins (PL‐I), and we characterize the major protamine‐like component of the fish Mullus surmuletus (striped red mullet). The native chromatin structure resulting from the association of these proteins with DNA was studied by micrococcal nuclease digestion as well as electron microscopy and X‐ray diffraction. It is shown that the PL‐I proteins organize chromatin in parallel DNA bundles of different thickness in a quite distinct arrangement that is reminiscent of the chromatin organization of those organisms that contain protamines (but not histones) in their sperm.

Effect of Hydrodynamic Forces on meso-(4-Sulfonatophenyl)-Substituted Porphyrin J-Aggregate Nanoparticles: Elasticity, Plasticity and Breaking

The J aggregates of 4-sulfonatophenyl meso-substituted porphyrins are non-covalent polymers obtained by self-assembly that form nanoparticles of different morphologies. In the case of high aspect-ratio nanoparticles (bilayered ribbons and monolayered nanotubes), shear hydrodynamic forces may modify their shape and size, as observed by peak force microscopy, transmission electron microscopy of frozen solutions, small-angle X-ray scattering measurements in a disk-plate rotational cell, and cone-plate rotational viscometry. These nanoparticles either show elastic or plastic behaviour: there is plasticity in the ribbons obtained upon nanotube collapse on solid/air interfaces and in viscous concentrated nanotube solutions, whereas elasticity occurs in the case of dilute nanotube solutions. Sonication and strong shear hydrodynamic forces lead to the breaking of the monolayered nanotubes into small particles, which then associate into large colloidal particles.

In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27

New features of an antiprotozoal DNA minor-groove binding drug, which acts as a cross-linking agent, are presented. It also fills the minor groove of DNA completely and prevents the access of proteins. These features are also expected for other minor-groove binding drugs when associated with suitable DNA targets.

A Geometric Approach to the Crystallographic Solution of Nonconventional DNA Structures: Helical Superstructures of d(CGATAT)

Oligonucleotides have been used extensively to build nanostructures and nanodevices. Mostly, rather long oligonucleotides (10–100 bases) are used to form either flat tiles or closed objects based on standard Watson–Crick base pairs. Only recently, self-assembled three-dimensional DNA lattices have been described. Such structures feature large cavities, allowing incorporation of globular shaped molecules. Also, short oligonucleotides (2–12 bases) may assemble into intricate lattices, such as cubes and other complex structures, containing large voids. X-ray crystallography provides the indispensable three-dimensional view into the atomic structure of such nanomaterials, but their crystals usually diffract far from atomic resolution, and thus their structures cannot be solved by direct methods. Herein, we present a new geometrical approach to solve nonconventional DNA structures and its application to the solution of the superstructure of new topology formed by d(CGATAT). Such unprecedented structures could result in materials with new properties, and their characterization should not be hindered for lack of a suitable phasing method. As it is well known from the pioneering work on the structure of the DNA double helix using fiber diffraction, in contrast to protein crystallography, meaningful information can be derived already from the diffraction pattern. Previous knowledge leads to the expectation that DNA forms basepaired, double-stranded helices in A, B, or Z geometry. Such helical moieties tend to stack on piles or to lean their ends on the grooves of other helices. Other motifs may play a role: quadruplexes, three-way and Holliday-junctions, or looping out unpaired bases have been described in the structures of oligonucleotides and their complexes. Major base-stacking directions can be identified from the diffraction images by the strong Bragg reflections at 3.3 spacing and fiber streaks. Thus, analysis of the diffraction data fixes the preferred orientation of piled base pairs (Figure S1a in the Supporting Information). The unit-cell geometry and the symmetry, along with the estimation of the solvent content from the atomic volumes, allow one to predict whether they fit a simple packing of regular helices or a distortion is required to build a three-dimensional structure. Figure S1b illustrates the relationship between the dimensions of a hexagonal projection and the requirements on the helical radii. Thus, examination of the geometrical parameters can be exploited to set up structural hypotheses as to the building blocks present and their packing, to be confirmed or discarded through molecular replacement or refinement of the models. To identify such models, we automated the analysis of the packing of all DNA structures deposited with the Protein or Nucleic Acid Databases (PDB/NDB). Our program SUBIX (Figure 1) allows one to establish the geometrical requirements of different projections and to classify DNA materials according to their building blocks, thus identifying or assembling the best candidates to be used alone or in combination

Functional and structural analysis of AT-specific minor groove binders that disrupt DNA-protein interactions and cause disintegration of the Trypanosoma brucei kinetoplast

Abstract Trypanosoma brucei, the causative agent of sleeping sickness (Human African Trypanosomiasis, HAT), contains a kinetoplast with the mitochondrial DNA (kDNA), comprising of >70% AT base pairs. This has prompted studies of drugs interacting with AT-rich DNA, such as the N-phenylbenzamide bis(2-aminoimidazoline) derivatives 1 [4-((4,5-dihydro-1H-imidazol-2-yl)amino)-N-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzamide dihydrochloride] and 2 [N-(3-chloro-4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)-4-((4,5-dihydro-1H-imidazol-2-yl)amino)benzamide] as potential drugs for HAT. Both compounds show in vitro effects against T. brucei and in vivo curative activity in a mouse model of HAT. The main objective was to identify their cellular target inside the parasite. We were able to demonstrate that the compounds have a clear effect on the S-phase of T. brucei cell cycle by inflicting specific damage on the kinetoplast. Surface plasmon resonance (SPR)–biosensor experiments show that the drug can displace HMG box-containing proteins essential for kDNA function from their kDNA binding sites. The crystal structure of the complex of the oligonucleotide d[AAATTT]2 with compound 1 solved at 1.25 Å (PDB-ID: 5LIT) shows that the drug covers the minor groove of DNA, displaces bound water and interacts with neighbouring DNA molecules as a cross-linking agent. We conclude that 1 and 2 are powerful trypanocides that act directly on the kinetoplast, a structure unique to the order Kinetoplastida.

Effect of solvent choice on the self-assembly properties of a diphenylalanine amphiphile stabilized by an ion pair

A diphenylalanine (FF) amphiphile blocked at the C terminus with a benzyl ester (OBzl) and stabilized at the N terminus with a trifluoroacetate (TFA) anion was synthetized and characterized. Aggregation of peptide molecules was studied by considering a peptide solution in an organic solvent and adding pure water, a KCl solution, or another organic solvent as co-solvent. The choice of the organic solvent and co-solvent and the solvent/co-solvent ratio allowed the mixture to be tuned by modulating the polarity, the ionic strength, and the peptide concentration. Differences in the properties of the media used to dissolve the peptides resulted in the formation of different self-assembled microstructures (e.g. fibers, branched-like structures, plates, and spherulites). Furthermore, crystals of TFA⋅FF-OBzl were obtained from the aqueous peptide solutions for X-ray diffraction analysis. The results revealed a hydrophilic core constituted by carboxylate (from TFA), ester, and amide groups, and the core was found to be surrounded by a hydrophobic crown with ten aromatic rings. This segregated organization explains the assemblies observed in the different solvent mixtures as a function of the environmental polarity, ionic strength, and peptide concentration.