DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers

The controlled arraying of DNA strands on adaptive polymeric platforms remains a challenge. Here, the noncovalent synthesis of DNA-grafted supramolecular polymers from short chimeric oligomers is presented. The oligomers are composed of an oligopyrenotide strand attached to the 5′-end of an oligodeoxynucleotide. The supramolecular polymerization of these oligomers in an aqueous medium leads to the formation of one-dimensional (1D) helical ribbon structures. Atomic force and transmission electron microscopy show rod-like polymers of several hundred nanometers in length. DNA-grafted polymers of the type described herein will serve as models for the development of structurally and functionally diverse supramolecular platforms with applications in materials science and diagnostics.

Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.

Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.

Synthesis and characterisation of photoreactive silanes for the self-assembly on functionalised silica surfaces

The aim of this thesis was to investigate novel techniques to create complex hierarchical chemical patterns on silica surfaces with micro to nanometer sized features. These surfaces were used for a site-selective assembly of colloidal particles and oligonucleotides. To do so, functionalised alkoxysilanes (commercial and synthesised ones) were deposited onto planar silica surfaces. The functional groups can form reversible attractive interactions with the complementary surface layers of the opposing objects that need to be assembled. These interactions determine the final location and density of the objects onto the surface. Photolithographically patterned silica surfaces were modified with commercial silanes, in order to create hydrophilic and hydrophobic regions on the surface. Assembly of hydrophobic silica particles onto these surfaces was investigated and finally, pH and charge effects on the colloidal assembly were analysed. In the second part of this thesis the concept of novel, "smart" alkoxysilanes is introduced that allows parallel surface activation and patterning in a one-step irradiation process. These novel species bear a photoreactive head-group in a protected form. Surface layers made from these molecules can be irradiated through a mask to remove the protecting group from selected regions and thus generate lateral chemical patterns of active and inert regions on the substrate. The synthesis of an azide-reactive alkoxysilane was successfully accomplished. Silanisation conditions were carefully optimised as to guarantee a smooth surface layer, without formation of micellar clusters. NMR and DLS experiments corroborated the absence of clusters when using neither water nor NaOH as catalysts during hydrolysis, but only the organic solvent itself. Upon irradiation of the azide layer, the resulting nitrene may undergo a variety of reactions depending on the irradiation conditions. Contact angle measurements demonstrated that the irradiated surfaces were more hydrophilic than the non-irradiated azide layer and therefore the formation of an amine upon irradiation was postulated. Successful photoactivation could be demonstrated using condensation patterns, which showed a change in wettability on the wafer surface upon irradiation. Colloidal deposition with COOH functionalised particles further underlined the formation of more hydrophilic species. Orthogonal photoreactive silanes are described in the third part of this thesis. The advantage of orthogonal photosensitive silanes is the possibility of having a coexistence of chemical functionalities homogeneously distributed in the same layer, by using appropriate protecting groups. For this purpose, a 3',5'-dimethoxybenzoin protected carboxylic acid silane was successfully synthesised and the kinetics of its hydrolysis and condensation in solution were analysed in order to optimise the silanisation conditions. This compound was used together with a nitroveratryl protected amino silane to obtain bicomponent surface layers. The optimum conditions for an orthogonal deprotection of surfaces modified with this two groups were determined. A 2-step deprotection process through a mask generated a complex pattern on the substrate by activating two different chemistries at different sites. This was demonstrated by colloidal adsorption and fluorescence labelling of the resulting substrates. Moreover, two different single stranded oligodeoxynucleotides were immobilised onto the two different activated areas and then hybrid captured with their respective complementary, fluorescent labelled strand. Selective hybridisation could be shown, although non-selective adsorption issues need to be resolved, making this technique attractive for possible DNA microarrays.

Hierarchical self-assembly of nucleotide-appended oligopyrenotides into defined supramolecular objects

Supramolecular DNA assembly blends DNA building blocks with synthetic organic and inorganic molecules giving structural and functional advantages both to the initial self-assembly process and to the final construct. Synthetic molecules can bring a number of additional interactions into DNA nanotechnology. Incorporating extended aromatic molecules as connectors of DNA strands allows folding of these strands through π-π stacking (DNA “foldamers”). In previous work it was shown that short oligopyrenotides (phosphodiester-linked pyrene oligomers) behave as staircase-like foldamers, which cooperatively self-assemble into two-dimensional supramolecular polymers in aqueous medium. Herein, we demonstrate that a 10-mer DNA-sequence modified with 7 pyrene units (see illustration) forms dimensionally-defined supramolecular polymers under thermodynamic conditions in water. We present the self-assembly behavior, morphological studies, and the spectroscopic properties of the investigated DNA-sequences (illustrative AFM picture shown below).

Hierarchical self-assembly of nucleotide-appended oligopyrenotides into defined supramolecular objects

Supramolecular DNA assembly blends DNA building blocks with synthetic organic molecules giving structural and functional advantages. Incorporating extended aromatic molecules as connectors of DNA strands allows folding of these strands through π-π stacking (DNA 'foldamers'). In previous work it was shown that short oligopyrenotides behave as staircase-like foldamers, which cooperatively self-assemble into 2D supramolecular polymers in aqueous medium. Herein, we demonstrate that 10-mer DNA-sequence conjugated with seven pyrene unites forms dimensionally-defined supramolecular polymers under thermodynamic conditions in water. We present the self-assembly behavior, morphologycal studies (AFM and TEM), and the spectroscopic properties (UV/vis, CD) of the investigated pyrene - conjugated DNA-sequence.

Self-assembly into nanoparticles is essential for receptor mediated uptake of therapeutic antisense oligonucleotides

Antisense oligonucleotides (ASOs) have the potential of revolutionizing medicine due to their ability to manipulate gene function for therapeutic purposes. ASOs are chemically modified and/or incorporated with nanoparticles to enhance their stability and cellular uptake; however, one of the biggest challenges is the poor understanding of their uptake mechanism, which is needed for designing better ASOs with high activity and low toxicity. Here, we study the uptake mechanism of three therapeutically relevant ASOs (peptide-conjugated phosphorodiamidate morpholino (P-PMO), 2?Omethyl phosphorothioate (2?OMe) and phosphorothioated tricyclo DNA (tcDNA) that have been optimized to induce exon skipping in models of Deuchenne muscular dystrophy (DMD). We show that P-PMO and tcDNA have high propensity to spontaneously self-assemble into nanoparticles. P-PMO forms micelles of defined size and their net charge (zeta potential) is dependent on the medium and concentration. In biomimetic conditions and at low concentrations P-PMO obtains net negative charge and its uptake is mediated by class A scavenger receptor subtypes (SCARAs) as shown by competitive inhibition and RNAi silencing experiments in-vitro. In-vivo, the activity of P-PMO was significantly decreased in SCARA1 knock-out mice compared to wild-type animals. Additionally, we show that SCARA1 is involved in the uptake of tcDNA and 2?OMe as shown by competitive inhibition and co-localization experiments. Surface plasmon resonance binding analysis to SCARA1 demonstrated that P-PMO and tcDNA have higher binding profiles to the receptor compared to 2?OMe. These results demonstrate receptor-mediated uptake for a range of ASO chemistries, a mechanism that is dependent on their self-assembly into nanoparticles.

Self-assembly of a heteroduplex helicate from two different ligand strands and Cu(II) cations.

Cu(II) ions have been reacted with a 1/1 mixture of two linear ligands, one containing three 2,2'- bipyridine groups and the other three 2,2':6',2"-terpyridine groups. Absorption spectroscopy and fast atom bombardment mass spectrometry indicate the formation of a trinuclear complex containing one ligand of each kind. Determination of the crystal structure of this compound has confirmed that it is indeed a linear trinuclear complex in which two different ligands are wrapped in a helical fashion around the pentacoordinated metal ions. The central coordination geometry is trigonal bipyramidal; the two lateral Cu(II) ions are in a square pyramidal environment. Thus, a heteroduplex helicate is formed by the self-assembly of two different ligand strands and three specific metal ions induced by the coordination number and geometry of the latter. The self-assembly process may be considered to result from the reading of the steric and binding information present in the two ligands by Cu(II) ions through a pentacoordination algorithm. The same ligands have been shown earlier to yield homoduplex helicates from ions of tetrahedral and octahedral coordination geometry and strands of bidentate bipyridines and tridentate terpyridines, respectively. These two types of artificial double helical species may be related on one hand to the natural homoduplex nucleic acids and on the other hand to the DNA:RNA heteroduplex.

Functionalized adamantane: Building blocks for nanostructure self-assembly

We report first-principles calculations on the electronic and structural properties of chemically functionalized adamantane molecules, either in isolated or crystalline forms. Boron and nitrogen functionalized molecules, aza-, tetra-aza-, bora-, and tetra-bora-adamantane, were found to be very stable in terms of energetics, consistent with available experimental data. Additionally, a hypothetical molecular crystal in a zincblende structure, involving the pair tetra-bora-adamantane and tetra-aza-adamantane, was investigated. This molecular crystal presented a direct and large electronic band gap and a bulk modulus of 20 GPa. The viability of using those functionalized molecules as fundamental building blocks for nanostructure self-assembly is discussed.

Self-assembly of a tetranuclear macrocyclic copper(II) complex

A dinuclear macrocyclic complex is synthesized via the one-pot reaction of dipotassium nitroacetate, formaldehyde and a linear tetraamine copper(II) complex; the X-ray crystal structure of the product reveals an association of two dinuclear complexes to form a novel tetracopper(II) species.

Equilibrium self-assembly of colloids with distinct interaction sites: Thermodynamics, percolation, and cluster distribution functions

We calculate the equilibrium thermodynamic properties, percolation threshold, and cluster distribution functions for a model of associating colloids, which consists of hard spherical particles having on their surfaces three short-ranged attractive sites (sticky spots) of two different types, A and B. The thermodynamic properties are calculated using Wertheim's perturbation theory of associating fluids. This also allows us to find the onset of self-assembly, which can be quantified by the maxima of the specific heat at constant volume. The percolation threshold is derived, under the no-loop assumption, for the correlated bond model: In all cases it is two percolated phases that become identical at a critical point, when one exists. Finally, the cluster size distributions are calculated by mapping the model onto an effective model, characterized by a-state-dependent-functionality (f) over bar and unique bonding probability (p) over bar. The mapping is based on the asymptotic limit of the cluster distributions functions of the generic model and the effective parameters are defined through the requirement that the equilibrium cluster distributions of the true and effective models have the same number-averaged and weight-averaged sizes at all densities and temperatures. We also study the model numerically in the case where BB interactions are missing. In this limit, AB bonds either provide branching between A-chains (Y-junctions) if epsilon(AB)/epsilon(AA) is small, or drive the formation of a hyperbranched polymer if epsilon(AB)/epsilon(AA) is large. We find that the theoretical predictions describe quite accurately the numerical data, especially in the region where Y-junctions are present. There is fairly good agreement between theoretical and numerical results both for the thermodynamic (number of bonds and phase coexistence) and the connectivity properties of the model (cluster size distributions and percolation locus).

Self-assembly in chains, rings, and branches: a single component system with two critical points

Agências financiadoras: FCT - PEstOE/FIS/UI0618/2011; PTDC/FIS/098254/2008 ERC-PATCHYCOLLOIDS e MIUR-PRIN

Quantitative description of the self-assembly of patchy particles into chains and rings

We numerically study a simple fluid composed of particles having a hard-core repulsion complemented by two patchy attractive sites on the particle poles. An appropriate choice of the patch angular width allows for the formation of ring structures which, at low temperatures and low densities, compete with the growth of linear aggregates. The simplicity of the model makes it possible to compare simulation results and theoretical predictions based on the Wertheim perturbation theory, specialized to the case in which ring formation is allowed. Such a comparison offers a unique framework for establishing the quality of the analytic predictions. We find that the Wertheim theory describes remarkably well the simulation results.

Natural and amyloid self-assembly of S100 proteins: structural basis of functional diversity

The S100 proteins are 10-12 kDa EF-hand proteins that act as central regulators in a multitude of cellular processes including cell survival, proliferation, differentiation and motility. Consequently, many S100 proteins are implicated and display marked changes in their expression levels in many types of cancer, neurodegenerative disorders, inflammatory and autoimmune diseases. The structure and function of S100 proteins are modulated by metal ions via Ca2+ binding through EF-hand motifs and binding of Zn2+ and Cu2+ at additional sites, usually at the homodimer interfaces. Ca2+ binding modulates S100 conformational opening and thus promotes and affects the interaction with p53, the receptor for advanced glycation endproducts and Toll-like receptor 4, among many others. Structural plasticity also occurs at the quaternary level, where several S100 proteins self-assemble into multiple oligomeric states, many being functionally relevant. Recently, we have found that the S100A8/A9 proteins are involved in amyloidogenic processes in corpora amylacea of prostate cancer patients, and undergo metal-mediated amyloid oligomerization and fibrillation in vitro. Here we review the unique chemical and structural properties of S100 proteins that underlie the conformational changes resulting in their oligomerization upon metal ion binding and ultimately in functional control. The possibility that S100 proteins have intrinsic amyloid-forming capacity is also addressed, as well as the hypothesis that amyloid self-assemblies may, under particular physiological conditions, affect the S100 functions within the cellular milieu.