Light Scattering and Cryo-Transmission Electron Microscopy Investigation of the Self-Assembling Behavior of Di-C12P-Nucleosides in Solution

Carbodiimide-Driven Dimerization and Self-Assembly of Artificial, Ribose-Based Amphiphiles

The aqueous self-assembly of amphiphiles into aggregates such as micelles and vesicles has been widely investigated over the past decades with applications ranging from materials science to drug delivery. The combination of characteristic properties of nucleic acids and amphiphiles is of substantial interest to mimic biological self-organization and compartmentalization. Herein, we present ribose- and ribonucleotide-based amphiphiles and investigate their self-assembly as well as their fundamental reactivity. We found that various types of aggregates are formed, ranging in size from nanometers to micrometers and all amphiphiles exhibit aggregation-induced emission (AIE) in solution as well as in the solid state. We also observed that the addition of 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) leads to rapid and selective dimerization of the amphiphiles into pyrophosphates, which decreases the critical aggregation concentration (CAC) by a factor of 25 when compared to the monomers. Since the propensity for amphiphile dimerization is correlated with their tendency to self-assemble, our results may be relevant for the formation of rudimentary compartments under prebiotic conditions.

Elongated self-assembled nanocarriers: From molecular organization to therapeutic applications

Self-assembled cylindrical aggregates made of amphiphilic molecules emerged almost 40 years ago. Due to their length up to micrometers, those particles display original physico-chemical properties such as important flexibility and, for concentrated samples, a high viscoelasticity making them suitable for a wide range of industrial applications. However, a quarter of century was needed to successfully take advantage of those improvements towards therapeutic purposes. Since then, a wide diversity of biocompatible materials such as polymers, lipids or peptides, have been developed to design self-assembling elongated drug nanocarriers, suitable for therapeutic or diagnostic applications. More recently, the investigation of the main forces driving the unidirectional growth of these nanodevices allowed a translation toward the formation of pure nanodrugs to avoid the use of unnecessary side materials and the possible toxicity concerns associated.

Stacking as a Key Property for Creating Nanoparticles with Tunable Shape: The Case of Squalenoyl-Doxorubicin

The development of elongated nanoparticles for drug delivery is of growing interest in recent years, due to longer blood circulation and improved efficacy compared to spherical counterparts. Squalenoyl-doxorubicin (SQ-Dox) conjugate was previously shown to form elongated nanoparticles with improved therapeutic efficacy and decreased toxicity compared to free doxorubicin. By using experimental and computational techniques, we demonstrate here that the specific physical properties of SQ-Dox, which include stacking and electrostatic interactions of doxorubicin as well as hydrophobic interactions of squalene, are involved in the formation of nanoassemblies with diverse elongated structures. We show that SQ-Dox bioconjugate concentration, ionic strength, and anion nature can be used to modulate the shape and stiffness of SQ-Dox nanoparticles. As those parameters are involved in nanoparticle behavior in biological media, these findings could bring interesting opportunities for drug delivery and serve as an example for the design of original nanodrugs with stacking properties tuned for particular clinical purposes.

Adenosine and lipids: A forced marriage or a love match?

Adenosine is a fascinating compound, crucial in many biochemical processes: this ubiquitous nucleoside serves as an essential building block of RNA, is also a component of ATP and regulates numerous pathophysiological mechanisms via binding to four extracellular receptors. Due to its hydrophilic nature, it belongs to a different world than lipids, and has no affinity for them. Since the 1970's, however, new discoveries have emerged and prompted the scientific community to associate adenosine with the lipid family, especially via liposomal preparations and bioconjugation. This seems to be an arranged marriage, but could it turn into a true love match? This review considered all types of unions established between adenosine and lipids. Even though exciting supramolecular structures were observed with adenosine-lipid conjugates, as well as with liposomal preparations which resulted in promising pre-clinical results, the translation of these technologies to the clinic is still limited.

Probing the Interaction between a DNA Nucleotide (Adenosine-5'-Monophosphate Disodium) and Surface Active Ionic Liquids by Rotational Relaxation Measurement and Fluorescence Correlation Spectroscopy

This article demonstrates the interaction of a deoxyribonucleic acid (DNA) nucleotide, adenosine-5'-monophosphate disodium (AMP) with a cationic surface active ionic liquid (SAIL) 1-dodecyl-3-methylimidazoium chloride (C₁₂mimCl), and an anionic SAIL, 1-butyl-3-methylimidazolium n-octylsulfate ([C₄mim][C₈SO₄]). Dynamic light scattering (DLS) measurements and ¹H NMR (nuclear magnetic resonance) studies indicate that substantial interaction is taking place among the DNA nucleotide (AMP) and the SAILs. Moreover, cryogenic transmission electron microscopy (cryo-TEM) suggests that SAILs containing micellar assemblies are transformed into larger micellar assemblies in the presence of DNA nucleotides. Additionally, the rotational motion of two oppositely charged molecules, rhodamine 6G perchlorate (R6G) and fluorescein sodium salt (Fl-Na), have been monitored in these aggregates. The rotational motion of R6G and Fl-Na differs significantly between SAILs micelles and SAILs-AMP containing larger micellar aggregates. The effect of negatively charged DNA nucleotide (AMP) addition into the cationic and anionic SAILs is more prominent for the cationic charged molecule R6G than that of anionic probe Fl-Na due to the favorable electrostatic interaction between the AMP and cationic R6G. Moreover, the influence of the anionic DNA nucleotide on the cationic and anionic SAIL micelles is monitored through the variation of the lateral diffusion motion of oppositely charged probe molecules (R6G and Fl-Na) inside these aggregates. This variation in diffusion coefficient values also suggests that the interaction pattern of these oppositely charged probes are different within the SAILs-nucleotide containing aggregates. Therefore, both rotational and translational diffusion measurements confirm that the DNA nucleotide (AMP) renders more rigid microenvironment within the micellar solution of SAILs.

Enhanced Molecular Recognition between Nucleobases and Guanine-5'-monophosphate-disodium (GMP) by Surfactant Aggregates in Aqueous Solution

Only specific base pairs on DNA can bind with each other through hydrogen bonds, which is called the Watson-Crick (W/C) pairing rule. However, without the constraint of DNA chains, the nucleobases in bulk aqueous solution usually do not follow the W/C pairing rule anymore because of the strong competitive effect of water and the multi-interaction edges of nucleobases. The present work applied surfactant aggregates noncovalently functionalized by nucleotide to enhance the recognition between nucleobases without DNA chains in aqueous solution, and it revealed the effects of their self-assembling ability and morphologies on the recognition. The cationic ammonium monomeric, dimeric, and trimeric surfactants DTAB, 12-3-12, and 12-3-12-3-12 were chosen. The surfactants with guanine-5'-monophosphate-disodium (GMP) form micelles, vesicles, and fingerprint-like and plate-like aggregates bearing the hydrogen-bonding sites of GMP, respectively. The binding parameters of these aggregates with adenine (A), uracil (U), guanine (G), and cytosine(C) indicate that the surfactants can promote W/C recognitions in aqueous solution when they form vesicles (GMP/DTAB) or plate-like aggregates (GMP/12-3-12) with proper molecular packing compactness, which not only provide hydrophobic environments but also shield non-W/C recognition edges. However, the GMP/12-3-12 micelles with loose molecular packing, the GMP/12-3-12 fingerprint-like aggregates where the hydrogen bond sites of GMP are occupied by itself, and the GMP/12-3-12-3-12 vesicles with too strong self-assembling ability cannot promote W/C recognition. This work provides insight into how to design self-assemblies with the performance of enhanced molecule recognition.

On the formation of dendrimer/nucleolipids surface films for directed self-assembly

We describe the formation and structure of nucleolipid/dendrimer multilayer films controlled by non-covalent interactions to obtain biomaterials that exhibit molecular recognition of nucleic acids. Layers of cationic poly(amidoamine) (PAMAM) dendrimers of generation 4 and the anionic nucleolipids 1,2-dilauroyl-sn-glycero-3-phosphatidylnucleosides (DLPNs) based on uridine (DLPU) and adenosine (DLPA) were first formed at the silica-water interface. The PAMAM/DLPN layers were then exposed to short oligonucleotides, polynucleotides and single stranded DNA (ssDNA). The interfacial properties were characterized using quartz crystal microbalance with dissipation monitoring, attenuated total reflection Fourier transform infrared spectroscopy and neutron reflectometry. Both types of DLPN were found to adsorb as aggregates to preadsorbed PAMAM monolayers with a similar interfacial structure and composition before rinsing with pure aqueous solution. Nucleic acids were found to interact with PAMAM/DLPA layers due to base pairing interactions, while the PAMAM/DLPU layers did not have the same capability. This was attributed to the structure of the DLPA layer, which is formed by aggregates that extend from the interface towards the bulk after rinsing with pure solvent, while the DLPU layer forms compact structures. In complementary experiments using a different protocol, premixed PAMAM/DLPN samples adsorbed to hydrophilic silica only when the mixtures contained positively charged aggregates, which is rationalized in terms of electrostatic forces. The PAMAM/DLPA layers formed from the adsorption of these mixtures also bind ssDNA although in this case the adsorption is mediated by the opposite charges of the film and the nucleic acid rather than specific base pairing. The observed molecular recognition of nucleic acids by dendrimers functionalized via non-covalent interactions with nucleolipids is discussed in terms of biomedical applications such as gene vectors and biosensors.

Molecular recognition of nucleic acids by nucleolipid/dendrimer surface complexes

We show for the first time that 1,2-dilauroyl-sn-glycero-3-phosphatidyladenosine nucleolipid surface complexes with cationic poly(amidoamine) dendrimers can be used to selectively bind DNA including oligonucleotides. This molecular recognition has high potential for applications involving biomedical and bioanalytic devices as well as drug delivery systems based on nucleic acids.

Self-assembled nucleolipids: from supramolecular structure to soft nucleic acid and drug delivery devices

This short review aims at presenting some recent illustrative examples of spontaneous nucleolipids self-assembly. High-resolution structural investigations reveal the diversity and complexity of assemblies formed by these bioinspired amphiphiles, resulting from the interplay between aggregation of the lipid chains and base–base interactions. Nucleolipids supramolecular assemblies are promising soft drug delivery systems, particularly for nucleic acids. Regarding prodrugs, squalenoylation is an innovative concept for improving efficacy and delivery of nucleosidic drugs.

DNA closed nanostructures: a structural and Monte Carlo simulation study

DNA nanoconstructs are obtained in solution by using six unique 42-mer DNA oligonucleotides, whose sequences have been designed to form a pseudohexagonal structure. The required flexibility is provided by the insertion of two non-base-paired thymines in the middle of each sequence that work as flexible hinges and constitute the corners of the nanostructure when formed. We show that hexagonally shaped nanostructures of about 7 nm diameter and their corresponding linear open constructs are formed by self-assembly of the specifically designed linear oligonucleotides. The structural and dynamical characterization of the nanostructure is obtained in situ for the first time by using dynamic light scattering (DLS), a noninvasive method that provides a fast dynamic and structural analysis and allows the characterization of the different synthetic DNA nanoconstructs in solution. A validation of the LS results is obtained through Monte Carlo (MC) simulations and atomic force microscopy (AFM). In particular, a mesoscale molecular model for DNA, developed by Knotts et al., is exploited to perform MC simulations and to obtain information about the conformations as well as the conformational flexibilities of these nanostructures, while AFM provides a very detailed particle analysis that yields an estimation of the particle size and size distribution. The structural features obtained by MC and AFM are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution.

Controlled self-assembly of nucleotide-lanthanide complexes: specific formation of nanofibers from dimeric guanine nucleotides

Monomeric and dimeric guanine nucleotides monophosphate spontaneously self-assemble into nanoparticles and nanofibers in the presence of lanthanide ions, which reflects differences in the unit coordination structures and their hierarchical assembly.

Collective headgroup conformational transition in twisted micellar superstructures

Predictions on amphiphilic self-assemblies traditionally rely on considerations on molecular shape and charge of the surfactant. In the case of functional surfactants a more sophisticated toolbox becomes necessary to design amphiphiles encoding chemical functionalities that provide additional responsive properties to their self-assemblies. Here we report on a comprehensive and combined structural-spectroscopic characterization of 1,2-dilauroyl-phosphatidyl-adenosine (DLPA) micelles in phosphate buffer. The temperature dependence, more precisely the thermal history of the sample, is explicitly taken into account. The experimental data, supplemented with MD simulations, indicate the presence of two possible states at room temperature, characterized by distinctly different structural properties that depend on the thermal history of the sample. The twisted superstructures, produced by aging DLPA micelles through intermicellar assembly of locally cylindrical aggregates at room temperature, collapse upon warming at 35 °C, yielding aligned filaments and/or wormlike structures. The initial superstructures cannot be recovered by thermal inversion. The reason for this behaviour is that the thermal activation causes a redistribution of syn-anti conformations of adenosine headgroups, as indicated by spectroscopic results (NMR, CD, FTIR), which is then collectively frozen thanks to molecular constraints present in the aggregate.

Self-assembly of nucleoamphiphiles: investigating nucleosides effect and the mechanism of micrometric helix formation

A new family of self-assembling systems based on nucleoamphiphiles is described. Nano to micrometric left-handed helix formation in aqueous solution was induced simply by complexing a GMP or an AMP with a nonchiral monocationic amphiphile. The assembling behavior such as micellar formation, monolayer at air-water interface, as well as the aggregates in solution of these nucleoamphiphiles are strongly influenced by the presence of nucleosides in solution. The observed effects depend on the properties of complexed nucleotides and nucleosides with a complex mixture of pi stacking, hydrophobicity of the bases, and hydrogen bonding.

Amphiphilic Self-Assemblies Decorated by Nucleobases

Phosphatidyl-nucleosides are a class of functional amphiphiles, where a nucleic acid monomer is conjugated to a lipid skeleton. These derivatives self-organize in aqueous solution as assemblies of various size, shape, and interfacial curvature. This paper presents a comparison of the aggregation behavior of different 1-R,2-R-sn-glycero-3-phosphatidyl-nucleosides, where R = 8 (DiC8PN) or R = 12 (DLPN) and N is either adenosine (a purine) or uridine (a pyrimidine), a complementary pair in RNA. Surface tension, small angle neutron scattering, cryo-TEM, and circular dichroism are used to highlight and distinguish the impact of the hydrophobic assembler and of the base substitution on the solution phase behavior. Our main conclusion is that the nucleic functionalization provides an additional parameter to control self-assembly through specific interactions among the polar heads. Further nonideal effects are induced by mixing nucleolipids with complementary base substitution. We show that these contributions alter the aggregation thresholds and modulate properties of the aggregates on the mesoscale.

Wormlike micelles: where do we stand? Recent developments, linear rheology and scattering techniques

Wormlike micelles are elongated flexible self-assembly structures formed by the aggregation of amphiphiles. Above a threshold concentration, they entangle into a dynamic network, reminiscent of polymer solutions, and display remarkable visco-elastic properties, which have been exploited in numerous industrial and technological fields. Relating the microstructure of these intricate structures with their bulk properties is still an ongoing quest. In this review, we present a classification of wormlike micelles, with a focus on novel systems and applications. We describe the current state of understanding of their linear rheology and give a detailed account of recent progress in small-angle neutron scattering, a particularly powerful technique to elucidate their microstructure on a wide range of length-scales.