The phase behavior of cationic lipid-DNA complexes

Mechanism of Cationic Lipid Induced DNA Condensation: Lipid-DNA Coordination and Divalent Cation Charge Fluctuations

The condensation of nucleic acids by lipids is a widespread phenomenon in biology with crucial implications for drug delivery. However, the mechanisms of DNA assembly in lipid bilayers remain insufficiently understood due to challenges in measuring and assessing each component's contribution in the lipid-DNA-cation system. This study uses all-atom molecular dynamics simulations to investigate DNA condensation in cationic lipid bilayers. Our exhaustive exploration of the thermodynamic factors reveals unique roles for phospholipid head groups and cations. We observed that bridging cations between lipid and DNA drastically reduce charges, while mobile magnesium cations "ping-ponging" between double strands create charge fluctuations. While the first factor stabilizes the DNA-lipid complex, the latter creates attractive forces to induce the spontaneous condensation of DNAs. This novel mechanism not only sheds light on the current data regarding cationic lipid-induced DNA condensation but also provides potential design strategies for creating efficient gene delivery vectors for drug delivery.

Polymyxin B-Enriched Exogenous Lung Surfactant: Thermodynamics and Structure

The use of an exogenous pulmonary surfactant (EPS) to deliver other relevant drugs to the lungs is a promising strategy for combined therapy. We evaluated the interaction of polymyxin B (PxB) with a clinically used EPS, the poractant alfa Curosurf (PSUR). The effect of PxB on the protein-free model system (MS) composed of four phospholipids (diC16:0PC/16:0-18:1PC/16:0-18:2PC/16:0-18:1PG) was examined in parallel to distinguish the specificity of the composition of PSUR. We used several experimental techniques (differential scanning calorimetry, small- and wide-angle X-ray scattering, small-angle neutron scattering, fluorescence spectroscopy, and electrophoretic light scattering) to characterize the binding of PxB to both EPS. Electrostatic interactions PxB-EPS are dominant. The results obtained support the concept of cationic PxB molecules lying on the surface of the PSUR bilayer, strengthening the multilamellar structure of PSUR as derived from SAXS and SANS. A protein-free MS mimics a natural EPS well but was found to be less resistant to penetration of PxB into the lipid bilayer. PxB does not affect the gel-to-fluid phase transition temperature, Tm, of PSUR, while Tm increased by ∼+ 2 °C in MS. The decrease of the thickness of the lipid bilayer (dL) of PSUR upon PxB binding is negligible. The hydrophobic tail of the PxB molecule does not penetrate the bilayer as derived from SANS data analysis and changes in lateral pressure monitored by excimer fluorescence at two depths of the hydrophobic region of the bilayer. Changes in dL of protein-free MS show a biphasic dependence on the adsorbed amount of PxB with a minimum close to the point of electroneutrality of the mixture. Our results do not discourage the concept of a combined treatment with PxB-enriched Curosurf. However, the amount of PxB must be carefully assessed (less than 5 wt % relative to the mass of the surfactant) to avoid inversion of the surface charge of the membrane.

Lipid nanovehicles overcome barriers to systemic RNA delivery: Lipid components, fabrication methods, and rational design

Lipid nanovehicles are currently the most advanced vehicles used for RNA delivery, as demonstrated by the approval of patisiran for amyloidosis therapy in 2018. To illuminate the unique superiority of lipid nanovehicles in RNA delivery, in this review, we first introduce various RNA therapeutics, describe systemic delivery barriers, and explain the lipid components and methods used for lipid nanovehicle preparation. Then, we emphasize crucial advances in lipid nanovehicle design for overcoming barriers to systemic RNA delivery. Finally, the current status and challenges of lipid nanovehicle-based RNA therapeutics in clinical applications are also discussed. Our objective is to provide a comprehensive overview showing how to utilize lipid nanovehicles to overcome multiple barriers to systemic RNA delivery, inspiring the development of more high-performance RNA lipid nanovesicles in the future.

Looking Back, Moving Forward: Lipid Nanoparticles as a Promising Frontier in Gene Delivery

Lipid nanoparticles (LNPs) have shown remarkable success in delivering genetic materials like COVID-19 LNP vaccines, such as mRNA-1273/SpikeVax by Moderna and BNT162b2/Comirnaty by BioNTech/Pfizer, as well as siRNA for rare inherited diseases, such as Onpattro from Alnylam Pharmaceuticals. These LNPs are advantageous since they minimize side effects, target specific cells, and regulate payload delivery. There has been a surge of interest in these particles due to their success stories; however, we still do not know much about how they work. This perspective will recapitulate the evolution of lipid-based gene delivery, starting with Felgner's pioneering 1987 PNAS paper, which introduced the initial DNA-transfection method utilizing a synthetic cationic lipid. Our journey takes us to the early 2020s, a time when advancements in bionano interactions enabled us to create biomimetic lipoplexes characterized by a remarkable ability to evade capture by immune cells in vivo. Through this overview, we propose leveraging previous achievements to assist us in formulating improved research goals when optimizing LNPs for medical conditions such as infectious diseases, cancer, and heritable disorders.

Theory of self-coacervation in semi-dilute and concentrated zwitterionic polymer solutions

Based on the random phase approximation, we develop a molecular theory of self-coacervation in zwitterionic polymer solutions. We show that the interplay between the volume interactions of the monomeric units and electrostatic correlations of charged groups on a polymer backbone can result in liquid-liquid phase separation (self-coacervation). We analyse the behavior of the coacervate phase polymer concentration depending on the electrostatic interaction strength - the ratio of the Bjerrum length to the bond length of the chain. We establish that in a wide range of polymer concentration values - from a semi-dilute to a rather concentrated solution - the chain connectivity and excluded volume interaction of the monomeric units have an extremely weak effect on the contribution of the electrostatic interactions of the dipolar monomeric units to the total free energy. We show that for rather weak electrostatic interactions, the electrostatic correlations manifest themselves as Keesom interactions of point-like freely rotating dipoles (Keesom regime), while in the region of strong electrostatic interactions the electrostatic free energy is described by the Debye-Hückel limiting law (Debye regime). We show that for real zwitterionic coacervates the Keesom regime is realized only for sufficiently small polymer concentrations of the coacervate phase, while the Debye regime is approximately realized for rather dense coacervates. Using the mean-field variant of the density functional theory, we calculate the surface tension (surface free energy) of the "coacervate-solvent" interface as a function of the bulk polymer concentration. Obtained results can be used to estimate the parameters of the polymer chains needed for practical applications such as drug encapsulation and delivery, as well as the design of adhesive materials.

Structural Entities Associated with Different Lipid Phases of Plant Thylakoid Membranes—Selective Susceptibilities to Different Lipases and Proteases

It is well established that plant thylakoid membranes (TMs), in addition to a bilayer, contain two isotropic lipid phases and an inverted hexagonal (H_II) phase. To elucidate the origin of non-bilayer lipid phases, we recorded the ³¹P-NMR spectra of isolated spinach plastoglobuli and TMs and tested their susceptibilities to lipases and proteases; the structural and functional characteristics of TMs were monitored using biophysical techniques and CN-PAGE. Phospholipase-A1 gradually destroyed all ³¹P-NMR-detectable lipid phases of isolated TMs, but the weak signal of isolated plastoglobuli was not affected. Parallel with the destabilization of their lamellar phase, TMs lost their impermeability; other effects, mainly on Photosystem-II, lagged behind the destruction of the original phases. Wheat-germ lipase selectively eliminated the isotropic phases but exerted little or no effect on the structural and functional parameters of TMs—indicating that the isotropic phases are located outside the protein-rich regions and might be involved in membrane fusion. Trypsin and Proteinase K selectively suppressed the H_II phase—suggesting that a large fraction of TM lipids encapsulate stroma-side proteins or polypeptides. We conclude that—in line with the Dynamic Exchange Model—the non-bilayer lipid phases of TMs are found in subdomains separated from but interconnected with the bilayer accommodating the main components of the photosynthetic machinery.

Influence of micellar size on the structure of surfactant-DNA complexes

We have studied the structure of complexes of the cationic surfactant dodecyltrimethylammonium bromide (DTAB) with DNA as a function of surfactant to DNA base molar ratio (R) and salt concentration. Small-angle x-ray scattering data show the formation of nematic gels at lower and higher salt concentrations, irrespective of the value of R. Two crystalline phases are observed over intermediate salt concentrations; a square (S) phase for R>3 and a hexagonal (H_{S}) phase for lower R. Electron density maps of these phases show intercalated structures, with DTAB micelles sandwiched between long DNA strands. The composition of these complexes, estimated using elemental analysis, indicates that the micelles are not very long, and they occupy only about half of the interstitial volume between the DNA strands. This phase behavior is strikingly different from that of complexes of DNA with longer chain surfactants cetyltrimethylammonium bromide (CTAB) and tetradecyltrimethylammonium bromide (TTAB), which show only a hexagonal (H) phase over similar ranges of R and salt concentration, the H_{S} structure observed in the present study being a sqrt[3]×sqrt[3] superlattice of the H structure. Madelung energies of the S and H structures, calculated from the electrostatic interaction between their cylindrical constituents, suggest that the former is preferred in DTAB-DNA complexes due to the smaller micellar radius of DTAB. The propensity of DTAB to form short micelles seems also to favor the H_{S} phase at lower R. These results illustrate the important role of micellar size in determining the structure of these two-dimensional macro-ion crystals.

Osmotic-pressure-induced phase transition of a surfactant-DNA complex

We have studied the effect of osmotic pressure on complexes formed by DNA with the cationic surfactant cetyltrimethylammonium tosylate using small-angle x-ray scattering. Earlier studies have shown that these complexes exhibit three different phases depending on the DNA and surfactant concentrations in the solution. The hexagonal superlattice phase (H_{I,s}^{c}) is found to be corralled into the hexagonal phase (H_{I}^{c}) above a threshold osmotic pressure. We have also estimated the DNA to surfactant micelle stoichiometry of the complexes in the three phases using elemental analysis. Our results provide further support for the structures of these complexes proposed earlier based on small-angle x-ray scattering data.

Cationic lipids for gene delivery: many players, one goal

Lipid-based carriers represent the most widely used alternative to viral vectors for gene expression and gene silencing purposes. This class of non-viral vectors is particularly attractive for their ease of synthesis and chemical modifications to endow them with desirable properties. Despite combinatorial approaches have led to the generation of a large number of cationic lipids displaying different supramolecular structures and improved behavior, additional effort is needed towards the development of more and more effective cationic lipids for transfection purposes. With this review, we seek to highlight the great progress made in the design of each and every constituent domain of cationic lipids, that is, the chemical structure of the headgroup, linker and hydrophobic moieties, and on the specific effect on the assembly with nucleic acids. Since the complexity of such systems is known to affect their performances, the role of formulation, stability and phase behavior on the transfection efficiency of such assemblies will be thoroughly discussed. Our objective is to provide a conceptual framework for the development of ever more performing lipid gene delivery vectors.

Structure and stoichiometry of CTAB-DNA complexes

We have studied the structure of cetyltrimethylammonium bromide-DNA complexes using small angle x-ray diffraction and elemental analysis. These complexes exhibit a two-dimensional hexagonal phase. The diffraction data have been analyzed using electron density models based on two different structures of these complexes proposed in the literature, which differ in the micelle to DNA stoichiometry. The structure with a 1:2 micelle-DNA stoichiometry is found to be more consistent with the diffraction data. Furthermore, this structure is also supported by the stoichiometry deduced from elemental analysis. Madelung energies of the two structures, calculated from the electrostatic interaction between their cylindrical constituents, give insight into their relative stability.

pH-Sensitive N,N-Dimethylalkane-1-amine N-Oxides in DNA Delivery: From Structure to Transfection Efficiency

pH-sensitive liposomes composed of homologues of series of N,N-dimethylalkane-1-amine N-oxides (CnNO, n = 8-18, where n is the number of carbon atoms in the alkyl substituent) and neutral phospholipid dioleoylphosphatidylethanolamine (DOPE) were prepared at two molar ratios (CnNO/DOPE = 0.4:1 and 1:1) and tested for their in vitro transfection activity. Several techniques (SAXS/WAXS, UV-vis, zeta potential measurements, confocal microscopy) were applied to characterize the system in an effort to unravel the relationship among the transfection efficiency, structure, and composition of the lipoplexes. The transfection efficiency of CnNO/DOPE for plasmid DNA in U2OS cells follows a quasi-parabolic dependence on CnNO's alkyl substituent length with a maximum at n = 16. The transfection efficiency of CnNO/DOPE (n = 12-18) lipoplexes was found to be higher than that of commercially available Lipofectamine 2000. C16NO/DOPE also positively transfected HEK 293T and HeLa cells. Small-angle X-ray scattering (SAXS) shows large structural diversity depending on the complex's composition and pH. Transfection efficiencies mediated by two structures, either a condensed lamellar (L_α^c) or epitaxially connected L_α^c and a condensed inverted hexagonal (H_II^c) phase (L_α^c & H_II^c), were found to be very similar. The change in pH from acidic to neutral induces phase transition L_α^c & H_II^c → Q_II + L_α, with cubic phase Q_II of the Pn3m space group. Q_II detected in lipoplexes of most efficient composition CnNO/DOPE (n = 16 and 18) facilitates DNA release and promotes its internalization in the cell.

Oligo-guanidyl targeted bioconjugates forming rod shaped polyplexes as a new nanoplatform for oligonucleotide delivery

Novel bioconjugates (Agm₆-M-PEG-FA) for active oligonucleotide (ON) delivery have been developed by conjugating a cationic oligo-guanidyl star-like shaped "head" (Agm₆-M) to a polymeric "tail" (PEG) terminating with folic acid (FA) as targeting agent or methoxy group (Agm₆-M-PEG-FA and Agm₆-M-PEG-OCH₃, respectively). Gel electrophoresis showed that the bioconjugates completely associated with ONs at 3 nitrogen/phosphate (N/P) ratio. Studies performed with folate receptor (FR)-overexpressing HeLa cells, showed that optimal cell up-take was obtained with the 75:25 w/w Agm₆-M-PEG-OCH₃:Agm₆-M-PEG-FA mixture. Dynamic light scattering and transmission electron microscopy showed that the polyplexes had size <80 nm with narrow polydispersity and rod-shaped morphology. The polyplexes were stable for several hours in plasma while ON was released in the presence of heparin concentration 16-times higher than the physiological one. The polyplexes displayed negligible cytotoxicity, hemolysis and low pro-inflammatory TNF-α release. Studies performed with FR-overexpressing HeLa and MDA-MB-231 cells using siRac1 revealed that the folated polyplexes caused significantly higher gene silencing (86.1 ± 9.6%) and inhibition of cell migration (40%) than the non-folated polyplexes obtained with Agm₆-M-PEG-OCH₃ only. Although cytofluorimetric analyses showed similar cell uptake for both folated and non-folated polyplexes, confocal, TEM and competition studies showed that the folated polyplexes were taken-up by lysosome escaping caveolin-mediated pathway with final polyplex localization within cytosol, while non-folated polyplexes were preferentially taken-up via clathrin-mediated pathway to localize in the lysosomes. Finally, preliminary in vivo studies carried out in mice revealed that the folated polyplexes dispose in the tumor mass.

Mesoscale Computational Modeling of Protein-Membrane Interactions Based on Continuum Mean-Field Theory

Quantitative computational modeling of protein-membrane interactions is of great importance as it aids in the interpretation of experimental results and enables design and exploration of new experimental systems. This review describes one such computational approach conceived specifically to treat electrostatically driven interactions between a lipid membrane and a protein (or protein domains) adsorbing onto the membrane. The methodology is based on self-consistent minimization of the governing free energy functional which is expressed in the mean-field approximation and has contributions from electrostatic interactions as well as from mixing entropy of lipids in the membrane and ions in the solution. The method enables calculation of the free energy of the binding process and quantification of the steady-state lipid distribution around the adsorbing protein. The extension of the method to include membrane deformation degrees of freedom further allows calculation of the equilibrium bilayer shape upon the protein binding.

DNA-surfactant complexes: self-assembly properties and applications

Over the last few years, DNA-surfactant complexes have gained traction as unique and powerful materials for potential applications ranging from optoelectronics to biomedicine because they self-assemble with outstanding flexibility spanning packing modes from ordered lamellar, hexagonal and cubic structures to disordered isotropic phases. These materials consist of a DNA backbone from which the surfactants protrude as non-covalently bound side chains. Their formation is electrostatically driven and they form bulk films, lyotropic as well as thermotropic liquid crystals and hydrogels. This structural versatility and their easy-to-tune properties render them ideal candidates for assembly in bulk films, for example granting directional conductivity along the DNA backbone, for dye dispersion minimizing fluorescence quenching allowing applications in lasing and nonlinear optics or as electron blocking and hole transporting layers, such as in LEDs or photovoltaic cells, owing to their extraordinary dielectric properties. However, they do not only act as host materials but also function as a chromophore itself. They can be employed within electrochromic DNA-surfactant liquid crystal displays exhibiting remarkable absorptivity in the visible range whose volatility can be controlled by the external temperature. Concomitantly, applications in the biological field based on DNA-surfactant bulk films, liquid crystals and hydrogels are rendered possible by their excellent gene and drug delivery capabilities. Beyond the mere exploitation of their material properties, DNA-surfactant complexes proved outstandingly useful for synthetic chemistry purposes when employed as scaffolds for DNA-templated reactions, nucleic acid modifications or polymerizations. These promising examples are by far not exhaustive but foreshadow their potential applications in yet unexplored fields. Here, we will give an insight into the peculiarities and perspectives of each material and are confident to inspire future developments and applications employing this emerging substance class.

Structural behaviour and gene delivery in complexes formed between DNA and arginine-containing peptide amphiphiles

We describe in depth the structure of complexes formed between DNA and two classes of arginine-containing peptide amphiphiles, namely, the lipopeptide PRW-C₁₆ (P = proline, R = arginine, W = tryptophan, C₁₆ = C16 : 0 alkyl chain) and the bolaamphiphile RFL₄FR (R = arginine, F = phenylalanine, L = leucine). A combination of X-ray and neutron scattering provided unprecedented insights into the local structure of these complexes. Lipopeptide-based complexes self-assembled into layered structures with large-scale fractal features, hosting DNA in the interstices. Bola-amphiphile scaffolds were characterized by planar structures with DNA strands presumably sandwiched in-between peptide nanotapes. Importantly, complexation did not affect the structural integrity of DNA in either of the two complexes. The bolaamphiphile conjugates displayed high levels of molecular ordering in contrast to the liquid-crystalline features observed in lipopeptide assemblies. Peptide-DNA complexes were assessed for their potential as a means to deliver the reporter vector pEGFP-N1 into SW480 human colon carcinoma cells. Successfully transfected cells expressed green fluorescent protein. The potentiating effect of PRW-C₁₆ on the cellular uptake of ectopic DNA was found to be much greater than that observed with RFL₄FR. In contrast to the bolaamphiphile-based conjugate, the liquid-crystalline nature of the lipopeptide complex is likely to play a key role in DNA release and transfection efficiency since these weakly bound structures require lower energy expenditure during disassembly and load release.

Interactions of rod-like particles on responsive elastic sheets

What are the physical laws of the mutual interactions of objects bound to cell membranes, such as various membrane proteins or elongated virus particles? To rationalise this, we here investigate by extensive computer simulations mutual interactions of rod-like particles adsorbed on the surface of responsive elastic two-dimensional sheets. Specifically, we quantify sheet deformations as a response to adhesion of such filamentous particles. We demonstrate that tip-to-tip contacts of rods are favoured for relatively soft sheets, while side-by-side contacts are preferred for stiffer elastic substrates. These attractive orientation-dependent substrate-mediated interactions between the rod-like particles on responsive sheets can drive their aggregation and self-assembly. The optimal orientation of the membrane-bound rods is established via responding to the elastic energy profiles created around the particles. We unveil the phase diagramme of attractive-repulsive rod-rod interactions in the plane of their separation and mutual orientation. Applications of our results to other systems featuring membrane-associated particles are also discussed.

The thermodynamics of endosomal escape and DNA release from lipoplexes

In this work we identify and characterize the entropic driving forces governing the process of transfection by lipid–DNA complexes.

Patterned Threadlike Micelles and DNA-Tethered Nanoparticles: A Structural Study of PEGylated Cationic Liposome-DNA Assemblies

The self-assembly of oppositely charged biomacromolecules has been extensively studied due to its pertinence in the design of functional nanomaterials. Using cryo electron microscopy (cryo-EM), optical light scattering, and fluorescence microscopy, we investigated the structure and phase behavior of PEGylated (PEG: poly(ethylene glycol)) cationic liposome-DNA nanoparticles (CL-DNA NPs) as a function of DNA length, topology (linear and circular), and ρ(chg) (the molar charge ratio of cationic lipid to anionic DNA). Although all NPs studied exhibited lamellar internal nanostructure, NPs formed with short (∼2 kbps), linear, polydisperse DNA were defect-rich and contained smaller domains. Unexpectedly, we found distinctly different equilibrium structures away from the isoelectric point. At ρ(chg) > 1, in the excess cationic lipid regime, threadlike micelles rich in PEG-lipid were found to coexist with NPs, cationic liposomes, and spherical micelles. At high concentrations these PEGylated threadlike micelles formed a well-ordered, patterned morphology with highly uniform intermicellar spacing. At ρ(chg) < 1, in the excess DNA regime and with no added salt, individual NPs were tethered together via long, linear DNA (48 kbps λ-phage DNA) into a biopolymer-mediated floc. Our results provide insight into what equilibrium nanostructures can form when oppositely charged macromolecules self-assemble in aqueous media. Self-assembled, well-ordered threadlike micelles and tethered nanoparticles may have a broad range of applications in bionanotechnology, including nanoscale lithograpy and the development of lipid-based multifunctional nanoparticle networks.

Modeling DNA condensation on freestanding cationic lipid membranes

Motivated by recent experimental observations of a rapid spontaneous DNA coil-globule transition on freestanding cationic lipid bilayers, we propose simple theoretical models for DNA condensation on cationic lipid membranes. First, for a single DNA rod, we examine the conditions of full wrapping of a cylindrical DNA-like semi-flexible polyelectrolyte by an oppositely charged membrane. Then, for two parallel DNA rods, we self-consistently analyze the shape and the extent of the membrane enveloping them, focusing on membrane elastic deformations and the membrane-DNA embracing angle, which enables us to compute the membrane-mediated DNA-DNA interactions. We examine the effects of the membrane composition and its charge density, which are the experimentally tunable parameters. We show that membrane-driven rod-rod attraction is more pronounced for higher charge densities and for smaller surface tensions of the membrane. Thus, we demonstrate that for a long DNA chain adhered to a cationic lipid membrane, such membrane-induced DNA-DNA attraction can trigger compaction of DNA.

Demixing and crystallization of DODAB in DPPC-DODAB binary mixtures

The crystallization mechanism of one lipid component within multicomponent lipid mixtures remains unclear. To shed light on this issue, we studied the demixing and crystallization behaviors of a binary lipid system using neutral dipalmitoylphosphatidylcholine (DPPC) and cationic dioctadecyldimethylammonium bromide (DODAB) as model molecules. The results indicate that when DODAB is no more than equimolar (e.g., DPPC/DODAB = 2/1 and 1/1), DPPC is miscible with DODAB and hinders the crystallization of DODAB, and the samples undergo reversible gel-fluid phase transitions upon heating and cooling. However, when DODAB is dominant in the mixture (DPPC/DODAB = 1/2), cooling of the mixed fluid phase results in the formation of a DODAB-rich gel domain and a DPPC-DODAB mixed gel domain. Such phase-separated mixed gels can undergo further demixing and crystallization, producing a DODAB-rich crystalline domain and a DPPC-rich tilted gel domain upon prolonged (or plus low-temperature) incubation. Besides, evidence has been given that the crystallized DODAB-rich domain remains in the same lipid bilayer as the DPPC-rich domain. All the three binary lipid mixtures can hold large amounts of water in the lipid interlamellar regions, allowing the incorporation of a large number of water-soluble substances such as DNA or proteins, which can be used for the fabrication of functional biofilms and biomaterials. Influences of water content and salt concentration on the phase structures (e.g., repeat distances) of the binary mixtures have also been studied.

Lamellar cationic lipid-DNA complexes from lipids with a strong preference for planar geometry: A Minimal Electrostatic Model

We formulate and analyze a minimal model, based on condensation theory, of the lamellar cationic lipid (CL)-DNA complex of alternately charged lipid bilayers and DNA monolayers in a salt solution. Each lipid bilayer, composed by a random mixture of cationic and neutral lipids, is assumed to be a rigid uniformly charged plane. Each DNA monolayer, located between two lipid bilayers, is formed by the same number of parallel DNAs with a uniform separation distance. For the electrostatic calculation, the model lipoplex is collapsed to a single plane with charge density equal to the net lipid and DNA charge. The free energy difference between the lamellar lipoplex and a reference state of the same number of free lipid bilayers and free DNAs, is calculated as a function of the fraction of CLs, of the ratio of the number of CL charges to the number of negative charges of the DNA phosphates, and of the total number of planes. At the isoelectric point the free energy difference is minimal. The complex formation, already favoured by the decrease of the electrostatic charging free energy, is driven further by the free energy gain due to the release of counterions from the DNAs and from the lipid bilayers, if strongly charged. This minimal model compares well with experiment for lipids having a strong preference for planar geometry and with major features of more detailed models of the lipoplex.

Formation of divalent ion mediated anionic disc bicelle-DNA complexes

Disc-shaped bicelles are formed by mixing long-chain lipids with short-chain lipids at suitable molar ratios and they have a relatively uniform size, typically around a few tens of nanometers in diameter. Different from the typically formulated cationic or anionic liposome–DNA complexes, which are used as nonviral vectors for improving the transfection efficiency of gene therapy, a novel way of packing the DNA can be developed by using the much smaller disc-like bicelles. We demonstrate that anionic lipid bicelle-ion–DNA (AB–DNA) complexes can be formed with the help of divalent ions. Multi-stacked AB–DNA complexes can be formed with diameters of around 50–100 nm and lengths of around 50–150 nm as revealed by TEM. Using the anionic lipid–DNA complexes has the advantage of lower cytotoxicity than using cationic lipids. The interaction of DNA with anionic bicelles was investigated by SAXS. It was found that the anionic bicelle could not form stable complexes with DNA at low calcium ion concentrations, such as 1 mM. The AB–DNA complexes can be formed in the investigated range of 10 mM to 100 mM calcium ion concentrations. However, for an equal anionic lipid charge and DNA charge system, an ion-membrane phase (multilamellar vesicles) would gradually appear as the calcium ion concentration is increased above a critical concentration. It indicates that DNA could be packed closer at above the critical divalent ion concentration. If more DNA is added to such a two-phase coexistence system (originally with the total anionic lipid charge equal to that of DNA), the ion-membrane phase could be transformed into the AB–DNA complexes. As a result, more DNA can be packed in the form of AB–DNA complexes at above the critical calcium ion concentration.

Supramolecular polymorphism of DNA in non-cationic Lα lipid phases

The structure of a complex between hydrated DNA and a non-cationic lipid is studied, including its phase diagram. The complex is spontaneously formed by adding DNA fragments (ca. 150 base pairs in length) to non-cationic lipids and water. The self-assembly process often leads to highly ordered structures. The structures were studied by combining X-ray scattering, fluorescence and polarized microscopy, as well as freeze-fracture experiments with transmission electron microscopy. We observe a significant increase of the smectic order as DNA is incorporated into the water layers of the lamellar host phase, and stabilization of single phase domains for large amounts of DNA. The effect of confinement on DNA ordering is investigated by varying the water content, following three dilution lines. A rich polymorphism is found, ranging from weakly correlated DNA-DNA in-plane organizations to highly ordered structures, where transmembrane correlations lead to the formation of columnar rectangular and columnar hexagonal superlattices of nucleotides embedded between lipid lamellae. From these observations, we suggest that addition of DNA to the lamellar phase significantly restricts membrane fluctuations above a certain concentration and helps the formation of the lipoplex. The alteration of membrane steric interactions, together with the appearance of interfacial interactions between membranes and DNA molecules may be a relevant mechanism for the emergence of highly ordered structures in the concentrated regime.

Role of temperature-independent lipoplex-cell membrane interactions in the efficiency boost of multicomponent lipoplexes

Multicomponent lipoplexes have recently emerged as especially promising transfection candidates, as they are from 10 to 100 times more efficient than binary complexes usually employed for gene delivery purposes. Previously, we investigated a number of chemical-physical properties of DNA-lipid complexes that were proposed to affect transfection efficiency (TE) of lipoplexes, such as nanoscale structure, size, surface potential, DNA-protection ability and DNA release from complexes upon interaction with cellular lipids. Although some minor differences between multicomponent and binary lipoplexes were found, they did not correlate clearly with efficiency. Instead, here we show that a marked difference between the cell internalization mechanism of binary and multicomponent lipoplexes does exist. Multicomponent lipoplexes significantly transfect cells at 4 °C, when endocytosis does not take place suggesting that they can enter cells via a temperature-independent mechanism. Confocal fluorescence microscopy experiments showed the existence of a correlation between endosomal escape and TE. Multicomponent lipoplexes exhibited a distinctive ability of endosomal escape and release DNA into the nucleus, whereas, poorly efficient binary lipoplexes exhibited minor, if any, endosomal rupture ability and remained confined in perinuclear late endosomes. Stopped-flow mixing measurements showed that the fusion rates of multicomponent cationic liposomes with anionic vesicles, used as model systems of cell membranes, were definitely shorter than those of binary liposomes. As either lipoplex uptake and endosomal escape involve fusion between lipoplex and cellular membranes, we suggest that a mechanism of lipoplex-cellular membrane interaction, driven by lipid mixing between cationic and anionic cellular lipids, does explain the TE boost of multicomponent lipoplexes.

Nucleic acid-lipid membrane interactions studied by DSC

The interactions of nucleic acids with lipid membranes are of great importance for biological mechanisms as well as for biotechnological applications in gene delivery and drug carriers. The optimization of liposomal vectors for clinical use is absolutely dependent upon the formation mechanisms, the morphology, and the molecular organization of the lipoplexes, that is, the complexes of lipid membranes with DNA. Differential scanning calorimetry (DSC) has emerged as an efficient and relatively easy-to-operate experimental technique that can straightforwardly provide data related to the thermodynamics and the kinetics of the DNA-lipid complexation and especially to the lipid organization and phase transitions within the membrane. In this review, we summarize DSC studies considering nucleic acid-membrane systems, accentuating DSC capabilities, and data analysis. Published work involving cationic, anionic, and zwitterionic lipids as well as lipid mixtures interacting with RNA and DNA of different sizes and conformations are included. It is shown that despite limitations, issues such as DNA- or RNA-induced phase separation and microdomain lipid segregation, liposomal aggregation and fusion, alterations of the lipid long-range molecular order, as well as membrane-induced structural changes of the nucleic acids can be efficiently treated by systematic high-sensitivity DSC studies.

Two-dimensional packing of short DNA with nonpairing overhangs in cationic liposome-DNA complexes: from Onsager nematics to columnar nematics with finite-length columns

We report the formation of liquid crystalline (LC) phases of short double-stranded DNA with nonpairing (nonsticky) overhangs, confined between two-dimensional (2D) lipid bilayers of cationic liposome-DNA complexes. In a landmark study (Science2007, 318, 1276), Nakata et al. reported on the discovery of strong end-to-end stacking interactions between short DNAs (sDNAs) with blunt ends, leading to the formation of 3D nematic (N) and columnar LC phases. Employing synchrotron small-angle X-ray scattering, we have studied the interplay between shape anisotropy-induced and DNA end-to-end interaction-induced N ordering for 11, 24, and 48 bp sDNA rods with single-stranded oligo-thymine (T) overhangs modulating the end-to-end interactions. For suppressed stacking interactions with 10-T overhangs, the volume fraction of sDNA at which the 2D isotropic (I)-to-N transition occurs for 24 and 48 bp sDNA rods depended on their length-to-width (L/D) shape anisotropy, qualitatively consistent with Onsager's theory for the entropic alignment of rigid rods. As the overhang length is reduced from 10 to 5 and 2 T for 24 and 48 bp sDNA, the N-to-I transition occurs at lower volume fractions, indicating the onset of some degree of end-to-end stacking interactions. The 11 bp sDNA rods with 5- and 10-T overhangs remain in the I phase, consistent with their small shape anisotropy (L/D ≈ 1.9) below the limit for Onsager LC ordering. Unexpectedly, in contrast to the behavior of 24 and 48 bp sDNA, the end-to-end interactions between 11 bp sDNA rods with 2-T overhangs set in dramatically, and a novel 2D columnar N phase (N(C)) with finite-length columns formed. The building blocks of this phase are comprised of 1D stacks of (on average) four 11 bp DNA-2T rods with an effective L(stacked)/D ≈ 8.2. Our findings have implications for the DNA-directed assembly of nanoparticles on 2D platforms via end-to-end interactions and in designing optimally packed LC phases of short anisotropic biomolecules (such as peptides and short-interfering RNAs) on nanoparticle membranes, which are used in gene silencing and chemical delivery.

DNA lipoplexes: formation of the inverse hexagonal phase observed by coarse-grained molecular dynamics simulation

Mixtures of dsDNA and lipids, so-called lipoplexes, are widely used as less toxic alternatives to viral vectors in transfection studies. However, the transfection efficiency achieved by lipoplexes is significantly lower than that of viral vectors and is a barrier to their use in the clinic. There is now significant evidence suggesting that the molecular organization and structure (nanoarchitecture) of lipoplexes might correlate with biological activity. As a consequence, the ability to predict quantitatively the nanoarchitecture of new systems, and how these might change intracellularly, would be a major tool in the development of rational discovery strategies for more efficient lipoplex formulations. Here we report the use of a coarse-grain molecular dynamics simulation to predict the phases formed by two lipoplex systems: dsDNA-DOPE and dsDNA-DOPE-DOTAP. The predictions of the simulations show excellent agreement with experimental data from polarized light microscopy and small-angle X-ray diffraction (SAXS); the simulations predicted the formation of phases with d-spacings that were comparable to those measured by SAXS. More significantly, the simulations were able to reproduce for the first time the experimentally observed change from a fluid lamellar to an inverse hexagonal phase in the dsDNA-DOPE-DOTAP system as a function of changes in lipid composition. Our studies indicate that coarse-grain MD simulations could provide a powerful tool to understand, and hence design, new lipoplex systems.

Toward the rational design of lipid gene vectors: shape coupling between lipoplex and anionic cellular lipids controls the phase evolution of lipoplexes and the efficiency of DNA release

A viewpoint now emerging is that a critical factor in lipid-mediated transfection (lipofection) is the structural evolution of lipoplexes upon interaction with anionic cellular lipids, resulting in DNA release. At the early stages of interaction, we found a universal behavior of lipoplex/anionic lipid (AL) mixtures: the lipoplex structure is slightly perturbed, while the one-dimensional DNA lattice between cationic membranes is largely diluted by ALs. This finding is in excellent agreement with previous suggestions on the mechanism of DNA unbinding from lipoplexes by ALs. Upon further interaction, the propensity of a given lipoplex structure to be solubilized by anionic cellular lipids strongly depends on the shape coupling between lipoplex and ALs. Furthermore, we investigated the effect of the membrane charge density and a general correlation resulted: the higher the membrane charge density of anionic membranes, the higher their ability to solubilize the structure of lipoplexes and to promote DNA release. Lastly, the formation of nonlamellar phases in lipoplex/AL mixtures is regulated by the propensity of anionic cellular lipids to adopt nonlamellar phases. Remarkably, also phase transition rates and DNA release were found to be strongly affected by the shape coupling between lipoplex and ALs. It thus seems likely that the structural and phase evolution of lipoplexes may only be meaningful in the context of specific anionic cellular membranes. These results highlight the phase properties of the carrier lipid/cellular lipid mixtures as a decisive factor for optimal DNA release and suggest a potential strategy for the rational design of efficient cationic lipid carriers.

Structural characterization of cationic lipid-tRNA complexes

Despite considerable interest and investigations on cationic lipid-DNA complexes, reports on lipid-RNA interaction are very limited. In contrast to lipid-DNA complexes where lipid binding induces partial B to A and B to C conformational changes, lipid-tRNA complexation preserves tRNA folded state. This study is the first attempt to investigate the binding of cationic lipid with transfer RNA and the effect of lipid complexation on tRNA aggregation and condensation. We examine the interaction of tRNA with cholesterol (Chol), 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), dioctadecyldimethylammoniumbromide (DDAB) and dioleoylphosphatidylethanolamine (DOPE), at physiological condition, using constant tRNA concentration and various lipid contents. FTIR, UV-visible, CD spectroscopic methods and atomic force microscopy (AFM) were used to analyze lipid binding site, the binding constant and the effects of lipid interaction on tRNA stability, conformation and condensation. Structural analysis showed lipid-tRNA interactions with G-C and A-U base pairs as well as the backbone phosphate group with overall binding constants of K(Chol) = 5.94 (+/- 0.8) x 10(4) M(-1), K(DDAB) = 8.33 (+/- 0.90) x 10(5) M(-1), K(DOTAP) = 1.05 (+/- 0.30) x 10(5) M(-1) and K(DOPE) = 2.75 (+/- 0.50) x 10(4) M(-1). The order of stability of lipid-tRNA complexation is DDAB > DOTAP > Chol > DOPE. Hydrophobic interactions between lipid aliphatic tails and tRNA were observed. RNA remains in A-family structure, while biopolymer aggregation and condensation occurred at high lipid concentrations.

Osmotically induced reversible transitions in lipid-DNA mesophases

We follow the effect of osmotic pressure on isoelectric complexes that self-assemble from mixtures of DNA and mixed neutral and cationic lipids. Using small angle x-ray diffraction and freeze-fracture cryo-electron microscopy, we find that lamellar complexes known to form in aqueous solutions can reversibly transition to hexagonal mesophases under high enough osmotic stress exerted by adding a neutral polymer. Using molecular spacings derived from x-ray diffraction, we estimate the reversible osmotic pressure-volume (Pi-V) work needed to induce this transition. We find that the transition free energy is comparable to the work required to elastically bend lipid layers around DNA. Consistent with this, the required work is significantly lowered by an addition of hexanol, which is known to soften lipid bilayers. Our findings not only help to resolve the free-energy contributions associated with lipid-DNA complex formation, but they also demonstrate the importance that osmotic stress can have to the macromolecular phase geometry in realistic biological environments.

Polyelectrolyte-induced aggregation of liposomes: a new cluster phase with interesting applications

Different charged colloidal particles have been shown to be able to self-assemble, when mixed in an aqueous solvent with oppositely charged linear polyelectrolytes, forming long-lived finite-size mesoscopic aggregates. On increasing the polyelectrolyte content, with the progressive reduction of the net charge of the primary polyelectrolyte-decorated particles, larger and larger clusters are observed. Close to the isoelectric point, where the charge of the adsorbed polyelectrolytes neutralizes the original charge of the particles' surface, the aggregates reach their maximum size, while beyond this point any further increase of the polyelectrolyte-particle charge ratio causes the formation of aggregates whose size is progressively reduced. This re-entrant condensation behavior is accompanied by a significant overcharging. Overcharging, or charge inversion, occurs when more polyelectrolyte chains adsorb on a particle than are needed to neutralize its original charge so that, eventually, the sign of the net charge of the polymer-decorated particle is inverted. The stability of the finite-size long-lived clusters that this aggregation process yields results from a fine balance between long-range repulsive and short-range attractive interactions, both of electrostatic nature. For the latter, besides the ubiquitous dispersion forces, whose supply becomes relevant only at high ionic strength, the main contribution appears due to the non-uniform correlated distribution of the charge on the surface of the polyelectrolyte-decorated particles ('charge-patch' attraction). The interesting phenomenology shown by these system has a high potential for biotechnological applications, particularly when the primary colloidal particles are bio-compatible lipid vesicles. Possible applications of these systems as multi-compartment vectors for the simultaneous intra-cellular delivery of different pharmacologically active substances will be briefly discussed.

The multiple faces of self-assembled lipidic systems

Lipids, the building blocks of cells, common to every living organisms, have the propensity to self-assemble into well-defined structures over short and long-range spatial scales. The driving forces have their roots mainly in the hydrophobic effect and electrostatic interactions. Membranes in lamellar phase are ubiquitous in cellular compartments and can phase-separate upon mixing lipids in different liquid-crystalline states. Hexagonal phases and especially cubic phases can be synthesized and observed in vivo as well. Membrane often closes up into a vesicle whose shape is determined by the interplay of curvature, area difference elasticity and line tension energies, and can adopt the form of a sphere, a tube, a prolate, a starfish and many more. Complexes made of lipids and polyelectrolytes or inorganic materials exhibit a rich diversity of structural morphologies due to additional interactions which become increasingly hard to track without the aid of suitable computer models. From the plasma membrane of archaebacteria to gene delivery, self-assembled lipidic systems have left their mark in cell biology and nanobiotechnology; however, the underlying physics is yet to be fully unraveled.PACS Codes: 87.14.Cc, 82.70.Uv.

Structural analysis of DNA complexation with cationic lipids

Complexes of cationic liposomes with DNA are promising tools to deliver genetic information into cells for gene therapy and vaccines. Electrostatic interaction is thought to be the major force in lipid–DNA interaction, while lipid-base binding and the stability of cationic lipid–DNA complexes have been the subject of more debate in recent years. The aim of this study was to examine the complexation of calf-thymus DNA with cholesterol (Chol), 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP), dioctadecyldimethylammoniumbromide (DDAB) and dioleoylphosphatidylethanolamine (DOPE), at physiological condition, using constant DNA concentration and various lipid contents. Fourier transform infrared (FTIR), UV-visible, circular dichroism spectroscopic methods and atomic force microscopy were used to analyse lipid-binding site, the binding constant and the effects of lipid interaction on DNA stability and conformation. Structural analysis showed a strong lipid–DNA interaction via major and minor grooves and the backbone phosphate group with overall binding constants of K_Chol = 1.4 (±0.5) × 10⁴ M⁻¹, K_DDAB = 2.4 (±0.80) × 10⁴ M⁻¹, K_DOTAP = 3.1 (±0.90) × 10⁴ M⁻¹ and K_DOPE = 1.45 (± 0.60) × 10⁴ M⁻¹. The order of stability of lipid–DNA complexation is DOTAP>DDAB>DOPE>Chol. Hydrophobic interactions between lipid aliphatic tails and DNA were observed. Chol and DOPE induced a partial B to A-DNA conformational transition, while a partial B to C-DNA alteration occurred for DDAB and DOTAP at high lipid concentrations. DNA aggregation was observed at high lipid content.

Structure-transfection activity studies of novel cationic cholesterol-based amphiphiles

Inclusion of DOPE in lipoplex formulations has hampered the establishment of a correlation between cationic lipid structure, biological specificity, and transfection activity, simply because the presence of a helper lipid not only alters the physicochemical properties of the lipoplex but also modifies cell surface specific interactions during the process of transfection. To this end, four cationic cholesterol-based derivatives were synthesized by systematically varying the methylation of the polar headgroup, after which the physicochemical properties, in the absence of DOPE and serum, were correlated with their transfection activity and interaction with cell membranes. It was found that only the primary and secondary amine derivatives, AC-Chol and MC-Chol, respectively, are able to mediate in vitro cell transfection. These results were consistent with fusion experiments and cell internalization studies which illustrated that although cell surface binding occurs for all of the cationic lipids, only the active analogues were able to gain entry into the cytosol. Given the minute differences in the physical properties of these cationic derivatives, we speculate that the biological specificity of the active cationic derivatives either triggers endocytotic pathways leading to eventual endosomal fusion allowing cytoplasmic access to the packaged DNA or other endocytotic pathways that avoid lysosomal degradation.

Electrostatics of DNA Complexes with Cationic Lipid Membranes

We present the exact solutions of the linear Poisson-Boltzmann equation for several problems relevant to electrostatics of DNA complexes with cationic lipids. We calculate the electrostatic potential and electrostatic energy for lamellar and inverted hexagonal phases, concentrating on the effects of dielectric boundaries. We compare our results for the complex energy with the known results of numerical solution of the nonlinear Poisson-Boltzmann equation. Using the solution for the lamellar phase, we calculate the compressibility modulus and compare our findings with the experimental data available. Also, we treat charge-charge interactions across, along, and between two low-dielectric membranes. We obtain an estimate for the strength of electrostatic interactions of one-dimensional DNA smectic layers across the lipid membrane. We discuss in the end some aspects of two-dimensional DNA condensation and DNA-DNA attraction in the DNA-lipid lamellar phase in the presence of di- and trivalent cations. We analyze the equilibrium DNA-DNA separations in lamellar complexes using the recently developed theory of electrostatic interactions of DNA helical charge motifs.