DNA at membrane surfaces: An experimental overview

Tools shaping drug discovery and development

Spectroscopic, scattering, and imaging methods play an important role in advancing the study of pharmaceutical and biopharmaceutical therapies. The tools more familiar to scientists within industry and beyond, such as nuclear magnetic resonance and fluorescence spectroscopy, serve two functions: as simple high-throughput techniques for identification and purity analysis, and as potential tools for measuring dynamics and structures of complex biological systems, from proteins and nucleic acids to membranes and nanoparticle delivery systems. With the expansion of commercial small-angle x-ray scattering instruments into the laboratory setting and the accessibility of industrial researchers to small-angle neutron scattering facilities, scattering methods are now used more frequently in the industrial research setting, and probe-less time-resolved small-angle scattering experiments are now able to be conducted to truly probe the mechanism of reactions and the location of individual components in complex model or biological systems. The availability of atomic force microscopes in the past several decades enables measurements that are, in some ways, complementary to the spectroscopic techniques, and wholly orthogonal in others, such as those related to nanomechanics. As therapies have advanced from small molecules to protein biologics and now messenger RNA vaccines, the depth of biophysical knowledge must continue to serve in drug discovery and development to ensure quality of the drug, and the characterization toolbox must be opened up to adapt traditional spectroscopic methods and adopt new techniques for unraveling the complexities of the new modalities. The overview of the biophysical methods in this review is meant to showcase the uses of multiple techniques for different modalities and present recent applications for tackling particularly challenging situations in drug development that can be solved with the aid of fluorescence spectroscopy, nuclear magnetic resonance spectroscopy, atomic force microscopy, and small-angle scattering.

Adsorption of Semiflexible Polymers in Cylindrical Tubes

Conformations of wormlike chains in cylindrical pores with attractive walls are explored for varying pore radius and strength of the attractive wall potential by molecular dynamics simulations of a coarse-grained model. Local quantities such as the fraction of monomeric units bound to the surface and the bond-orientational order parameter as well as the radial density distribution are studied, as well as the global chain extensions parallel to the cylinder axis and perpendicular to the cylinder surface. A nonmonotonic convergence of these properties to their counterparts for adsorption on a planar substrate is observed due to the conflict between pore surface curvature and chain stiffness. Also the interpretation of partially adsorbed chains in terms of trains, loops, and tails is discussed.

Impact of lipid nanoparticle size on mRNA vaccine immunogenicity

Lipid nanoparticles (LNP) are effective delivery vehicles for messenger RNA (mRNA) and have shown promise for vaccine applications. Yet there are no published reports detailing how LNP biophysical properties can impact vaccine performance. In our hands, a retrospective analysis of mRNA LNP vaccine in vivo studies revealed a relationship between LNP particle size and immunogenicity in mice using LNPs of various compositions. To further investigate this, we designed a series of studies to systematically change LNP particle size without altering lipid composition and evaluated biophysical properties and immunogenicity of the resulting LNPs. While small diameter LNPs were substantially less immunogenic in mice, all particle sizes tested yielded a robust immune response in non-human primates (NHP).

Protein-induced metamorphosis of unilamellar lipid vesicles to multilamellar hybrid vesicles

Protein encapsulation into nanocarriers has been extensively studied to improve the efficacy and stability of therapeutic proteins. However, the chemical modification of proteins or new synthetic carrier materials are essential to achieve a high encapsulation efficiency and structural stability of proteins, which hinders their clinical applications. New strategies to physically incorporate proteins into nanocarriers feasible for clinical uses are required to overcome the current limitation. Here we report the spontaneous protein-induced reorganization of 'pre-formed' unilamellar lipid vesicles to efficiently incorporate proteins within multilamellar protein-lipid hybrid vesicles without chemical modification. Epidermal growth factor (EGF) binds to the surface of cationic unilamellar lipid vesicles and induces layer-by-layer self-assembly of the vesicles. The protein is spontaneously entrapped in the interstitial layers of a multilamellar structure with extremely high loading efficiency, ~99%, through polyionic interactions as predicted by molecular dynamics simulation. The loaded protein exhibits much higher structural, chemical, and biological stability compared to free protein. The method is also successfully applied to several other proteins. This work provides a promising method for the highly efficient encapsulation of therapeutic proteins into multilamellar lipid vesicles without the use of specialized instruments, high energy, coupling agents, or organic solvents.

Semiflexible Polymers Interacting With Planar Surfaces: Weak versus Strong Adsorption

Semiflexible polymers bound to planar substrates by a short-range surface potential are studied by Molecular Dynamics simulations to clarify the extent to which these chain molecules can be considered as strictly two-dimensional. Applying a coarse-grained bead-spring model, the chain length N and stiffness κ as well as the strength of the adsorption potential ϵwall are varied over a wide range. The excluded-volume (EV) interactions inherent in this model can also be “switched off” to provide a discretized version of the Kratky–Porod wormlike chain model. We study both local order parameters (fraction f of monomers within the range of the potential, bond-orientational order parameter η) and the mean square gyration radius parallel, 〈Rg2〉||, and perpendicular, 〈Rg2〉⊥, to the wall. While for strongly adsorbed chains EV has negligible effect on f and η, we find that 〈Rg2〉|| is strongly affected when the chain contour length exceeds the persistence length. Monomer coordinates in perpendicular (⊥) direction are correlated over the scale of the deflection length which is estimated. It is found that f,η, and 〈Rg2〉⊥ converge to their asymptotic values with 1/N corrections. For both weakly and strongly adsorbed chains, the distribution functions of “loops”, “trains”, and “tails” are analyzed. Some consequences pertaining to the analysis of experiments on adsorbed semiflexible polymers are pointed out.

Smectic C and Nematic Phases in Strongly Adsorbed Layers of Semiflexible Polymers

Molecular dynamics simulations of semiflexible polymers in a good solvent reveal a dense adsorbed layer when the solution is exposed to an attractive planar wall. This layer exhibits both a nematic and a smectic phase (smA for short and smC for longer chains) with bond vectors aligned strictly parallel to the wall. The tilt angle of the smC phase increases strongly with the contour length of the polymers. The isotropic-nematic transition is a Kosterlitz-Thouless transition and also the nematic-smectic transition is continuous. Our finding demonstrates thus a two-dimensional realization of different liquid crystalline phases, ubiquitous in three dimensions, that occurs in a single monomolecular layer ordered at least over mesoscopic scales.

Kinetic arrest in polyion-induced inhomogeneously charged colloidal particle aggregation

Polymer chains adsorbed onto oppositely charged colloidal particles can significantly modify the particle-particle interactions. For sufficient amounts of added polymers, the original electrostatic repulsion can even turn into an effective attraction and relatively large aggregates can form. The attractive interaction contribution between two particles arises from the correlated adsorption of polyions at the oppositely charged particle surfaces, resulting in a non-homogeneous surface charge distribution. Here, we investigate the aggregation kinetics of polyion-induced colloidal complexes through Monte Carlo simulation, in which the effect of charge anisotropy is taken into account by a DLVO-like inter-particle potential, as recently proposed by Velegol and Thwar (Langmuir 17, 7687 (2001)). The results reveal that the aggregation process slows down due to the progressive increase of the potential barrier height upon clustering. Within this framework, the experimentally observed cluster phases in polyelectrolyte-liposome solutions can be interpreted as a kinetic arrested state.

Effect of the preparation procedure on the structural properties of oligonucleotide/cationic liposome complexes (lipoplexes) studied by electron spin resonance and Zeta potential

Lipoplexes with different surface charge were prepared from a short oligonucleotide (20 mer, dsAT) inserted into liposomes of 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and 1,2-dioleoyl-sn-glycero-3-phospho-ethanolamine (DOPE). The starting liposomes were prepared by two different procedures, i.e. progressive dsAT addition starting from plain liposomes (titration) and direct mixing of dsAT with pure liposomes (point to point preparation). Lipoplexes were characterized from a molecular point of view by Electron Spin Resonance (ESR) of a cationic spin probe and by Nuclear Magnetic Resonance. Structural and surface features were analysed by Zeta potential (zeta) measurements and Cryo-TEM micrographs. The complete set of results allowed to demonstrate that: i) the interactions between dsAT and cationic lipids were strong and occurred at the liposome surface; ii) the overall shape and physicochemical properties of liposomes did not change when short nucleic acid fragments were added before surface charge neutralization; iii) the bilayer structure of the lipids in lipoplexes was substantially preserved at all charge ratios; iv) the physical status of lipoplexes with electrical charge far from neutrality did not depend on the preparation method.

Conductometric evidence for intact polyion-induced liposome clusters

In this note, we present a set of electrical conductivity measurements of polyion-induced liposome aggregate aqueous suspensions that supports evidence for the existence of a cluster phase in low-density colloidal systems. Heavily NaCl-loaded liposomes, dispersed in a low-conductivity aqueous solution, are forced by electrostatic interactions with oppositely charged polyions to build up into individual aggregates, where the single vesicles maintain their integrity and, upon an external force, are able to release their ionic content. The conductivity data, within the effective medium approximation theory for heterogeneous systems, are in agreement with the picture of a suspension built up by clusters of vesicles which are able to preserve their content from the external medium. This finding opens new possibilities in multicompartment drug delivery techniques.

Physico-chemical characterization and transfection efficacy of cationic liposomes containing the pEGFP plasmid

Cationic liposomes-DNA complexes (lipoplexes) are largely used in gene delivery. Deciphering specific chemical and physical properties of lipoplexes is a necessary step to unravel the mechanisms underlying transfection and to improve transfection efficacy in each experimental model. In the present paper we investigated the physico-chemical features of lipoplexes containing a plasmid encoding for the GFP protein, in order to correlate these results with transfection efficacy. Cationic unilamellar vesicles (mean diameter 100 nm) were prepared, from the cationic DC-Chol lipid and the zwitterionic phospholipid DOPE. The two components of the liposome bilayer were used at molar ratio close to unity. ESR spectra were recorded and zeta potential zeta was measured on liposomes complexed with the plasmid. One of the main points of interest in this paper resided in the fact that both kinds of measurements were carried out in the same conditions (i.e. lipid concentration, medium composition, and pH) employed for cell transfection experiments. Transfection was performed on CHO cells; the percentage of fluorescent cells was evaluated and compared with the above physico-chemical features. It emerged that the composition and pH of the medium, the lipoplex/cell ratio, as well as the amount of lipoplex added to the cell culture were critical parameters for transfection efficacy. Finally, lipoplex surface charge played a fundamental role to achieve a high transfection level.

The structure of DNA–DLPC–cationic gemini surfactant aggregates: a small angle synchrotron X-ray diffraction study

The structure of aggregates formed by interaction of DNA with unilamellar dilauroylphosphatidylcholine (DLPC) vesicles (DNA:DLPC=1:1 base/mol) in the presence of gemini surfactant butane-1,4-diyl-bis(dodecyldimethylammonium bromide) (C12GS) was investigated using synchrotron small angle X-ray diffraction. In the concentration range C12GS+:DLPC< or =1 mol/mol, a condensed lamellar Lalphac phase was found with a repeat period of lipid bilayer stacking in the range d approximately 5.70-6.53 nm and the DNA interhelical distance d(DNA) approximately 3.52-3.99 nm, depending on the concentration of C12GS. At molar ratio C12GS+:DLPC> or =0.35:1, the diffractograms have shown the presence of a second lamellar phase with the repeat period d approximately 5.31 nm which slightly decreases with increasing concentration of C12GS+. The increasing fraction of this phase in the aggregates with increasing concentration of C12GS supports the association of this phase with microscopic domains enriched by surfactant molecules. The temperature behaviour of aggregates was investigated in the range 25-60 degrees C and the transversal thermal expansivities of the observed phases were determined.

Correlation between structure and transfection efficiency: a study of DC-Chol−DOPE/DNA complexes

The supramolecular structural nature of some cationic liposomes-DNA complexes, currently used as vehicles in non-viral gene delivery, has been elucidated by recent X-ray diffraction experiments. The relationship between the chemico-physical properties of these self-assembled structures and their transfection efficiency is extensively studied. Here we report a first comprehensive structural study by using energy dispersive X-ray diffraction, of the complex DC-Chol--DOPE/DNA (3beta[N-(N',N'-dimethylaminoethane)-carbamoyl]cholesterol dioleoylphosphatidylethanolamine/DNA), which has been classified as one of the most effective in in-vivo experiments. Our results show that DC-Chol--DOPE/DNA lipoplexes have a columnar inverted hexagonal structure, which is not influenced by the cationic liposome/DNA charge ratio. The transfection efficiency of C6 rat glioma cells by DC-Chol--DOPE/DNA lipoplexes and the toxicity of lipoplexes to cells are dramatically affected by cationic liposome/DNA weight ratio. It seems therefore that the lipoplex structures have not any influence on transfection efficiency and toxicity in our experimental system.

Langmuir monolayers to study interactions at model membrane surfaces

Langmuir monolayers at the liquid-air interface are well-defined interfacial systems and, therefore, excellent model systems to learn about interactions at interfaces beyond the classical DLVO description. Many parameters can be independently varied over a broad range and the structure can be analyzed with A precision. In the first part of the paper, the rich polymorphism in monolayers composed of amphiphilic molecules is demonstrated. Using homologues series generic phase diagrams can be derived. The delicate interplay of interactions causes a richness of phases which in turn can be used to measure fine variations in these interactions. Based on the understanding of the polymorphism in pure or mixed lipid monolayers, one can study the interaction of molecules dissolved in the subphase with monolayers. Samples presented are chemical reactions catalyzed by enzymes and coupling of polyelectrolytes to oppositely charged monolayers. To relate structure and reactivity, the activity of enzymes at the interface can be studied, predominantly combining X-ray diffraction and FTIR-spectroscopy. It is shown that the activity depends on monolayer structure. In one case, the reaction product leads to structural changes in the monolayer and stops the reaction, hence, indicating a subtle case of product inhibition via the membrane. On the other hand it has become possible to manipulate the organization of polyelectrolytes at interfaces via lipid charge density and ionic strength. In the most important case of DNA interacting with a membrane surface we show that DNA arranges at the interface in a lamellar manner, and the intermolecular distances, measured by Synchrotron X-ray diffraction can be varied by the lipid density.

Condensed lamellar phase in ternary DNA-DLPC-cationic gemini surfactant system: a small-angle synchrotron X-ray diffraction study

We report on a small-angle synchrotron X-ray diffraction study of dilauroylphosphatidylcholine (DLPC) liposomes aggregated with high molecular DNA in the presence of 1,4-butanediammonium-N,N'-dilauryl-N,N,N',N'-tetramethyl gemini surfactant cations (C12GS). The aggregates prepared at the DLPC/C12GS/DNA phosphate group=2:1:1.6 molar ratio in 0.0015 mol x l(-1) NaCl aqueous solution exhibit Bragg reflections due to lamellar lipid bilayer stacking and the Bragg reflection typical of one-dimensional DNA lattice with parallel strands intercalated between lipid bilayers. In this condensed fluid lamellar L(alpha)(c) phase, the interactions between DNA and charged bilayers damp the thermally induced bilayer undulations. The diffraction data obtained with the mixture of DLPC liposomes and DNA (at DNA phosphate group/DLPC=0.8:1 molar ratio) indicate a DNA-lipid interaction in the absence of C12GS.

Real time monitoring of lipoplex molar mass, size and density

Time-resolved multiangle laser light scattering (TR-MALLS) is used to monitor the temporal variation of DNA/cationic liposome lipoplex molar masses and geometric sizes throughout the complexation process. The measured molar masses and geometric sizes are in turn used to estimate lipoplex density. The DNA/cationic lipid charge ratio is found to be the primary factor governing lipoplex formation kinetics and the final lipoplex molar mass, geometric size and density. Charge ratios near unity lead to a growing kinetic regime in which initially formed primary lipoplexes undergo further aggregation eventually forming large molar mass lipoplexes of high density, while charge ratios very far from unity yield low molar mass lipoplexes of lower density. It is also noted that solvent composition can play a significant role in the lipoplex formation process with lipoplexes formed in ion-containing media being larger and denser than those formed in dextrose solution.

Advantage of the ether linkage between the positive charge and the cholesteryl skeleton in cholesterol-based amphiphiles as vectors for gene delivery

Twelve novel cationic cholesterol derivatives with different linkage types between the cationic headgroup and the cholesteryl backbone have been developed. These have been tested for their efficacies as gene transfer agents as mixtures with dioleoyl phosphatidylethanolamine (DOPE). A pronounced improvement in transfection efficiency was observed when the cationic center was linked to the steroid backbone using an ether type bond. Among these, cholest-5-en-3b-oxyethane-N,N,N-trimethylammonium bromide (2a) and cholest-5-en-3b-oxyethane-N,N-dimethyl-N-2-hydroxyethylammonium bromide (3d) showed transfection efficiencies considerably greater than commercially available reagents such as Lipofectin or Lipofectamine. To achieve transfection, 3d did not require DOPE. Increasing hydration at the headgroup level for both ester- and ether-linked amphiphiles resulted in progressive loss of transfection efficiency. Transfection efficiency was also greatly reduced when a 'disorder'-inducing chain like an oleyl (cis-9-octadecenyl) segment was added to these cholesteryl amphiphiles. Importantly, the transfection ability of 2a with DOPE in the presence of serum was significantly greater than for a commercially available reagent, Lipofectamine. This suggests that these novel cholesterol-based amphiphiles might prove promising in applications involving liposome-mediated gene transfection. This investigation demonstrates the importance of structural features at the molecular level for the design of cholesterol-based gene delivery reagents that would aid the development of newer, more efficient formulations based on this class of molecules.

Structure and structure-function studies of lipid/plasmid DNA complexes

Recent synchrotron-based X-ray diffraction studies have enabled us to comprehensively solve the self-assembled structures in mixtures of cationic liposomes (CLs) complexed with linear lambda-DNA. In one case the CL-DNA complexes were found to consist of a higher ordered multilamellar structure (labeled L(alpha)C with DNA sandwiched between cationic bilayer membranes. The membrane charge density is found to control the DNA interaxial spacing with high densities leading to high DNA compaction between lipid bilayers. A second self-assembled structure (labeled H(II)C) consists of linear DNA strands coated by cationic lipid monolayers and arranged on a 2D hexagonal lattice. In this paper we report on a combined X-ray diffraction and optical microscopy study of CLs complexed with functional supercoiled plasmid DNA. We describe the self-assembled structures in cell culture medium for both a high transfectant complex (DOTAP/DOPE, phiDOPE = 0.72) and a low transfectant complex (DOTAP/DOPC, (phiDOPC = 0.72). Fluorescence optica microscopy shows two distinct interactions between these two types of complexes and mouse fibroblast L-cells, demonstrating the existence of a correlation between structure and transfection efficiency.

Gene transfection efficiency of tracheal epithelial cells by DC-chol-DOPE/DNA complexes

We evaluated the transfection efficiency of five different cationic liposome/plasmid DNA complexes, during the in vitro gene transfer into human epithelial tracheal cell lines. A dramatic correlation between the transfection efficiency and the charge ratio (positive charge of liposome to negative charge of DNA) has been found. DC-Chol-DOPE was found to be the most effective liposome formulation. Therefore, a morphological and structural analysis of DC-Chol-DOPE liposomes and DC-Chol-DOPE/DNA complexes, has been performed by transmission electron microscopy (TEM) and by confocal laser scanning microscopy (CLSM), respectively. The process of interaction between DC-Chol-DOPE/DNA complexes and human epithelial tracheal cells has been studied by CLSM. These results raise some issues for in vivo gene therapy.