RNA and DNA association to zwitterionic and charged monolayers at the air-liquid interface

Neutron reflectometry as a powerful tool to elucidate membrane interactions of drug delivery systems

The last couple of decades have seen an explosion of novel colloidal drug delivery systems, which have been demonstrated to increase drug efficacy, reduce side-effects, and provide various other advantages for both small-molecule and biomacromolecular drugs. The interactions of delivery systems with biomembranes are increasingly recognized to play a key role for efficient eradication of pathogens and cancer cells, as well as for intracellular delivery of protein and nucleic acid drugs. In parallel, there has been a broadening of methodologies for investigating such systems. For example, advanced microscopy, mass-spectroscopic "omic"-techniques, as well as small-angle X-ray and neutron scattering techniques, which only a few years ago were largely restricted to rather specialized areas within basic research, are currently seeing increased interest from researchers within wide application fields. In the present discussion, focus is placed on the use of neutron reflectometry to investigate membrane interactions of colloidal drug delivery systems. Although the technique is still less extensively employed for investigations of drug delivery systems than, e.g., X-ray scattering, such studies may provide key mechanistic information regarding membrane binding, re-modelling, translocation, and permeation, of key importance for efficacy and toxicity of antimicrobial, cancer, and other therapeutics. In the following, examples of this are discussed and gaps/opportunities in the research field identified.

mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria

Signal-sequence-dependent protein targeting is essential for the spatiotemporal organization of eukaryotic and prokaryotic cells and is facilitated by dedicated protein targeting factors such as the signal recognition particle (SRP). However, targeting signals are not exclusively contained within proteins but can also be present within mRNAs. By in vivo and in vitro assays, we show that mRNA targeting is controlled by the nucleotide content and by secondary structures within mRNAs. mRNA binding to bacterial membranes occurs independently of soluble targeting factors but is dependent on the SecYEG translocon and YidC. Importantly, membrane insertion of proteins translated from membrane-bound mRNAs occurs independently of the SRP pathway, while the latter is strictly required for proteins translated from cytosolic mRNAs. In summary, our data indicate that mRNA targeting acts in parallel to the canonical SRP-dependent protein targeting and serves as an alternative strategy for safeguarding membrane protein insertion when the SRP pathway is compromised.

Effects of the structure of lipid-based agents in their complexation with a single stranded mRNA fragment: a computational study

In this work we employed fully atomistic molecular dynamics simulations, aiming towards a better understanding of the mechanisms associated with the formation and the stability of lipid-based RNA nanoassemblies, in an aqueous environment. We examined two groups of lipid-based complexation agents, differing in the degree of hydrophobicity and in the overall charge. The first group was comprised of cationic ionizable agents while the second included electrically neutral amphoteric phosphatidylcholine lipids. It was found that the overall charge of the complexation agents played the most decisive role in the energetics of the lipid/RNA association, while their degree of hydrophobicity affected their self-assembly and their complexation kinetics. The latter also affected the structural stability of the formed complexes since the water entrapped within the clusters of the less hydrophobic agents appeared to reduce the coherence of the lipid-RNA nanoassemblies. The combined effects of the aforementioned attributes dictated also the RNA conformation after complexation. The results from the present study provide thus new insight towards controlling the morphology, the energetic stability and the structural integrity of the formed complexes.

pH-temperature dual-sensitive nucleolipid-containing stealth liposomes anchored with PEGylated AuNPs for triggering delivery of doxorubicin

Liposomes (Lip) are useful nanocarriers for drug delivery and cancer nanomedicine because of their ability to efficiently encapsulate drugs with different physical and chemical properties. The pH gradient between normal and tumoral tissues, and their rapid metabolism that induces hyperthermia encourage the development of pH- and thermo-sensitive Lip for delivering anticancer drugs. Nucleolipids have been studied as scaffolding material to prepare Lip, mainly for cancer therapy. Herein, we report for the first time the use of 1,2-dipalmitoyl-sn-glycero-3-(cytidine diphosphate) (DG-CDP) to develop pH/thermo-sensitive nucleolipid-containing stealth Lip stabilized by combination with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and cholesterol, anchored with NH₂-PEGylated gold nanoparticles (PEG-AuNPs, 15 nm) for triggering delivery of doxorubicin (Dox). The optimal composition of DPPC, DG-CDP and cholesterol (94:3:3) was established by Langmuir isotherms. Unloaded and Dox-loaded Lip and AuNPs-Lip exhibited nano-scale sizes (415-650 nm), acceptable polydispersity indexes (<0.33), spherical shapes, and negative Z-potential (-23- -6.6 mV) due to the phosphate groups of DG-CDP, which allowed the anchoring with positively charged AuNPs. High EE% were achieved (>78%) and although efficient control in the Dox release towards different receptor media was observed, the release of Dox from PEG-AuNPs-Lip-Dox was significantly triggered at acidic pH and hyperthermia temperature, demonstrating its responsiveness to both stimuli. Dox-loaded Lip showed high cytotoxic activity against MDA-MB-231 breast cancer cells and SK-OV-3 ovarian cancer cells, suggesting that Dox was released from these nanocarriers over time. Overall, the liposomal formulations showed promising properties as stimuli-responsive nanocarriers for cancer nanomedicine, with prospects for hyperthermia therapy.

Lipid membranes modulate the activity of RNA through sequence-dependent interactions

RNA is a ubiquitous biomolecule that can serve as both catalyst and information carrier. Understanding how RNA bioactivity is controlled is crucial for elucidating its physiological roles and potential applications in synthetic biology. Here, we show that lipid membranes can act as RNA organization platforms, introducing a mechanism for riboregulation. The activity of R3C ribozyme can be modified by the presence of lipid membranes, with direct RNA-lipid interactions dependent on RNA nucleotide content, base pairing, and length. In particular, the presence of guanine in short RNAs is crucial for RNA-lipid interactions, and G-quadruplex formation further promotes lipid binding. Lastly, by artificially modifying the R3C substrate sequence to enhance membrane binding, we generated a lipid-sensitive ribozyme reaction with riboswitch-like behavior. These findings introduce RNA-lipid interactions as a tool for developing synthetic riboswitches and RNA-based lipid biosensors and bear significant implications for RNA world scenarios for the origin of life.

Kelvin probe force microscopy to study electrostatic interactions of DNA with lipid-gemini surfactant monolayers for gene delivery

In novel gene therapy mechanisms utilising gemini surfactants, electrostatic interactions of the surfactant molecules with the DNA strands is a primary mechanism by which the two components of the delivery vehicle bind. In this work, we show for the first time direct evidence of electrostatic interactions of these compounds visualised with Kelvin probe force microscopy (KPFM) and correlated to their topography from atomic force microscopy (AFM). We construct monolayers of lipids and gemini surfactant to simulate interactions on a cellular level, using lipids commonly found in cell membranes, and allow DNA to bind to the monolayer as it is formed on a Langmuir-Blodgett trough. The difference in topography and electrical surface potential between monolayers with and without DNA is striking. In fact, KPFM reveals a strongly positive relative electrical surface potential in between where we identify a background lipid and the DNA strands, evidenced by the height profiles of the domains. Such identification is not possible without KPFM. We conclude that it is likely we are seeing cationic surfactant molecules surrounding DNA strands within a sea of background lipid.

Membrane affinity and fluorescent labelling: comparative study of monolayer interaction, cellular uptake and cytotoxicity profile of carboxyfluorescein-conjugated cationic peptides

Fluorescent labelling is a common approach to reveal the molecular details of cellular uptake, internalisation, transport, distribution processes in biological systems. The conjugation with a fluorescent moiety might affect relevant physico-chemical and in vitro transport properties of the bioactive component. A representative set of seven cationic peptides-including cell-penetrating peptides as well as antimicrobial peptides and synthetic derivatives-was selected for our comparative study. Membrane affinity of the peptides and their 5(6)-carboxyfluorescein (Cf) derivatives was determined quantitatively and compared applying Langmuir monolayer of zwitterionic (DPPC) and negatively charged (DPPC + DPPG) lipids as cell membrane models. The interaction with neutral lipid layer is mainly governed by the overall hydrophobicity of the molecule which is remarkably increased by Cf-conjugation for the most hydrophobic Magainin, Melittin and Transportan. A significantly enhanced membrane affinity was detected in negatively charged lipid model monolayer for all of the peptides since the combination of electrostatic and hydrophobic interaction is active in that case. The Cf-conjugation improved the penetration ability of Penetratin and Dhvar4 suggesting that both the highly charged character (Z/n) and the increased hydrophobicity by Cf-conjugation present important contribution to membrane interaction. This effect might also responsible for the observed high in vitro internalisation rate of Penetratin and Dhvar4, while according to in vitro studies they did not cause damage of cell membrane. From the experiments with the given seven cationic peptides, it can be concluded that the Cf-conjugation alters the degree of membrane interaction of such peptides which are moderately hydrophobic and highly charged.

Organelle-mimicking liposome dissociates G-quadruplexes and facilitates transcription

Important biological reactions involving nucleic acids occur near the surface of membranes such as the nuclear membrane (NM) and rough endoplasmic reticulum (ER); however, the interactions between biomembranes and nucleic acids are poorly understood. We report here that transcription was facilitated in solution with liposomes, which mimic a biomembrane surface, relative to the reaction in a homogeneous aqueous solution when the template was able to form a G-quadruplex. The G-quadruplex is known to be an inhibitor of transcription, but the stability of the G-quadruplex was decreased at the liposome surface because of unfavourable enthalpy. The destabilization of the G-quadruplex was greater at the surface of NM- and ER-mimicking liposomes than at the surfaces of liposomes designed to mimic other organelles. Thermodynamic analyses revealed that the G-rich oligonucleotides adopted an extended structure at the liposome surface, whereas in solution the compact G-quadruplex was formed. Our data suggest that changes in structure and stability of nucleic acids regulate biological reactions at membrane surfaces.

Adsorption of DNA onto anionic lipid surfaces

Currently self-assembled DNA delivery systems composed of DNA multivalent cations and anionic lipids are considered to be promising tools for gene therapy. These systems become an alternative to traditional cationic lipid-DNA complexes because of their low cytotoxicity lipids. However, currently these nonviral gene delivery methods exhibit low transfection efficiencies. This feature is in large part due to the poorly understood DNA complexation mechanisms at the molecular level. It is well-known that the adsorption of DNA onto like charged lipid surfaces requires the presence of multivalent cations that act as bridges between DNA and anionic lipids. Unfortunately, the molecular mechanisms behind such adsorption phenomenon still remain unclear. Accordingly a historical background of experimental evidence related to adsorption and complexation of DNA onto anionic lipid surfaces mediated by different multivalent cations is firstly reviewed. Next, recent experiments aimed to characterise the interfacial adsorption of DNA onto a model anionic phospholipid monolayer mediated by Ca(2+) (including AFM images) are discussed. Afterwards, modelling studies of DNA adsorption onto charged surfaces are summarised before presenting preliminary results obtained from both CG and all-atomic MD computer simulations. Our results allow us to establish the optimal conditions for cation-mediated adsorption of DNA onto negatively charged surfaces. Moreover, atomistic simulations provide an excellent framework to understand the interaction between DNA and anionic lipids in the presence of divalent cations. Accordingly,our simulation results in conjunction go beyond the macroscopic picture in which DNA is stuck to anionic membranes by using multivalent cations that form glue layers between them. Structural aspects of the DNA adsorption and molecular binding between the different charged groups from DNA and lipids in the presence of divalent cations are reported in the last part of the study. Although this research work is far from biomedical applications, we truly believe that scientific advances in this line will assist, at least in part, in the rational design and development of optimal carrier systems for genes and applicable to other drugs.

The interaction between the outer layer of a mixed ion pair amphiphile/double-chained cationic surfactant vesicle and DNA: a Langmuir monolayer study

The charge density of vesicular bilayers plays an important role in the structure characteristic of the vesicle-DNA complex for gene delivery. In this work, the charge density effect of catanionic vesicle surfaces on the association behavior of the vesicle with DNA was explored with the model Langmuir monolayer approach. The interaction of negatively charged DNA with positively charged Langmuir monolayers composed of catanionic vesicle-forming materials, hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dihexadecyldimethylammonium bromide (DHDAB), was investigated with surface pressure-area isotherms, area-time relaxation curves and Brewster angle microscope images. The results showed that the adsorption of DNA molecules onto the monolayers was enhanced with an increased DHDAB molar fraction (XDHDAB), which was apparently related to the increased charge density of the monolayers. With XDHDAB being increased up to 0.5, the mixed monolayers with a higher XDHDAB, or higher charge density, possessed a more stable characteristic at high surface pressures, at which the molecular status was close to that in a corresponding vesicular bilayer, due to the DHDAB-improved molecular packing/interaction. It was found that the composition of the mixed HTMA-DS-DHDAB monolayers at high surface pressures would be affected by the adsorbed DNA with the extent depending on XDHDAB. For the formation of stable HTMA-DS-DHDAB monolayer-DNA complexes, a strong electrostatic interaction of DNA with a monolayer of high charge density and a high monolayer stability characteristic resulting from DHDAB-improved molecular packing/interaction were thus required. The finding has an implication for the formulation of catanionic vesicles composed of an ion pair amphiphile, HTMA-DS, with DHDAB in gene delivery applications.

Calcium-mediated binding of DNA to 1,2-distearoyl-sn-glycero-3-phosphocholine-containing mixed lipid monolayers

The calcium-mediated interaction of DNA with monolayers of the non-toxic, zwitterionic phospholipid, 1,2-distearoyl-sn-glycero-3-phosphocholine when mixed with 50 mol% of a second lipid, either the zwitteronic 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine or neutral cholesterol was investigated using a combination of surface pressure-area isotherms, Brewster angle microscopy, external reflectance Fourier transform infrared spectroscopy and specular neutron reflectivity in combination with contrast variation. When calcium and DNA were both present in the aqueous subphase, changes were observed in the compression isotherms as well as the surface morphologies of the mixed lipid monolayers. In the presence of calcium and DNA, specular neutron reflectivity showed that directly underneath the head groups of the lipids comprising the monolayers, DNA occupied a layer comprising approximately 13 and 18% v/v DNA for the 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine and cholesterol-containing monolayers, respectively. The volume of the corresponding layer for 1,2-distearoyl-sn-glycero-3-phosphocholine only containing monolayers was ∼15% v/v DNA. Furthermore regardless of the presence and nature of the second lipid and the surface pressure of the monolayer, the specular neutron reflectivity experiments showed that the DNA-containing layer was 20-27 Å thick, suggesting the presence of a well-hydrated layer of double-stranded DNA. External reflectance Fourier transform infrared studies confirmed the presence of double stranded DNA, and indicated that the strands are in the B-form conformation. The results shed light on the interaction between lipids and nucleic acid cargo as well as the role of a second lipid in lipid-based carriers for drug delivery.

Density functional analysis of like-charged attraction between two similarly charged cylinder polyelectrolytes

A systematic theoretical investigation is performed for electrostatic potential of mean force (EPMF) between two similarly charged rods (modeling DNA) immersed in a primitive model electrolyte solution. Two scientific anomalies are disclosed: (i) although a like-charge attraction (LCA) generally becomes stronger with bulk electrolyte concentration, the opposite effect unexpectedly occurs if the two rod surfaces involved are sufficiently charged and (2) contrary to what is often asserted, that the presence of multivalent counterion is necessary to induce the LCA, it is found that the univalent counterion induces the LCA solely only if bulk electrolyte concentration rises sufficiently and the rod surface charge quantities are high. On the basis of the system energetics calculated first by a classical density functional theory in three-dimensional space, a hydrogen-bonding style mechanism is advanced to reveal the origin of the LCA, and by appealing to fairly common-sense concepts such as bond energy, bond length, number of hydrogen bonds formed, and counterion single-layer saturation adsorption capacity, the present mechanism successfully explains the scientific anomalies and effects of counterion and co-ion diameters in eliciting the LCA first investigated in this work. To add weight to the hydrogen-bonding style mechanism, a theoretical investigation is further performed regarding the effects of the rod surface charge density, co-ion valence, relative permittivity of the medium, temperature, nonelectrostatic interion interactions, and rod diameter in modifying the EPMF, and several novel phenomena are first confirmed, which is self-consistently explained by the present hydrogen-bonding style mechanism.