Stoichiometry of dipalmitoylphosphatidylcholine-DNA interaction in the presence of Ca2+: a temperature-scanning ultrasonic study

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.

Lipoplex-Mediated Deintercalation of Doxorubicin from Calf Thymus DNA-Doxorubicin Complex

In this paper, we report the lipoplex-mediated deintercalation of anticancer drug doxorubicin (DOX) from the DOX-DNA complex under controlled experimental conditions. We used three zwitterionic liposomes, namely, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC), which are widely different in their phase transition temperatures to form a lipoplex with calf thymus DNA in the presence of Ca(2+) ions. The study revealed that DPPC being in sol-gel phase was more effective in releasing the drug from the DOX-DNA complex compared with liposomes that remain in liquid crystalline phase (DMPC and POPC). The higher extent of drug release in the case of DPPC liposomes was attributed to the stronger lipoplex formation with DNA as compared with that of other liposomes. Owing to the relatively smaller head group area, the DPPC liposomes in their sol-gel phase can absorb a larger number of Ca(2+) ions and hence offer a strong electrostatic interaction with DNA. This interaction was confirmed by time-resolved anisotropy and circular dichroism spectroscopy. Apart from the electrostatic interaction, the possible hydrophobic interaction between the liposomes and DNA was also taken into account for the observed deintercalation. The successful uptake of drug molecules by liposomes from the drug-DNA complex in the post-release period was also confirmed using confocal laser scanning microscopy (CLSM).

X-DNA origami-networked core-supported lipid stratum

DNA hydrogels are promising materials for various fields of research, such as in vitro protein production, drug carrier systems, and cell transplantation. For effective application and further utilization of DNA hydrogels, highly effective methods of nano- and microscale DNA hydrogel fabrication are needed. In this respect, the fundamental advantages of a core-shell structure can provide a simple remedy. An isolated reaction chamber and massive production platform can be provided by a core-shell structure, and lipids are one of the best shell precursor candidates because of their intrinsic biocompatibility and potential for easy modification. Here, we demonstrate a novel core-shell nanostructure made of gene-knitted X-shaped DNA (X-DNA) origami-networked gel core-supported lipid strata. It was simply organized by cross-linking DNA molecules via T4 enzymatic ligation and enclosing them in lipid strata. As a condensed core structure, the DNA gel shows Brownian behavior in a confined area. It has been speculated that they could, in the future, be utilized for in vitro protein synthesis, gene-integration transporters, and even new molecular bottom-up biological machineries.

Supramolecular assemblies of zwitterionic nanoliposome-polynucleotide complexes as gene transfer vectors: Nanolipoplex formulation and in vitro characterisation

Synthetic gene transfer vectors based on zwitterionic nanoliposome-DNA assemblies (nanolipoplexes), formed by the mediation of magnesium ions, were prepared by a scalable method without employing volatile solvents, high-shear force treatments or extrusion. The zwitterionic nanolipoplexes (NLP) were formulated with PC (phosphatidylcholine) and DPPC (a natural lung surfactant) incorporating different amounts of cholesterol (CHOL). The resulting structures were characterised in terms of their morphology, size and DNA content. In addition, the toxicity and transfection efficiency of the nanolipoplexes were evaluated in cultured Chinese hamster ovary-K1 (CHO-K1) cells. The effects of the multivalent cation Mg(2+) on nanoliposome-DNA transfection potency were evaluated. Formulations containing 10% CHOL showed maximum transfection efficiency and the optimum amount of Mg(2+) ions for transfection with minimum cytotoxicity was ca. 20 mM. The zwitterionic formulations showed significantly less cytotoxicity compared to a commercially available cationic liposome reagent or polyethylenimine (PEI) while they were superior in terms of gene transfer potency. The zwitterionic vectors formulated in this study avoid the use of toxic cationic lipids as well as toxic solvents and may have potential application in gene therapy. The new method will enable scale-up and manufacture of safe and efficacious transfection vehicles required for preclinical and clinical studies. Based on the advantages and superiority of the formulated nanolipoplexes, this method allows for the acceleration of nanolipoplex formulation, enabling the rapid development and evaluation of novel carrier systems for genes and other drugs.

Assembly of zwitterionic phospholipid/conjugated polyelectrolyte complexes: structure and photophysical properties

We report on the formation of complexes between zwitterionic phospholipid vesicles and an anionic fluorescent conjugated polyelectrolyte and the effect of mono- and divalent cations on the photophysical properties of these complexes. Our goal is to gain an understanding of the interplay of morphology and exciton transport in these complexes, information that is critical to designing efficient lipid/conjugated polymer-based sensors. Our studies further underscore the potential application of lipid/conjugated polymer complexes in light-harvesting devices. Our work focuses on the negatively charged conjugated polyelectrolyte poly[5-methoxy-2-(3-sulfopropoxy)-1,4-phenylenevinylene] (MPS-PPV) and its interaction with the zwitterionic lipid dioleoylphosphatidylcholine (DOPC). We utilize monovalent and divalent cations as a tool to control and explore the interaction of MPS-PPV with lipids. We show that Ca(2+) ions promote the complexation of zwitterionic lipids and MPS-PPV in comparison to Na(+) ions. The addition of increasing amounts of zwitterionic phospholipids in the form of vesicles gradually disrupts MPS-PPV aggregates albeit vesicle structure is preserved in Na(+) buffer. Lipid complexation and the resulting MPS-PPV aggregate disruption produces an intensity enhancement and blue shifting of the MPS-PPV emission peak. In the absence of Ca(2+), the intensity enhancement and blue shift reach a plateau at larger than a 10:1 lipid/MPS-PPV monomer mole ratio. In the presence of Ca(2+), a plateau is reached at equimolar concentrations of MPS-PPV and lipid. Vesicle particle coalescence and agglomerate formation are observed herein. Lipid complexation and concomitant MPS-PPV shielding is shown to diminish the quenching of MPS-PPV emission by water-soluble quencher methyl viologen. FRET experiments conducted with membrane-intercalating acceptor dye DiD further underscore the large lipid/polymer interaction mediated by Ca(2+). We observe efficient light harvesting and MPS-PPV-amplified emission quenching in Ca(2+) buffer and to a lesser extent in Na(+) buffer. Our results highlight how the interplay of a zwitterionic lipid, cations, and buffer, in combination with the conjugated polyelectrolyte MPS-PPV, provides rich diversity in architecture and photophysical properties.

DNA binding to zwitterionic model membranes

This study shows that DNA (linearized plasmid, 4331 base pairs and salmon sperm, 2000 base pairs, respectively) adsorbs to model membranes of zwitterionic liquid crystalline phospholipid bilayers in solutions containing divalent Ca(2+) cations, and also in solutions containing monovalent Na(+). The interaction between DNA and surface-supported model membranes was followed in situ using null ellipsometry, quartz crystal microbalance with dissipation, as well as neutron reflectometry. In the presence of Na(+) (in the absence of multivalent ions), DNA adopts an extended coil conformation upon adsorption. The solvent content in the adsorbed layer is high, and DNA is positioned on top of the membrane. In the presence of divalent Ca(2+), the driving force for the adsorption of DNA is electrostatic, and the adsorbed DNA film is not as dilute as in a solution containing Na(+). Cryo-TEM and SANS were further used to investigate the interaction in bulk solution using vesicles as model membrane systems. DNA adsorption could not be identified in the presence of Na(+) using SANS, but cryo-TEM indicates the presence of DNA between neighboring unilamellar vesicles. In the presence of Ca(2+), DNA induces the formation of multilamellar vesicles in which DNA intercalates the lamellae. Possible electrostatic and hydrophobic mechanisms for the adsorption of DNA in solutions containing monovalent salt are discussed and compared to the observations in divalent salt.

The structural diversity of DNA–neutral phospholipids–divalent metal cations aggregates: a small-angle synchrotron X-ray diffraction study

We investigate the structure of aggregates formed due to DNA interaction with saturated neutral phosphatidylcholines [dipalmitoylphosphatidylcholine (DPPC) and dimyristoylphosphatidylcholine] in presence of Ca(2+) and Mg(2+) cations using simultaneous synchrotron small- and wide-angle X-ray diffractions. For DPPC:DNA = 3:1 mol/base and in the range of 1-50 mM Ca(2+), the diffractograms show structural heterogeneity of aggregates. We observe the coexistence of two lamellar phases in aggregates prepared at 1 mM Ca(2+): L(x) phase with the DNA strands (of unknown organization) intercalated in water layers between adjacent lipid bilayers and L(DPPC) phase of DPPC bilayers without any divalent cations and DNA strands. Aggregates prepared in the range 2-50 mM Ca(2+) show a condensed gel lamellar phase L (g) (c) with the lipid bilayer periodicity d approximately 8.0 nm, and the DNA-DNA interhelical distance d (DNA) approximately 5.1 nm. The increase of temperature induces the decrease in the intensity and the increase in the width of the DNA related peak. In the fluid state, the condensed lamellar phase L (alpha) (c) gradually converts into L(x) phase. The aggregates do not exhibit rippled P(beta) phase. The thermal behaviour of aggregates was investigated in the range 20-80 degrees C. Applying heating-cooling cycles, the aggregates converted into energetically more favourable structure: a condensed lamellar phase L(c) (or L(x)) is preserved or we observe lateral segregation of the DNA strands and metal cations (L(x) phase) in coexistence with L(PC) phase of pure phospholipids.

AFM images of short oligonucleotides on a surface of supported lipid films

Atomic force microscopy (AFM) was used to study the topography of lipid films on a gold support with immobilized 19 mer single stranded DNA (ssDNA) chemically modified by oleylamine and after hybridization with complementary DNA. The topography of various surfaces was analyzed, including alkanethiol layer chemisorbed on a gold support, lipid films formed on alkanethiol layer without and with immobilized single or double stranded DNA (dsDNA). The value of root means square roughness (RMS) for each surface was determined. RMS value for sBLM with immobilized ssDNA was 2.98 nm, while slightly higher value of 3.37 nm was typical for dsDNA. The analysis of AFM images revealed that both ssDNA and dsDNA form clusters. The clusters formed by ssDNA are not uniform, but that formed by dsDNA are almost of circular shape with diameter of 13.6+/-0.5 nm. Formation of the clusters could be consequence of lower hydration of lipids and DNA at an air. The water deficit and hence increased ion concentration probably facilitate the attraction between oligonucleotides.

DNA condensation and interaction with zwitterionic phospholipids mediated by divalent cations

Artificial viruses are considered to be a promising tool in gene therapy. To find lipid-DNA complexes with high transfection efficiency but without toxicity is a fundamental aim. Although cationic lipids are frequently toxic for cells, neutral lipids are completely nontoxic. Zwitterionic lipids do not interact with DNA directly; however, the interaction can be mediated by divalent cations. Langmuir monolayers represent a well-defined model system to study the DNA-lipid complexes at the air/water interface (quasi-2D systems). In this work, isotherms, infrared reflection absorption spectroscopy (IRRAS), X-ray reflectivity (XR), grazing incidence X-ray diffraction (GIXD), and Brewster angle microscopy (BAM) measurements are used to study the interaction of calf thymus DNA with DMPE (1,2-dimyristoyl-phosphatidylethanolamine) monolayers mediated by Ca2+ or Mg2+ ions. DNA adsorption is observed only in the presence of divalent cations. At low lateral pressure, the DNA partially penetrates into the lipid monolayer but is squeezed out at high pressure. The adsorption layer has a thickness of 18-19 A. Additionally, GIXD provides information about a one-dimensional ordering of adsorbed DNA. The periodic distance between DNA strands depends on the type of the divalent cation.

Structure and Phase Behavior of Self-Assembled DPPC−DNA−Metal Cation Complexes

Multilamellar liposomes of dipalmitoylphosphatidylcholine (DPPC) in solution with DNA and bivalent metal cations (Ca2+, Mn2+, Mg2+) self-assemble into a ternary DPPC-DNA-Me2+ complex. The supramolecular structure of the complex consists of an ordered multilamellar assembly where hydrated DNA helices are sandwiched between the lipid bilayers and the metal cations bind the phosphate groups of DNA to the lipid polar heads. In the range of explored incubation times, the complex coexists with the uncomplexed DPPC over the whole temperature range investigated (20-55 degrees C). Accordingly, two distinct coexisting lamellar phases are observed, one corresponding to the ternary complex and the other to the uncomplexed lipid. The structure and thermotropic phase behavior of both of these have been investigated by means of synchrotron X-ray diffraction, and the relevant structural data are deduced from experimental electron density profiles. While the uncomplexed lipid exhibits the same phase behavior as pure DPPC, that is, L beta'-P beta'-L alpha, the thermotropic behavior of the bound lipid in the complex is partially altered. This is manifested as an increase in the main transition temperature and the disappearance of the ripple phase leading to the single -phase transition. The role of the different metal cations in promoting and stabilizing the DNA condensation into the ternary complex is also discussed.

Completing the cycles; the dynamics of endonuclear lipidomics

Signal transductions via periodic generation and mobilisation of lipid second messengers within the nuclear matrix of eukaryotic cells have focused renewed attention on their precursor phospholipids' location, structure, form and function. The nuclear matrix contains and supports dynamic pools of phosphatidylcholine and phosphatidylinositol which serve as parent molecules of lipid second messengers but also of other phospholipids requiring cyclical replacement as cells proliferate. Applications of new, highly sensitive and specific analytical methodologies based on tandem electrospray ionisation mass spectrometry and the use of stable isotopes have allowed both static and dynamic lipidomic profiling of these endonuclear phospholipid pools. Together with more conventional enzymatic analyses and evaluation of the effect of specific "knock-out" of phospholipid transfer capacity, a number of important principles have been established. Specifically, a compartmental capacity to synthesise and remodel highly saturated phosphatidylcholine exists alongside transport mechanisms that facilitate the nuclear import of phosphatidylinositol and other phospholipids synthesised elsewhere within the cell. Subnuclear fractionation and the use of newly emerging techniques for sensitive lipidomic profiling of polyphosphoinositides, diacylglycerols and phosphatidate molecular species offer the potential for further significant advances in the near future.

Role of calcium in gene delivery

The treatment of genetic diseases using therapeutic gene transfer is considered to be a significant development. This development has brought with it certain limitations, and the process of overcoming these barriers has seen a drastic change in gene delivery. Many metal ions such as Mg2+, Mn2+, Ba2+ and, most importantly, Ca2+ have been demonstrated to have significant roles in gene delivery. Recently, calcium phosphate alone, or in combination with viral and nonviral vectors, was found to exert a positive effect on gene transfer when incorporated in the colloidal particulate system, which is an advancing approach to gene delivery. This review elaborates on various successful methods of using calcium in gene delivery.

Interfacial ternary complex DNA/Ca/lipids at anionic vesicle surfaces

The electroporative transfer of gene DNA and other bioactive substances into tissue cells by electric pulses gains increasing importance in the new disciplines of electrochemotherapy and electrogenetherapy. The efficiency of the electrotransfer depends crucially on the adsorption of the gene DNA and oligonucleotides to the plasma cell membranes. Here it is shown that the adsorption of larger oligonucleotides such as fragments (ca. 300 bp) of sonicated calf-thymus DNA, to anionic lipids of unilamellar vesicles (diameter Phi=300+/-90 nm) is greatly enhanced by divalent cations such as Ca(2+)-ions. Applying centrifugation, bound and free DNA are monitored optically at the wavelength lambda=260 nm. Using arsenazo III as a Ca(2+)-indicator and atomic absorption spectroscopy (AAS), Ca(2+)-titrations of DNA and vesicles yield the individual equilibrium constants of Ca(2+)- and DNA-binding not only for the binary complexes: Ca/lipids, Ca/DNA and DNA/lipids, respectively, but also for the various processes to form the ternary complex DNA/Ca/lipids. The data provide the basis for goal-directed optimization protocols for the adsorption and thus efficient electrotransfer of oligonucleotides and polynucleotides into cells.

The structure of DNA–DOPC aggregates formed in presence of calcium and magnesium ions: A small-angle synchrotron X-ray diffraction study

The structure of aggregates formed due to DNA interaction with dioleoylphosphatidylcholine (DOPC) vesicles in presence of Ca(2+) and Mg(2+) cations was investigated using synchrotron small-angle X-ray diffraction. For DOPC/DNA=1:1 mol/base and in the range of concentration of the cation(2+) 0-76.5 mM, the diffractograms show the coexistence of two lamellar phases: L(x) phase with repeat distance d(Lx) approximately 8.26-7.39 nm identified as a phase where the DNA strands are intercalated in water layers between adjacent lipid bilayers, and L(DOPC) phase with repeat distance d(DOPC) approximately 6.45-5.65 nm identified as a phase of partially dehydrated DOPC bilayers without any divalent cations and DNA strands. The coexistence of these phases was investigated as a function of DOPC/DNA molar ratio, length of DNA fragments and temperature. If the amount of lipid increases, the fraction of partially dehydrated L(DOPC) phase is limited, depends on the portion of DNA in the sample and also on the length of DNA fragments. Thermal behaviour of DOPC+DNA+Ca(2+) aggregates was investigated in the range 20-80 degrees C. The transversal thermal expansivities of both phases were evaluated.

Observation of a rectangular columnar phase in a DNA-calcium-zwitterionic lipid complex

In the presence of calcium, DNA and unilamellar liposomes of the zwitterionic lipid DPPC form a complex in which DNA strands are embedded between a lamellar phase of DPPC. In some complexes, in-plane alignment of the DNA strands occurs, where a DNA-DNA interaxial distance can be measured using small-angle X-ray scattering. Here we report a higher level of DNA organization, with a rectangular columnar phase of DNA identified within this complex structure. This observation is important in view of recent interests in creating new synthetic systems at the interface of biology.

DNA-Induced Aggregation of Zwitterionic Oligolamellar Liposome

Liposome consisting of a single zwitterionic lipid as the potential vector for gene therapy has been reported recently; however, whether polyanionic DNA can bind directly with zwitterionic lipid without the aid of multivalent salt still remains unresolved. In this study, we reveal the aggregation of zwitterionic oligolamellar liposomes composed of 1,2-di(cis-9-octadecenoyl)-sn-glycero-3-phosphocholine induced by DNA without the presence of multivalent salt. Our results demonstrate that only a small fraction (<10%) of DNA can bind electrostatically with a portion of the liposomes. Such a low degree of binding, however, induces significant aggregation of these oligolamellar liposomes, yielding large multilamellar particles in which the number of hydrophilic/hydrophobic layer stacking becomes sufficiently large to yield multiple diffraction peaks in the small-angle X-ray scattering profile. Addition of monovalent salt such as NaCl tends to disrupt the multilamellar structure.

Liposome-mediated conformation transition of DNA detected by molecular probe: methyl green

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper, we take methyl green (MG) as a probe molecule to detect the conformational change of DNA molecule induced by dimethyldioctadecylammonium bromide (DDAB) liposomes before the condensation process of DNA begins. DDAB-induced DNA topology changes were investigated by cyclic voltammetry (CV), circular dichroism (CD) and UV-VIS spectrometry. We find that upon binding to DNA, positively charged liposomes induce a conformational transition of DNA molecules from the native B-form to the C motif. Conformational transition in DNA results in the binding modes of MG to DNA, changing and being isolated from DNA to the solution. More stable complexes are formed between DNA and DDAB. That is also proved by the melting study of DNA.

Electrostriction of supported lipid films at presence of cationic surfactants, surfactant-DNA and DNA-Mg(2+) complexes

The method of electrostriction has been applied to study the physical properties of supported lipid membranes (sBLM) during membrane formation at application of negative potential. Application of negative potential -350 mV to the sBLM during its formation resulted in more compact membrane structure as revealed by higher elastic modulus in comparison with sBLM formed without application of this potential. We also studied interaction with sBLM cationic surfactant hexadecylamine (HDA), HDA-DNA and DNA-Mg(2+) complexes. Interaction of HDA with sBLM resulted in decrease of membrane capacitance and two-directional effect on elasticity modulus (increase or decrease), which can be caused by different aggregation state of surfactant at the surface of sBLM. In contrast with effect of HDA, the complexes of HDA-DNA resulted, in most cases, increase of elasticity modulus and increase of membrane capacitance, which can be caused by incorporation of these complexes into the hydrophobic interior of the membrane. Certain part of these complexes can, however, be adsorbed on the sBLM surface. DNA itself does not cause substantial changes of physical properties of sBLM; however, addition of bivalent cations Mg(2+) to the electrolyte-contained DNA caused substantial increase of elasticity modulus and surface potential. These changes are, however, much slower than that observed for HDA-DNA complexes, which can be caused by slow competitive exchange between Na(+) and Mg(2+) ions.

Efficient encapsulation of DNA plasmids in small neutral liposomes induced by ethanol and calcium

Efficient encapsulation of DNA plasmids inside small, neutral liposomes composed of 1,2-dioleoyl-sn-phosphatidylcholine (DOPC), DOPC/DOPE (1,2-dioleoyl-sn-phosphatidylethanolamine) (1:1) and DOPC/DOPE/cholesterol (1:1:1) was achieved by the addition of ethanol and calcium chloride to an aqueous mixture of small unilamellar vesicles (SUVs) and plasmid. Following dialysis against low-salt buffer, the neutral lipid complexes (NLCs) had average effective diameters less than 200 nm and encapsulated up to 80% of the DNA. Optimum Ca(2+) and ethanol concentrations for each lipid mixture were determined by statistically designed experiments and mathematical modeling of trapping efficiency. NLCs are unilamellar, have neutral surface potentials, and retain entrapped DNA at pH 4.0 and in serum at 37 degrees C. The circulation and clearance properties of the complexes following intravenous administration in mice are similar to empty neutral liposomes, and the toxicity of NLCs are expected to be significantly reduced compared to other non-viral gene-delivery systems. The NLC encapsulation method, if it can be combined with effective targeting and endosome-release technologies to achieve efficient and tissue-specific transfection, may represent an important alternative to current systemic gene therapy approaches.