A stopped-flow kinetic study of the assembly of nonviral gene delivery complexes

Controlling Nanoparticle Formulation: A Low-Budget Prototype for the Automation of a Microfluidic Platform

Active pharmaceutical ingredients (API) with suboptimal pharmacokinetic properties may require formulation into nanoparticles. In addition to the quality of the excipients, production parameters are crucial for producing nanoparticles which reliably deliver APIs to their target. Microfluidic platforms promise increased control over the formulation process due to the decreased degrees of freedom at the micro- and nanoscale. Publications about these platforms usually provide only limited information about the soft- and hardware required to integrate the microfluidic chip seamlessly into an experimental set-up. We describe a modular, low-budget prototype for microfluidic mixing in detail. The prototype consists of four modules. The control module is a raspberry pi executing customizable python scripts to control the syringe pumps and the fraction collector. The feeding module consists of up to three commercially available, programable syringe pumps. The formulation module can be any macro- or microfluidic chip connectable to syringe pumps. The collection module is a custom-built fraction collector. We describe each feature of the working prototype and demonstrate its power with polyplexes formulated from siRNA and two different oligomers that are fed to the chip at two different stages during the assembly of the nanoparticles.

Can microfluidics address biomanufacturing challenges in drug/gene/cell therapies?

Translation of any inventions into products requires manufacturing. Development of drug/gene/cell delivery systems will eventually face manufacturing challenges, which require the establishment of standardized processes to produce biologically-relevant products of high quality without incurring prohibitive cost. Microfluidicu technologies present many advantages to improve the quality of drug/gene/cell delivery systems. They also offer the benefits of automation. What remains unclear is whether they can meet the scale-up requirement. In this perspective, we discuss the advantages of microfluidic-assisted synthesis of nanoscale drug/gene delivery systems, formation of microscale drug/cell-encapsulated particles, generation of genetically engineered cells and fabrication of macroscale drug/cell-loaded micro-/nano-fibers. We also highlight the scale-up challenges one would face in adopting microfluidic technologies for the manufacturing of these therapeutic delivery systems.

Interaction between calf thymus DNA and cationic bottle-brush copolymers: equilibrium and stopped-flow kinetic studies

Polyplex formation betweenctDNA and PEGylated cationic bottle-brush copolymers: PEG influences the DNA compaction behavior and the kinetics of polyplex formation.

Time resolved SAXS to study the complexation of siRNA with cationic micelles of divalent surfactants

The complexation of siRNA (small interfering RNA) with cationic micelles was studied using time dependent synchrotron SAXS. Micelles were formed by two types of divalent cationic surfactants, i.e. Gemini bis(quaternary ammonium) bromide with variable spacer length (12-3-12, 12-6-12, 12-12-12) and a weak electrolyte surfactant (SH14) with triazine head. Immediately after mixing (t < 50 ms), new large aggregates appeared in solution and the scattering intensity at low q increased. Concomitantly, the presence of a quasi-Bragg peak at q ∼ 1.5 nm(-1) indicated core structuring within the complexes. We hypothesize that siRNA and micelles are alternately arranged into "sandwiches", forming domains with internal structural coherence. The process of complex reorganization followed a first-order kinetics and was completed in less than about 5 minutes, after which a steady state was reached. Aggregates containing Geminis were compact globular structures whose gyration radii Rg depended on the spacer length and were in the order of 7-27 nm. Complexes containing SH14 (Rg = 14-16 nm) were less ordered and possessed a looser internal arrangement. The obtained data, joint with previous structural investigation using Dynamic Light Scattering, Zeta Potential and Small Angle Neutron Scattering, are encouraging evidence for using these systems in biological trials. In fact we showed that transfection agents can be obtained by simply mixing a micelle solution of the cationic surfactant and a siRNA solution, both of which are easily prepared and stable.

Structure and kinetics of lipid-nucleic acid complexes

The structure and function of lipid-based complexes (lipoplexes) have been widely investigated as cellular delivery vehicles for nucleic acids-DNA and siRNA. Transfection efficiency in applications such as gene therapy and gene silencing has been clearly linked to the local, nano-scale organization of the nucleic acid in the vehicle, as well as to the global properties (e.g. size) of the carriers. This review focuses on both the structure of DNA and siRNA complexes with cationic lipids, and the kinetics of structure evolution during complex formation. The local organization of the lipoplexes is largely set by thermodynamic, equilibrium forces, dominated by the lipid preferred phase. As a result, complexation of linear lambda-phage DNA, circular plasmid DNA, or siRNA with lamellae-favoring lipids (or lipid mixtures) forms multi-lamellar L(α)(C) liquid crystalline arrays. Complexes created with lipids that have bulky tail groups may form inverted hexagonal HII(C) phases, or bicontinuous cubic Q(II)(C) phases. The kinetics of complex formation dominates the large-scale, global structure and the properties of lipoplexes. Furthermore, the time-scales required for the evolution of the equilibrium structure may be much longer than expected. In general, the process may be divided into three distinct stages: An initial binding, or adsorption step, where the nucleic acid binds onto the surface of the cationic vesicles. This step is relatively rapid, occurring on time scales of order of milliseconds, and largely insensitive to system parameters. In the second step, vesicles carrying adsorbed nucleic acid aggregate to form larger complexes. This step is sensitive to the lipid characteristics, in particular the bilayer rigidity and propensity to rupture, and to the lipid to nucleic acid (L/D) charge ratio, and is characterized by time scales of order seconds. The last and final step is that of internal rearrangement, where the overall global structure remains constant while local adjustment of the nucleic acid/lipid organization takes place. This step may occur on unusually long time scales of order hours or longer. This rate, as well, is highly sensitive to lipid characteristics, including membrane fluidity and rigidity. While the three step process is consistent with many experimental observations to date, improving the performance of these non-viral vectors requires better understanding of the correlations between the parameters that influence lipoplexes' formation and stability and the specific rate constants i.e., the timescales required to obtain the equilibrium structures. Moreover, new types of cellular delivery agents are now emerging, such as antimicrobial peptide complexes with anionic lipids, and other proteins and small-molecule lipid carriers, suggesting that better understanding of lipoplex kinetics would apply to a variety of new systems in biotechnology and nanomedicine.

Poly-amidoamine structure characterization: amide resonance structure of imidic acid (HO–CN) and tertiary ammonium

The dendrimer PAMAM has an amide resonance structure,i.e.imidic acid (HO–CN), and a tertiary ammonium structure, which can be characterized using¹⁵N/¹H/2D NH/¹³C NMR, IR and MS.

A study using quantum chemical theory methods on the intrinsic fluorescence emission and the possible emission mechanisms of PAMAM

Structural units imidic acid (HO–CN) and tertiary ammonium in PAMAM dendrimers were proven to give fluorescence emission by TDDFT methods.

Microfluidic preparation of polymer-nucleic acid nanocomplexes improves nonviral gene transfer

As the designs of polymer systems used to deliver nucleic acids continue to evolve, it is becoming increasingly apparent that the basic bulk manufacturing techniques of the past will be insufficient to produce polymer-nucleic acid nanocomplexes that possess the uniformity, stability, and potency required for their successful clinical translation and widespread commercialization. Traditional bulk-prepared products are often physicochemically heterogeneous and may vary significantly from one batch to the next. Here we show that preparation of bioreducible nanocomplexes with an emulsion-based droplet microfluidic system produces significantly improved nanoparticles that are up to fifty percent smaller, more uniform, and are less prone to aggregation. The intracellular integrity of nanocomplexes prepared with this microfluidic method is significantly prolonged, as detected using a high-throughput flow cytometric quantum dot Förster resonance energy transfer nanosensor system. These physical attributes conspire to consistently enhance the delivery of both plasmid DNA and messenger RNA payloads in stem cells, primary cells, and human cell lines. Innovation in processing is necessary to move the field toward the broader clinical implementation of safe and effective nonviral nucleic acid therapeutics, and preparation with droplet microfluidics represents a step forward in addressing the critical barrier of robust and reproducible nanocomplex production.

Stopped-flow kinetic studies of poly(amidoamine) dendrimer-calf thymus DNA to form dendriplexes

Poly(amidoamine) (PAMAM) dendrimers are known to be highly efficient nonviral carriers in gene delivery. Dendrimer-mediated transfection is known to be a function of the dendrimer to DNA charge ratio as well as the size of the dendrimer. In the present study, the binding kinetics of four PAMAM dendrimers (G1, G2, G3, and G4) with calf thymus DNA (CT-DNA) has been studied using stopped-flow fluorescence spectroscopy. The effect of dendrimer-to-DNA charge ratio and dendrimer generation on the binding kinetics was investigated. In most cases, the results of dendrimer-CT-DNA binding can be explained by a two-step reaction mechanism: a rapid electrostatic binding between the dendrimer and DNA, followed by a conformational change of the dendrimer-DNA complex that ultimately leads to DNA condensation. It was observed that the charge ratio on the dendrimer and the DNA phosphate groups, as well as the dendrimer generation (size), has a marked effect on the kinetics of binding between the DNA and the dendrimers. The rate constant (k'1) of the first step was much higher compared to that of the second step (k'2), and both were found to increase with an increase in dendrimer concentration. Among the four generations of dendrimers, G4 exhibited significantly faster binding kinetics compared to the three smaller generation dendrimers.

Potential Use of Polyamidoamine Dendrimer Conjugates with Cyclodextrins as Novel Carriers for siRNA

Cyclodextrin (CyD)-based nanoparticles and polyamidoamine (PAMAM) starburst dendrimers (dendrimers) are used as novel carriers for DNA and RNA. Recently, small interfering RNA (siRNA) complex with β-CyD-containing polycations (CDP) having adamantine-PEG or adamantine-PEG-transferrin underwent a phase I study for treatment of solid tumors. Multifunctional dendrimers can be used for a wide range of biomedical applications, including the interaction and intracellular delivery of DNA and RNA. The present review will address the latest developments in dendrimer conjugates with cyclodextrins for siRNA delivery including the novel sustained release system.

Peptide dendrimers as efficient and biocompatible gene delivery vectors: Synthesis and in vitro characterization

We report the synthesis and characterization of different generations of dendritic poly(l-lysine) vectors, and their use for in vitro gene transfection. Gel retardation assay revealed that the dendrimers could form complexes with plasmid DNAs (pDNAs), evident from the inhibition of the migration of pDNA at the N/P ratios of 0.5, 1 and 2 by G3, G4 and G5 dendritic generations, respectively. DNase I assay revealed the protection of pDNA acquired from the complexation with dendrimers from nuclease-catalyzed degradation, with the protection capacity of G5 being even stronger than poly(ethyleneimine) (PEI). Atomic force microscopy (AFM) revealed that all 4 generations of dendrimer/DNA complexes studied were of similar particle sizes within 100-200nm. Zeta potential measurements showed that as the N/P ratio increased from 1 to 25, all dendrimer/pDNA complexes gradually changed from negative to positive charges. The higher generations tended to produce the greater positive potentials, indicating a stronger potency of the complexes to interact with negatively charged cell membranes. In vitro and in vivo cytotoxicity evaluations showed good biocompatibility of the dendrimers and their complexes over the different N/P ratios studied. In vitro gene transfection revealed higher efficiency of G5 than other dendrimers and insensitive variation to the presence of serum. Given its similar transfection efficiency to PEI but lower toxicity to cultured cells, dendrimer G5 could be a better candidate for gene delivery.

The mechanism of polyplex internalization into cells: testing the GM1/caveolin-1 lipid raft mediated endocytosis pathway

The GM1/caveolin-1 lipid raft mediated endocytosis mechanism was explored for generation 5 and 7 poly(amidoamine) dendrimer polyplexes employing the Cos-7, 293A, C6, HeLa, KB, and HepG2 cell lines. Expression levels of GM1 and caveolin-1 were measured using dot blot and Western blot, respectively. The level of GM1 in the cell plasma membrane was adjusted by incubation with exogenous GM1 or ganglioside inhibitor PPMP, and the level of CAV-1 was adjusted by upregulation with the adenovirus vector expressed caveolin-1 (AdCav-1). Cholera toxin B subunit was employed as a positive control for uptake in all cases. No evidence was found for a GM1/caveolin-1 lipid raft mediated endocytosis mechanism for the generation 5 and 7 poly(amidoamine) dendrimer polyplexes.

Watching DNA condensation induced by poly(amido amine) dendrimers with time-resolved cryo-TEM

The condensation of DNA by poly(amido amine) dendrimers of generation 1, 2, and 4 has been followed by time-resolved cryogenic transmission electron microscopy (cryo-TEM). The recorded images show that significant morphological rearrangement occurs for DNA condensed with the lower generation dendrimers leading to the formation of toroidal aggregates. Higher charge density dendrimers, on the other hand, give rise to globular aggregates, where no transient morphologies are observed. We suggest that the dendrimers in this case are kinetically trapped as soon as they bind to the DNA strand.

How to study dendriplexes II: Transfection and cytotoxicity

This paper reviews different techniques for analyzing the transfection efficiencies and cytotoxicities of dendriplexes-complexes of nucleic acids with dendrimers. Analysis shows that three plasmids are mainly used in transfection experiments: plasmid DNA encoding luciferase from the firefly Photinus pyralis, beta-galactosidase, or green fluorescent protein. The effective charge ratio of transfection does not directly correlate with the charge ratio obtained from gel electrophoresis, zeta-potential or ethidium bromide intercalation data. The most popular cells for transfection studies are human embryonic kidney cells (HEK293), mouse embryonic cells (NIH/3T3), SV40 transformed monkey kidney fibroblasts (COS-7) and human epithelioid cervical carcinoma cells (HeLa). Cellular uptake is estimated using fluorescently-labeled dendrimers or nucleic acids. Transfection efficiency is measured by the luciferase reporter assay for luciferase, X-Gal staining or beta-galactosidase assay for beta-galactosidase, and confocal microscopy for green fluorescent protein. Cytotoxicity is determined by the MTT test and lactate dehydrogenase assays. On the basis of the papers reviewed, a standard essential set of techniques for characterizing dendriplexes was constructed: (1) analysis of size and shape of dendriplexes in dried/frozen state by electron or atomic force microscopy; (2) analysis of charge/molar ratio of complexes by gel electrophoresis or ethidium bromide intercalation assay or zeta-potential measurement; (3) analysis of hydrodynamic diameter of dendriplexes in solution by dynamic light scattering. For the evaluation of transfection efficiency the essential techniques are (4) luciferase reporter assay, beta-galactosidase assay or green fluorescent protein microscopy, and (5) cytotoxicity by the MTT test. All these tests allow the transfection efficiencies and cytotoxicities of different kinds of dendrimers to be compared.

The convergence of quantum-dot-mediated fluorescence resonance energy transfer and microfluidics for monitoring DNA polyplex self-assembly in real time

We present a novel convergence of quantum-dot-mediated fluorescence resonance energy transfer (QD-FRET) and microfluidics, through which molecular interactions were precisely controlled and monitored using highly sensitive quantum-dot-mediated FRET. We demonstrate its potential in studying the kinetics of self-assembly of DNA polyplexes under laminar flow in real time with millisecond resolution. The integration of nanophotonics and microfluidics offers a powerful tool for elucidating the formation of polyelectrolyte polyplexes, which is expected to provide better control and synthesis of uniform and customizable polyplexes for future nucleic acid-based therapeutics.

Studies on the interactions between DNA and PAMAM with fluorescent probe [Ru(phen)2dppz]2+

The interactions between plasmid DNA and cationic polymers are of interest for their potential biological applications. In this paper, the interactions of DNA with polyamidoamine (PAMAM) dendrimer were studied by fluorescence spectroscopy and stopped-flow technique. A rapid and reproducible fluorescent assay method had been developed for assessing PAMAM and DNA interactions using [Ru(phen)2 dppz]2+ as a probe. We further studied the kinetics of PAMAM binding to DNA and the reverse process of DNA dissociation from the complexes. The results indicated that DNA condensation was the rate-determining step during the complexation process, while DNA unfolding and expansion was the rate-determining step during the DNA dissociation process. At N/P ratios before reaching the thermodynamically most stable state, the complexes of DNA and PAMAM were incompact and could dissociate to some extent. And at N/P ratios above 2.0, DNA was fully condensed by PAMAM and dissociation was increasingly difficult. These results provided some useful instructions for self-assembling and disassembling of DNA as well as efficient gene delivery applications.