Self-assembly of stable monomolecular nucleic acid lipid particles with a size of 30 nm

Sub-100 nm carriers by template polymerization for drug delivery applications

Size-controlled drug delivery systems (DDSs) have gained significant attention in the field of pharmaceutical sciences due to their potential to enhance drug efficacy, minimize side effects, and improve patient compliance. This review provides a concise overview of the preparation method, advancements, and applications of size-controlled drug delivery systems focusing on the sub-100 nm size DDSs. The importance of tailoring the size for achieving therapeutic goals is briefly mentioned. We highlight the concept of "template polymerization", a well-established method in covalent polymerization that offers precise control over molecular weight. We demonstrate the utility of this approach in crafting a monolayer of a polymer around biomolecule templates such as DNA, RNA, and protein, achieving the generation of DDSs with sizes ranging from several tens of nanometers. A few representative examples of small-size DDSs that share a conceptual similarity to "template polymerization" are also discussed. This review concludes by briefly discussing the drug release behaviors and the future prospects of "template polymerization" for the development of innovative size-controlled drug delivery systems, which promise to optimize drug delivery precision, efficacy, and safety.

Computational analysis of protein synthesis, diffusion, and binding in compartmental biochips

Protein complex assembly facilitates the combination of individual protein subunits into functional entities, and thus plays a crucial role in biology and biotechnology. Recently, we developed quasi-twodimensional, silicon-based compartmental biochips that are designed to study and administer the synthesis and assembly of protein complexes. At these biochips, individual protein subunits are synthesized from locally confined high-density DNA brushes and are captured on the chip surface by molecular traps. Here, we investigate single-gene versions of our quasi-twodimensional synthesis systems and introduce the trap-binding efficiency to characterize their performance. We show by mathematical and computational modeling how a finite trap density determines the dynamics of protein-trap binding and identify three distinct regimes of the trap-binding efficiency. We systematically study how protein-trap binding is governed by the system's three key parameters, which are the synthesis rate, the diffusion constant and the trap-binding affinity of the expressed protein. In addition, we describe how spatially differential patterns of traps modulate the protein-trap binding dynamics. In this way, we extend the theoretical knowledge base for synthesis, diffusion, and binding in compartmental systems, which helps to achieve better control of directed molecular self-assembly required for the fabrication of nanomachines for synthetic biology applications or nanotechnological purposes.

Size-tunable lipid vectors for controlled local delivery of siRNA from gene activated matrix

Tissue engineering aims to restore or replace different types of biological tissues through the association of cells, biologic factors and biomaterials. Currently, stem cells arise as a major cell source for many therapeutic indications, and their association with 3D scaffolds allow increasing regenerative medicine efficiency. In this context, the use of RNA interference to enhance or control stem cell differentiation into the desired phenotype appears as a promising strategy. However, achieving high transfection efficiency of cells in a 3D structure requires the use of a vector allowing for the spatiotemporally controlled release of the genetic material from these scaffolds. In this study, we report a new siRNA nanovector, called solvent exchange lipoplexe formulation (SELF), which has a tunable size, is stable over time in cell culture conditions and possess a high efficiency to transfect primary human mesenchymal stromal cells (hMSC). We associated SELFs with porous 3D collagen microspheres and demonstrated that the loading capacity and release kinetics were different depending on the size of the associated SELF. Interestingly, these different release profiles resulted in differences in the transfection kinetics of hMSCs. This original and unique type of gene activated matrix, with adaptable release kinetics, could be of interest for long-term and/or sequential transfection profiles of stem cells in 3D culture. STATEMENT OF SIGNIFICANCE: This work combines the use of human mesenchymal stromal cell (hMSC) and gene therapy for tissue engineering. Here, a gene-activated matrix was elaborated with collagen microspheres supporting hMSCs and acting as a reservoir for transfection vectors. This injectable GAM allows for the local and sustained delivery of nucleic acids, hence long-lasting transfection of the supported cells. With the original synthesis protocol presented herein, the size of the nanocarriers can be easily adapted, resulting in different siRNA release profiles from the microspheres. Most interestingly, different siRNA release profiles gave rise to different cell transfection profiles as assessed by the downregulation of a target gene. This highlights the versatility of the system and its suitability for various pathophysiological needs in regenerative medicine.

siRNA-based nanotherapeutics as emerging modalities for immune-mediated diseases: A preliminary review

Immune‐mediated diseases (IMDs) are chronic conditions that have an immune‐mediated etiology. Clinically, these diseases appear to be unrelated, but pathogenic pathways have been shown to connect them. While inflammation is a common occurrence in the body, it may either stimulate a favorable immune response to protect against harmful signals or cause illness by damaging cells and tissues. Nanomedicine has tremendous promise for regulating inflammation and treating IMIDs. Various nanoparticles coated with nanotherapeutics have been recently fabricated for effective targeted delivery to inflammatory tissues. RNA interference (RNAi) offers a tremendous genetic approach, particularly if traditional treatments are ineffective against IMDs. In cells, several signaling pathways can be suppressed by using RNAi, which blocks the expression of particular messenger RNAs. Using this molecular approach, the undesirable effects of anti‐inflammatory medications can be reduced. Still, there are many problems with using short‐interfering RNAs (siRNAs) to treat IMDs, including poor localization of the siRNAs in target tissues, unstable gene expression, and quick removal from the blood. Nanotherapeutics have been widely used in designing siRNA‐based carriers because of the restricted therapy options for IMIDs. In this review, we have discussed recent trends in the fabrication of siRNA nanodelivery systems, including lipid‐based siRNA nanocarriers, liposomes, and cationic lipids, stable nucleic acid‐lipid particles, polymeric‐based siRNA nanocarriers, polyethylenimine (PEI)‐based nanosystems, chitosan‐based nanoformulations, inorganic material‐based siRNA nanocarriers, and hybrid‐based delivery systems. We have also introduced novel siRNA‐based nanocarriers to control IMIDs, such as pulmonary inflammation, psoriasis, inflammatory bowel disease, ulcerative colitis, rheumatoid arthritis, etc. This study will pave the way for new avenues of research into the diagnosis and treatment of IMDs.

Binding between an amine cationic surfactant and DNA and surface properties of the resultant aggregates

Binding between cetyltrimethylammonium bromide, a cationic surfactant, and a variety of lengths of single stranded DNA was measured using fluorescence polarization and a simple cooperative model was used to obtain dissociation constants on the order of 1 × 10^-5 for the aggregates that formed. Aggregation depended on strand length where strands much shorter than 40 nucleotides (for example strands of 24-nucleotides) were too short to form the same size aggregates. Other factors such as salt concentration and temperature also affected aggregate formation: increasing either the salt concentration or performing binding at the highest temperature studied (60 °C) made it more difficult for aggregates to form. Both heating and dilution of aggregates caused the anisotropy signal to decrease, which suggested that the complexes fell apart under these conditions. Force spectroscopy of aggregate surfaces showed that both electrostatic and hydrophobic adhesive forces were present between aggregates and derivatized AFM tips. These findings can be used to better understand the stability of cationic surfactant-DNA aggregates and may provide guidance for lipid nanoparticle design used in vaccine development and therapeutics.

Lipid-Nucleic Acid Complexes: Physicochemical Aspects and Prospects for Cancer Treatment

Cancer is an extremely complex disease, typically caused by mutations in cancer-critical genes. By delivering therapeutic nucleic acids (NAs) to patients, gene therapy offers the possibility to supplement, repair or silence such faulty genes or to stimulate their immune system to fight the disease. While the challenges of gene therapy for cancer are significant, the latter approach (a type of immunotherapy) starts showing promising results in early-stage clinical trials. One important advantage of NA-based cancer therapies over synthetic drugs and protein treatments is the prospect of a more universal approach to designing therapies. Designing NAs with different sequences, for different targets, can be achieved by using the same technologies. This versatility and scalability of NA drug design and production on demand open the way for more efficient, affordable and personalized cancer treatments in the future. However, the delivery of exogenous therapeutic NAs into the patients’ targeted cells is also challenging. Membrane-type lipids exhibiting permanent or transient cationic character have been shown to associate with NAs (anionic), forming nanosized lipid-NA complexes. These complexes form a wide variety of nanostructures, depending on the global formulation composition and properties of the lipids and NAs. Importantly, these different lipid-NA nanostructures interact with cells via different mechanisms and their therapeutic potential can be optimized to promising levels in vitro. The complexes are also highly customizable in terms of surface charge and functionalization to allow a wide range of targeting and smart-release properties. Most importantly, these synthetic particles offer possibilities for scaling-up and affordability for the population at large. Hence, the versatility and scalability of these particles seem ideal to accommodate the versatility that NA therapies offer. While in vivo efficiency of lipid-NA complexes is still poor in most cases, the advances achieved in the last three decades are significant and very recently a lipid-based gene therapy medicine was approved for the first time (for treatment of hereditary transthyretin amyloidosis). Although the path to achieve efficient NA-delivery in cancer therapy is still long and tenuous, these advances set a new hope for more treatments in the future. In this review, we attempt to cover the most important biophysical and physicochemical aspects of non-viral lipid-based gene therapy formulations, with a perspective on future cancer treatments in mind.

Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment

Nucleic acid-based technologies are an emerging research focus area for pharmacological and biological studies because they are biocompatible and can be designed to produce a variety of scaffolds at the nanometer scale. The use of nucleic acids (ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) as building materials in programming the assemblies and their further functionalization has recently established a new exciting field of RNA and DNA nanotechnology, which have both already produced a variety of different functional nanostructures and nanodevices. It is evident that the resultant architectures require detailed structural and functional characterization and that a variety of technical approaches must be employed to promote the development of the emerging fields. Small-angle X-ray and neutron scattering (SAS) are structural characterization techniques that are well placed to determine the conformation of nucleic acid nanoparticles (NANPs) under varying solution conditions, thus allowing for the optimization of their design. SAS experiments provide information on the overall shapes and particle dimensions of macromolecules and are ideal for following conformational changes of the molecular ensemble as it behaves in solution. In addition, the inherent differences in the neutron scattering of nucleic acids, lipids, and proteins, as well as the different neutron scattering properties of the isotopes of hydrogen, combined with the ability to uniformly label biological macromolecules with deuterium, allow one to characterize the conformations and relative dispositions of the individual components within an assembly of biomolecules. This article will review the application of SAS methods and provide a summary of their successful utilization in the emerging field of NANP technology to date, as well as share our vision on its use in complementing a broad suite of structural characterization tools with some simulated results that have never been shared before.

Cucurbit[8]uril-based supramolecular polymer nanocapsules as an effective siRNA delivery platform for gene therapy

An effective siRNA delivery platform was constructed by supramolecular self-assembly to achieve enhanced transfection efficiency and the gene silencing effect.

Microfluidic self-assembly of folate-targeted monomolecular siRNA-lipid nanoparticles

Non-viral delivery of nucleic acids for therapies based on RNA interference requires a rational design and optimal self-assembly strategies. Nucleic acid particles need to be small, stable and functional in terms of selective cell uptake and controlled release of encapsulated nucleic acids. Here we report on small (∼38 nm) monomolecular nucleic acid/lipid particles (mNALPs) that contain single molecules of short double-stranded oligonucleotides covered by a tight, highly curved lipid bilayer. The particles consist of DOPE, DOTAP, DOPC and DSPE-PEG(2000) and are assembled with 21 bp double-stranded DNA or small interfering RNA by solvent exchange on a hydrodynamic-focusing microfluidic chip. In comparison to vortex mixing by hand this method increases the encapsulation efficiency by 20%, and yields particles with a narrower size distribution, negligible aggregate formation and high stability in blood plasma and serum. Modification of mNALPs with folate-conjugated PEG-lipids results in specific binding and uptake by epithelial carcinoma KB cells overexpressing folate receptors. Binding is significantly reduced by competitive inhibition using free folate and is not observed with non-targeted mNALPs, revealing high specificity. The functionalized mNALPs show gene silencing in the presence of chloroquine, an endosome-destabilizing agent. Together, the robust self-assembly of small-sized mNALPs with their high stability and receptor-specific cell uptake demonstrate that the tight, PEG-grafted lipid-bilayer encapsulation may offer a promising approach towards the delivery of short double-stranded oligonucleotides.

Controllable Acoustic Mixing of Fluids in Microchannels for the Fabrication of Therapeutic Nanoparticles

Fifteen years ago, surface acoustic waves (SAW) were found to be able to drive fluids and numerous applications in microfluidics have been developed since. Here, we review the progress made and report on new approaches in setting-up microfluidic, continuous flow acoustic mixing. In a microchannel, chaotic advection is achieved by generation of a SAW driven fluid jet perpendicular to the mean flow direction. Using a high speed video camera and particle image velocimetry, we measure the flow velocities and show that mixing is achieved in a particularly controllable and fast way. The mixing quality is determined as a function of system parameters: SAW power, volume flux and fluid viscosity. Exploring the parameter space of mixing provides a practical guide for acoustic mixing in microchannels and allows for adopting conditions to different solvents, as e.g., required for the generation of nanoscale particles from alcoholic phases. We exemplarily demonstrate the potential of SAW based continuous flow mixing for the production of therapeutic nucleic acid nanoparticles assembled from polymer and lipid solutions.

On-chip controlled surfactant-DNA coil-globule transition by rapid solvent exchange using hydrodynamic flow focusing

This paper presents a microfluidic method for precise control of the size and polydispersity of surfactant-DNA nanoparticles. A mixture of surfactant and DNA dispersed in 35% ethanol is focused between two streams of pure water in a microfluidic channel. As a result, a rapid change of solvent quality takes place in the central stream, and the surfactant-bound DNA molecules undergo a fast coil-globule transition. By adjusting the concentrations of DNA and surfactant, fine-tuning of the nanoparticle size, down to a hydrodynamic diameter of 70 nm with a polydispersity index below 0.2, can be achieved with a good reproducibility.

Biocompatible, chimeric peptide-condensed supramolecular nanoparticles for tumor cell-specific siRNA delivery and gene silencing

A practical and tumor cell-specific siRNA delivery system was developedviasingle-step self-assembly of an arginine-rich chimeric peptide with siRNA.

Lipid-based nanoparticles in the systemic delivery of siRNA

RNAi therapeutics are believed to be the future of personalized medicine and have shown promise in early clinical trials. However, many physiological barriers exist in the systemic delivery of siRNAs to the cytoplasm of targeted cells to perform their function. To overcome these barriers, many siRNA delivery systems have been developed. Among these, lipid-based nanoparticles have great potential owing to their biocompatibility and low toxicity in comparison with inorganic nanoparticles and viral systems. This review discusses the hurdles of systemic siRNA delivery and highlights the recent progress made in lipid-based nanoparticles, which are categorized based on their key lipid components, including cationic lipid, lipoprotein, lipidoid, neutral lipid and anionic lipid-based nanoparticles. It is expected that these lipid nanoparticle-based siRNA delivery systems will have an enabling role for personalized cancer medicine, where siRNA delivery will join forces with genetic profiling of individual patients to achieve the best treatment outcome.

Precisely tunable engineering of sub-30 nm monodisperse oligonucleotide nanoparticles

Advancement of RNAi therapies is mainly hindered by the development of efficient delivery vehicles. The ability to create small size (<30 nm) oligonucleotide nanoparticles is essential for many aspects of the delivery process but is often overlooked. In this report, we describe diblock star polymers that can reproducibly complex double-stranded oligonucleotides into monodisperse nanoparticles with 15, 23, or 30 nm in diameter. The polymer-nucleic acid nanoparticles have a core-shell architecture with dense PEG brush coating. We characterized these nanoparticles using ITC, DLS, FRET, FCS, TIRF, and TEM. In addition to small size, these nanoparticles have neutral zeta-potentials, making the presented polymer architecture a very attractive platform for investigation of yet poorly studied polyplex size range for siRNA and antisense oligonucleotide delivery applications.

Nucleic acid nanostructures for biomedical applications

We review the current developments of DNA-based nanostructures for drug delivery, immunotherapy, diagnostics and molecular biology. DNA is a powerful building block, which by the nature of predictable base pairing, allows the creation of molecular scaffolds, cages and multifunctional carriers with nanoscale dimensions. These engineered constructs have unsurpassed structural qualities such as full control over size, shape and dispersity. Site-specific surface modification enables the presentation of biomolecules at defined distances and stochiometries, which allows tailored cell targeting and substance delivery on demand. As the first successful in vivo applications of DNA nanostructures have recently been demonstrated, we now expect a burst of biomedical studies involving this rapidly progressing technology.

Nucleation in mesoscopic systems under transient conditions: peptide-induced pore formation in vesicles

Attachment of lytic peptides to the lipid membrane of virions or bacteria is often accompanied by their aggregation and pore formation, resulting eventually in membrane rupture and pathogen neutralization. The membrane rupture may occur gradually via formation of many pores or abruptly after the formation of the first pore. In academic studies, this process is observed during interaction of peptides with lipid vesicles. We present an analytical model and the corresponding Monte Carlo simulations focused on the pore formation in such situations. Specifically, we calculate the time of the first nucleation-limited pore-formation event and show the distribution of this time in the regime when the fluctuations of the number of peptides attached to a vesicle are appreciable. The results obtained are used to clarify the mechanism of the pore formation and membrane destabilization observed recently during interaction of highly active α-helical peptide with sub-100-nm lipid vesicles that mimic enveloped viruses with nanoscale membrane curvature. The model proposed and the analysis presented are generic and may be applicable to other meso- and nanosystems.