DNA-Polyelectrolyte Complexation Study: The Effect of Polyion Charge Density and Chemical Nature of the Counterions

Complexation of Poly(ethylene glycol)-(ds)OligoDNA Conjugates with Ionic Liquids

We report the complexation of poly(ethylene glycol) conjugated double-stranded oligoDNA (PEG-(ds)oligoDNA) with imidazolium-based ionic liquids (ILs) to form polyelectrolyte complex aggregates (PCAs). The PEG-(ds)oligoDNA conjugates are prepared following a solution-phase coupling reaction. The binding of PEG-(ds)oligoDNA with either 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) or 1-hexyl-3-methylimidazolium tetrafluoroborate ([HMIM][BF4]) is confirmed by a fluorescence displacement assay. Both ILs show stronger binding affinity to PEG-(ds)oligoDNA than bare (ds)oligoDNA due to the PEG-assisted increase in IL cation concentration in the vicinity of (ds)oligoDNA. The complex morphology formed at various amine (N) to phosphate (P) ratios is also examined. At high N/P ratios above 4, nanosized PCAs are formed, driven by a counterion-mediated attraction among the IL-bound (ds)oligoDNA segments and stabilized by the conjugated PEG segments. The PCAs exhibit near-neutral surface charges and resistance to DNase degradation, suggesting their potential use in gene delivery applications.

Ionic mononuclear [Fe] and heterodinuclear [Fe,Ru] bis(diphenylphosphino)alkane complexes: Synthesis, spectroscopy, DFT structures, cytotoxicity, and biomolecular interactions

Iron(II) and Ru(II) half-sandwich compounds encompass some promising pre-clinical anticancer agents whose efficacy may be tuned by structural modification of the coordinated ligands. Here, we combine two such bioactive metal centres in cationic bis(diphenylphosphino)alkane-bridged heterodinuclear [Fe²⁺, Ru²⁺] complexes to delineate how ligand structural variations modulate compound cytotoxicity. Specifically, Fe(II) complexes of the type [(η⁵-C₅H₅)Fe(CO)₂(κ¹-PPh₂(CH₂)_nPPh₂)]{PF₆} (n = 1-5), compounds 1-5, and heterodinuclear [Fe²⁺, Ru²⁺] complexes, [(η⁵-C₅H₅)Fe(CO)₂(μ-PPh₂(CH₂)_nPPh₂))(η⁶-p-cymene)RuCl₂]{PF₆} (n = 2-5) (compounds 7-10), were synthesized and characterised. The mononuclear complexes were moderately cytotoxic against two ovarian cancer cell lines (A2780 and cisplatin resistant A2780cis) with IC₅₀ values ranging from 2.3 ± 0.5 μM to 9.0 ± 1.4 μM. For 7-10, the cytotoxicity increased with increasing Fe⋅⋅⋅Ru distance, consistent with their DNA affinity. UV-visible spectroscopy suggested the chloride ligands in heterodinuclear 8-10 undergo stepwise substitution by water on the timescale of the DNA interaction experiments, probably affording the species [RuCl(OH₂)(η⁶-p-cymene)(PRPh₂)]²⁺ and [Ru(OH)(OH₂)(η⁶-p-cymene)(PRPh₂)]²⁺ (where PRPh₂ has R = [-(CH₂)₅PPh₂-Fe(C₅H₅)(CO)₂]⁺). One interpretation of the combined DNA-interaction and kinetic data is that the mono(aqua) complex may interact with dsDNA through nucleobase coordination. Heterodinuclear 10 reacts with glutathione (GSH) to form stable mono- and bis(thiolate) adducts, 10-SG and 10-SG₂, with no evidence of metal ion reduction (k₁ = 1.07 ± 0.17 × 10^-1 min^-1 and k₂ = 6.04 ± 0.59 × 10^-3 min^-1 at 37 °C). This work highlights the synergistic effect of the Fe²⁺/Ru²⁺ centres on both the cytotoxicity and biomolecular interactions of the present heterodinuclear complexes.

In silico study of PEI-PEG-squalene-dsDNA polyplex formation: the delicate role of the PEG length in the binding of PEI to DNA

Biocompatible hydrophilic polyethylene glycol (PEG) is widely used in biomedical applications, such as drug or gene delivery, tissue engineering or as an antifouling component in biomedical devices. Experimental studies have shown that the size of PEG can weaken polycation-polyanion interactions, like those between branched polyethyleneimine (b-PEI) and DNA in gene carriers, but details of its cause and underlying interactions on the atomic scale are still not clear. To better understand the interaction mechanisms in the formation of polyplexes between b-PEI-PEG based carriers and DNA, we have used a combination of in silico tools and experiments on three multicomponent systems differing in PEG MW. Using the PEI-PEG-squalene-dsDNA systems of the same size, both in the all-atom MD simulations and in experimental in-gel electrophoresis measurements, we found that the binding between DNA and the vectors is highly influenced by the size of PEG, with the binding efficiency increasing with a shorter PEG length. The mechanism of how PEG interferes with the binding between PEI and DNA is explained using a two-step MD simulation protocol that showed that the DNA-vector interactions are influenced by the PEG length due to the hydrogen bond formation between PEI and PEG. Although computationally demanding we find it important to study molecular systems of the same size both in silico and in a laboratory and to simulate the behaviour of the carrier prior to the addition of bioactive molecules to understand the molecular mechanisms involved in the formation of the polyplex.

Polymeric Delivery of Therapeutic Nucleic Acids

The advent of genome editing has transformed the therapeutic landscape for several debilitating diseases, and the clinical outlook for gene therapeutics has never been more promising. The therapeutic potential of nucleic acids has been limited by a reliance on engineered viral vectors for delivery. Chemically defined polymers can remediate technological, regulatory, and clinical challenges associated with viral modes of gene delivery. Because of their scalability, versatility, and exquisite tunability, polymers are ideal biomaterial platforms for delivering nucleic acid payloads efficiently while minimizing immune response and cellular toxicity. While polymeric gene delivery has progressed significantly in the past four decades, clinical translation of polymeric vehicles faces several formidable challenges. The aim of our Account is to illustrate diverse concepts in designing polymeric vectors towards meeting therapeutic goals of in vivo and ex vivo gene therapy. Here, we highlight several classes of polymers employed in gene delivery and summarize the recent work on understanding the contributions of chemical and architectural design parameters. We touch upon characterization methods used to visualize and understand events transpiring at the interfaces between polymer, nucleic acids, and the physiological environment. We conclude that interdisciplinary approaches and methodologies motivated by fundamental questions are key to designing high-performing polymeric vehicles for gene therapy.

Interaction of Ionenes with Lipid Membrane: Unusual Impact of Charge Density

Synthetic water-soluble polymers are increasingly used for gene delivery, stabilization, and delivery of proteins, and as prospective antimicrobial and antiviral agents. Therefore, study of their interaction with lipid membranes is of special importance. Herein, we studied interaction of aliphatic cationic ionenes (recently tested for gene delivery efficiency) differed in the length of spacer between charged groups (and therefore in charge density) with anionic lipid membrane. A range of approaches such as measurement of particle size and electrophoretic mobility, liposome integrity, ATR-FTIR spectroscopy, isothermal titration calorimetry as well as atomistic molecular modeling was used. Ionene with a spacer of 10 methylene groups has been shown to be incorporated into membrane and interact with its inner hydrophobic part in contrast to ionenes with shorter spacer, which interacted only with outer polar head groups of lipids staying at the water-membrane interface. It affects membrane integrity and results in a different behavior of the polymer-liposome complexes. These findings are relevant for potential biomedical application of ionenes, including creation of composite polymer-liposome systems for drug delivery.

Recent Advances in Hybrid Biomimetic Polymer-Based Films: from Assembly to Applications

Biological membranes, in addition to being a cell boundary, can host a variety of proteins that are involved in different biological functions, including selective nutrient transport, signal transduction, inter- and intra-cellular communication, and cell-cell recognition. Due to their extreme complexity, there has been an increasing interest in developing model membrane systems of controlled properties based on combinations of polymers and different biomacromolecules, i.e., polymer-based hybrid films. In this review, we have highlighted recent advances in the development and applications of hybrid biomimetic planar systems based on different polymeric species. We have focused in particular on hybrid films based on (i) polyelectrolytes, (ii) polymer brushes, as well as (iii) tethers and cushions formed from synthetic polymers, and (iv) block copolymers and their combinations with biomacromolecules, such as lipids, proteins, enzymes, biopolymers, and chosen nanoparticles. In this respect, multiple approaches to the synthesis, characterization, and processing of such hybrid films have been presented. The review has further exemplified their bioengineering, biomedical, and environmental applications, in dependence on the composition and properties of the respective hybrids. We believed that this comprehensive review would be of interest to both the specialists in the field of biomimicry as well as persons entering the field.

Critical Assessment of the Interaction between DNA and Choline Amino Acid Ionic Liquids: Evidences of Multimodal Binding and Stability Enhancement

Long-term storage and stability of DNA is of paramount importance in biomedical applications. Ever since the emergence of ionic liquids (ILs) as alternate green solvents to aqueous and organic solvents, their exploration for the extraction and application of DNA need conscientious understanding of the binding characteristics and molecular interactions between IL and DNA. Choline amino acid ILs (CAAILs) in this regard seem to be promising due to their non-cytotoxic, completely biobased and environment-friendly nature. To unravel the key factors for the strength and binding mechanism of CAAILs with DNA, various spectroscopic techniques, molecular docking, and molecular dynamics simulations were employed in this work. UV-Vis spectra indicate multimodal binding of CAAILs with DNA, whereas dye displacement studies through fluorescence emission confirm the intrusion of IL molecules into the minor groove of DNA. Circular dichorism spectra show that DNA retains its native B-conformation in CAAILs. Both isothermal titration calorimetry and molecular docking studies provide an estimate of the binding affinity of DNA with CAAILs ≈ 4 kcal/mol. The heterogeneity in binding modes of CAAIL-DNA system with evolution of time was established by molecular dynamics simulations. Choline cation while approaching DNA first binds at surface through electrostatic interactions, whereas a stronger binding at minor groove occurs via van der Waals and hydrophobic interactions irrespective of anions considered in this study. We hope this result can encourage and guide the researchers in designing new bio-ILs for biomolecular studies in future.

Structure optimization of dendritic lipopeptide based gene vectors with the assistance from molecular dynamic simulation

Disulfide modified lipopeptide assemblies with an arginine-rich dendritic periphery provide a promising platform for effective gene transfer. Dendritic arginine peptides that mimic the cell-penetrating peptides of a virus envelope are vital for complexation, interaction with physical barriers, and final gene release. Here, we report three lipopeptides with different-generation dendritic peripheries (R₁LS, R₂LS and R₃LS), each of which contains a dioleoyl-l-lysinate hydrophobic tail. Such molecules were proven to self-assemble in aqueous solution with different morphologies, sizes, and surface zeta potentials. R₂LS and R₃LS assemblies showed spherical and spindle shapes with zeta potentials of 27.2 and 32.8 mV, respectively. They exhibited complete condensation of pDNA at a low N/P ratio, while R₁LS assemblies displayed a fiber pattern with a relatively low electric potential of 10.9 mV with poor DNA binding ability. In a cellular viability experiment, R₁LS and R₂LS have no significant cytotoxicity even at high dosage, while R₃LS showed conspicuous toxicity. As a gene vector, R₂LS presented high gene transfection efficiency either in the presence or the absence of serum, which was 58.7% greater than liposome 2000 and PEI in the condition of 10% fetal bovine serum for HeLa cells. While R₃LS showed good results just without serum and R₁LS was unserviceable in all situations. Moreover, molecular dynamic simulation was exploited to analyze the kinestate of the signal molecule and the interactions of multiple molecules, which could assist us in better understanding the experimental phenomena. The simulation results indicated that the R₂LS molecule has better flexibility, which was favorable for interaction with the cell membrane. And it could generate tight integration in self-assembly while R₁LS and R₃LS assemblies have a large molecular interval, which led to a controllable release of cargos for R₂LS in a reductive environment. In summary, the generation of the dendrimer in lipopeptides is vital for the gene transfer effect. For optimization, it is necessary to study the structure-function relationship, and molecular dynamic simulation is an effective strategy for screening the molecular structure and even for predicting experimental results.

Role of Associative Charging in the Entropy-Energy Balance of Polyelectrolyte Complexes

Polyelectrolytes may be classified into two primary categories (strong and weak) depending on how their charge state responds to the local environment. Both of these find use in many applications, including drug delivery, gene therapy, layer-by-layer films, and fabrication of ion filtration membranes. The mechanism of polyelectrolyte complexation is, however, still not completely understood, though experimental investigations suggest that entropy gain due to release of counterions is the key driving force for strong polyelectrolyte complexation. Here we perform a comprehensive thermodynamic investigation through coarse-grained molecular simulations permitting us to calculate the free energy of complex formation. Importantly, our expanded-ensemble methods permit the explicit separation of energetic and entropic contributions to the free energy. Our investigations indicate that entropic contributions indeed dominate the free energy of complex formation for strong polyelectrolytes, but are less important than energetic contributions when weak electrostatic coupling or weak polyelectrolytes are present. Our results provide a new view of the free energy of polyelectrolyte complex formation driven by polymer association, which should also arise in systems with large charge spacings or bulky counterions, both of which act to weaken ion-polymer binding.