DNA Condensation by Peptide-Conjugated PAMAM Dendrimers. Influence of Peptide Charge.

Nucleic acid delivery to cells is an important therapeutic strategy that requires the transport of nucleic acids to intracellular compartments and their protection from enzymatic degradation. This can be achieved through the complexation of the nucleic acids with polycations. Poly(amidoamine) (PAMAM) dendrimers and peptide-conjugated dendrimers have been investigated as delivery vectors.

Efficient DNA Condensation Induced by Chiral β-Amino Acid-Based Cationic Surfactants.

Four cationic chiral amino acid-based surfactants, - and - and - and -, have been studied as DNA-condensing agents with enhanced properties and the absence of cell toxicity. The polar head of the surfactant is made of a cyclobutane β-amino acid in which the amino group is a hydrochloride salt and the carboxyl group is involved in an amide bond, allowing the link with hydrophobic C (surfactant ) or C (surfactant ) chains. The ability of these surfactants to condense DNA was investigated using a dye exclusion assay, gel electrophoresis, and circular dichroism and compared with the well-studied dodecyltrimethylammonium bromide (DTAB) and cetyltrimethylammonium bromide (CTAB).

Influence of macromolecular crowding on the charge regulation of intrinsically disordered proteins.

In this work we study the coupling between ionization and conformational properties of two IDPs, histatin-5 and β-amyloid 42, in the presence of neutral and charged crowders. The latter is modeled to resemble bovine serum albumin (BSA). With this aim, semi-grand canonical Monte Carlo simulations are performed, so that the IDP charge is a dynamic property, undergoing protonation/deprotonation processes.

Role of Protein Self-Association on DNA Condensation and Nucleoid Stability in a Bacterial Cell Model.

Bacterial cells do not have a nuclear membrane that encompasses and isolates the genetic material. In addition, they do not possess histone proteins, which are responsible for the first levels of genome condensation in eukaryotes. Instead, there is a number of more or less specific nucleoid-associated proteins that induce DNA bridging, wrapping and bending.

Nanoparticle-Hydrogel Composites: From Molecular Interactions to Macroscopic Behavior.

Hydrogels are materials used in a variety of applications, ranging from tissue engineering to drug delivery. The incorporation of nanoparticles to yield composite hydrogels has gained substantial momentum over the years since these afford tailor-making and extend material mechanical properties far beyond those achievable through molecular design of the network component. Here, we review different procedures that have been used to integrate nanoparticles into hydrogels; the types of interactions acting between polymers and nanoparticles; and how these underpin the improved mechanical and optical properties of the gels, including the self-healing ability of these composite gels, as well as serving as the basis for future development.

pH-Dependent Polyelectrolyte Bridging of Charged Nanoparticles.

Systems comprised of polyelectrolytes and charged nanoparticles are of great technological interest, being common components in formulations among other uses. The colloidal stability of formulations is an important issue, and thus a lot of effort has been made to study the interactions of individual components in these systems. Here, the complexation and adsorption of an annealed (pH-dependent) polyelectrolyte to two spherical nanoparticles has been studied using coarse-grained Monte Carlo simulations.

Adsorption of charged macromolecules upon multicomponent responsive surfaces.

Adsorption of polyions onto charged surfaces has long been recognized as a crucial phenomenon in biological and technological applications. An intuitive model relating polyelectrolyte adsorption with the imposed features of polarizable surfaces of different compositions and charges is proposed based on Monte Carlo simulations using a coarse-grained approach. The excellent performance of the equation allows simultaneously describing a wide range of adsorption regimes and accounting for specific non-monotonic trends.

In vitro studies of DNA condensation by bridging protein in a crowding environment.

The macromolecules of the bacterial cell occupy 20-40% of the total cytosol volume, and crowded environments have long been known to compact and stabilize DNA. Nevertheless, investigations on DNA-protein binding are generally performed in the absence of crowding, which may yield an incomplete understanding of how nucleoid-assembling proteins work. A family of such proteins, abundant in Gram-negative bacteria, is the histone-like nucleoid structuring proteins (H-NS).

Combining polyethylenimine and Fe(III) for mediating pDNA transfection.

Background: The potential use of Fe(III) ions in biomedical applications may predict the interest of its combination with pDNA-PEI polyplexes. The present work aims at assessing the impact of this metal on pDNA complex properties.

Methods: Variations in the formation of complexes were imposed by using two types of biological buffers at different salt conditions.

Complexes formed between DNA and poly(amido amine) dendrimers of different generations--modelling DNA wrapping and penetration.

This study deals with the build-up of biomaterials consisting of biopolymers, namely DNA, and soft particles, poly(amido amine) (PAMAM) dendrimers, and how to model their interactions. We adopted and applied an analytical model to provide further insight into the complexation between DNA (4331 bp) and positively charged PAMAM dendrimers of generations 1, 2, 4, 6 and 8, previously studied experimentally. The theoretical models applied describe the DNA as a semiflexible polyelectrolyte that interacts with dendrimers considered as either hard (impenetrable) spheres or as penetrable and soft spheres.

DNA compaction induced by a cationic polymer or surfactant impact gene expression and DNA degradation.

There is an increasing interest in achieving gene regulation in biotechnological and biomedical applications by using synthetic DNA-binding agents. Most studies have so far focused on synthetic sequence-specific DNA-binding agents. Such approaches are relatively complicated and cost intensive and their level of sophistication is not always required, in particular for biotechnological application.

Interpreting the rich behavior of ternary DNA-PEI-Fe(III) complexes.

This work aims to shed light on the mechanism of interaction between components of ternary DNA-PEI-Fe(III) complexes, using experimental and theoretical approaches. In the experimental part, the chelation between PEI-Fe(III) was inspected by potentiometry and electrical conductance measurements and the respective importance for the condensation of DNA analyzed. To this end, three different mixing protocols for the components were imposed using different PEIs, branched (bPEI1.

Enhanced condensation and facilitated release of DNA using mixed cationic agents: a combined experimental and Monte Carlo study.

Efficient DNA condensation and decondensation, as well as low toxicity, are required for an efficient gene delivery vehicle. We report on the condensation of DNA by a mixture of cationic agents, low-molecular-weight polyethylenimine (PEI, 1.2 KDa) and Fe(III) ions, and respective decondensation, using experimental and theoretical methods.

Effect of the architecture on polyelectrolyte adsorption and condensation at responsive surfaces.

Adsorption profiles and conformational properties of negatively charged polyions at responsive surfaces were investigated by Monte Carlo simulations using a simple coarse-grained model. The surface, carrying both negative and positively charged groups, presents different overall charge, ranging from -10 to +50 e, and states, where the surface groups are either in a liquid-like structure (frozen surface) or laterally mobile (fluid surface). Polyions with both linear and ring architectures are considered.

Kinetic studies of amino acid-based surfactant binding to DNA.

In this work, the binding kinetics of amino acid-based surfactants, presenting different linkers and head groups, with calf thymus (CT)-DNA was studied using stopped-flow fluorescence spectroscopy. The kinetic studies were carried out as a function of Na(+) concentration and surfactant-to-DNA charge ratio. The surfactant binding on DNA took place in two consecutive steps, for which the corresponding first and second relative rate constants (k(1) and k(2)) were determined.

Condensation and decondensation of DNA by cationic surfactant, spermine, or cationic surfactant-cyclodextrin mixtures: macroscopic phase behavior, aggregate properties, and dissolution mechanisms.

The macroscopic phase behavior and other physicochemical properties of dilute aqueous mixtures of DNA and the cationic surfactant hexadecyltrimethylammounium bromide (CTAB), DNA and the polyamine spermine, or DNA, CTAB, and (2-hydroxypropyl)-β-cyclodextrin (2HPβCD) were investigated. When DNA is mixed with CTAB we found, with increasing surfactant concentration, (1) free DNA coexisting with surfactant unimers, (2) free DNA coexisting with aggregates of condensed DNA and CTAB, (3) a miscibility gap where macroscopic phase separation is observed, and (4) positively overcharged aggregates of condensed DNA and CTAB. The presence of a clear solution beyond the miscibility gap cannot be ascribed to self-screening by the charges from the DNA and/or the surfactant; instead, hydrophobic interactions among the surfactants are instrumental for the observed behavior.

DNA condensation by pH-responsive polycations.

This work addresses the impact of pH variation on DNA-polyethylenimine (PEI) complex formation, in aqueous solution and at constant ionic strength. An initial potentiometric characterization of the acid-base behavior of PEI is carried out to measure the concentration of ionized species in the relevant systems. The characterization of the DNA-PEI complexes is performed by precipitation assays, agarose gel electrophoresis, photon correlation spectroscopy, and zeta potential analysis.

Release of DNA from surfactant complexes induced by 2-hydroxypropyl-beta-cyclodextrin.

Decompaction of DNA-CTA self-assembled complexes by 2-hydroxypropyl-beta-cyclodextrin (2-HP-beta-CD) was studied and the results were compared with beta-CD. Different degrees of 2-HP substitution (0.6, 0.

Re-dissolution and de-compaction of DNA-cationic surfactant complexes using non-ionic surfactants.

Addition of a cationic surfactant to a solution of DNA causes the formation of compacted DNA-cationic surfactant complexes which precipitate from aqueous solution. It has been shown previously that addition of anionic surfactant will re-dissolve and de-compact the DNA-cationic surfactant complexes and we find that addition of non-ionic surfactants of the alkylpolyoxyethylene type can be used similarly. In principle, these de-compaction and re-dissolution processes could occur either by stripping of the cationic surfactant from the DNA into mixed micelles with the non-ionic surfactant or by solubilisation of the DNA-cationic surfactant complexes within the non-ionic micelles.

Cyclodextrins in DNA decompaction.

Individual T4DNA molecules, previously compacted by using a cationic surfactant (cetyltrimethylammonium bromide, CTAB), were successfully decompacted by the addition of an appropriate concentration of either alpha-cyclodextrin or beta-cyclodextrin (alpha-CD and beta-CD, respectively) due to the formation of inclusion complexes with the surfactant. The process was shown to be a non first-order transition from globules to coils. Density and sound velocity measurements as well as steady state fluorescence spectroscopy have confirmed the approximate CD concentration at which the globule-to-coil transition occurs.

Role of linker groups between hydrophilic and hydrophobic moieties of cationic surfactants on oligonucleotide-surfactant interactions.

The interaction between DNA and amino-acid-based surfactants with different linker groups was investigated by gel electrophoresis, ethidium bromide exclusion assays, circular dichroism, and melting temperature determinations. The studies showed that the strength of the interaction between the oligonucleotides and the surfactants is highly dependent on the linker of the surfactant. For ester surfactants, no significant interaction was observed for surfactant-to-DNA charge ratios up to 12.

Different strategies for controlling DNA conformation: compaction and decompaction.

In the present review we summarize different strategies to induce DNA compaction and decompaction. DNA compaction is achieved using different cationic co-solutes, such as trivalent ions, surfactant, and polycations. In addition, single-chained DNA compaction can also be achieved in solvents with low dielectric constants and by confinement.

Interaction between DNA and cationic surfactants: effect of DNA conformation and surfactant headgroup.

The interactions between DNA and a number of different cationic surfactants, differing in headgroup polarity, were investigated by electric conductivity measurements and fluorescence microscopy. It was observed that, the critical association concentration (cac), characterizing the onset of surfactant binding to DNA, does not vary significantly with the architecture of the headgroup. However, comparing with the critical micelle concentration (cmc) in the absence of DNA, it can be inferred that the micelles of a surfactant with a simple quaternary ammonium headgroup are much more stabilized by the presence of DNA than those of surfactants with hydroxylated head-groups.

Effect of the head-group geometry of amino acid-based cationic surfactants on interaction with plasmid DNA.

The interaction between DNA and different types of amino acid-based cationic surfactants was investigated. Particular attention was directed to determine the extent of influence of surfactant head-group geometry toward tuning the interaction behavior of these surfactants with DNA. An overview is obtained by gel retardation assay, isothermal titration calorimetry, fluorescence spectroscopy, and circular dichroism at different mole ratios of surfactant/DNA; also, cell viability was assessed.

Cationic agents for DNA compaction.

Fluorescence microscopy was used to investigate the conformational changes of individual T4 DNA molecules induced by different compacting agents, namely the cationic surfactants, cetyltrimethylammonium bromide (CTAB) and chloride (CTAC), iron(III), lysozyme, and protamine sulfate. A protocol for establishing size estimates is suggested to obtain reproducible results. Observations show that in the presence of lysozyme and protamine sulfate, DNA molecules exhibit a conformational change from an elongated coil structure to compact globules, usually interpreted as a first-order transition.