Cationic dendrimers are promising vectors for nonviral gene therapies due to their well-defined size and chemistry. We have synthesized a series of succinylated fourth generation (G4) PAMAM dendrimers to control the DNA packaging in dendriplexes, allowing us to probe the role of charge on DNA packaging. The self-assembly of DNA induced by these zwitterionic PAMAM (zPAMAM) was investigated using small-angle X-ray scattering (SAXS). We demonstrate that changing the degree of modification in zPAMAM–DNA significantly alters the packing density of the resulting dendriplexes. Salt sensitivities and pH dependence on the inter-DNA spacing were also examined. The swelling and stability to salt are reduced with increasing degree of PAMAM modification. Lowering the pH leads to significantly tighter hexagonal DNA packaging. In combination, these results show zPAMAM is an effective means to modulate nucleic acid packaging in a deterministic manner.

Short arginine-rich proteins called protamines mediate the near crystalline DNA packaging in most vertebrate sperm cells. Protamines are synthesized during spermiogenesis and condense the paternal genome into a transcriptionally inactive state in late-stage spermatids. Protamines from eutherian mammals, including bulls and humans, also contain multiple cysteine residues that form intra- and interprotamine sulfur-sulfur bonds during the final stages of sperm maturation. Although the cross-linked protamine network is known to stabilize the resulting nucleoprotamine structure, little is known about the role of disulfide bonds on DNA condensation in the mammalian sperm. Using small angle x-ray scattering, we show that isolated bull nuclei achieve slightly lower DNA packing densities compared to salmon nuclei despite salmon protamine lacking cysteine residues. Surprisingly, reduction of the intermolecular sulfur-sulfur bonds of bull protamine results in tighter DNA packing. Complete reduction of the intraprotamine disulfide bonds ultimately leads to decondensation, suggesting that disulfide-mediated secondary structure is also critical for proper protamine function. Lastly, comparison of multiple bull collections showed some to have aberrant x-ray scattering profiles consistent with incorrect disulfide bond formation. Together, these observations shed light on the biological functions of disulfide linkages for in vivo DNA packaging in sperm chromatin.

Cationic polymers are capable of spontaneously condensing DNA into complexes suitable for nonviral gene therapy. The precisely defined molecular weights and highly symmetric surface chemistries of dendrimers, such as poly(amidoamine) (PAMAM), have made them attractive alternatives to conventional linear polymers for DNA delivery applications. In this paper, we use small-angle X-ray scattering (SAXS) coupled with osmotic stress to directly measure the effect of pH on the packaging and forces in low generation (G0 and G1) PAMAM–DNA complexes or dendriplexes. Because of the presence of both primary and tertiary amines with differing pKas, PAMAM changes its net charge with pH. We show that changing the pH at condensation results in large differences in the packaging and intermolecular forces in PAMAM dendriplexes. Both dendrimer/DNA systems show a large increase in attractions with decreasing pH scaling linearly with the inverse of the dendrimer charge, while repulsions in the system are nearly unaffected. pH also greatly influences the resulting phase behavior and salt sensitivities of the PAMAM–DNA complexes. With increasing salt concentration, a discontinuous phase transition is observed from a hexagonal packaging of DNA helices to a more loosely ordered cholesteric phase for both PAMAM dendriplex systems studied. The phase transition occurs at a critical salt concentration, c*, that is dependent on both the PAMAM generation number and the pH. When normalized by c*, this salt-induced melting transition is found to be universal for a given dendrimer/DNA system.

Using osmotic stress coupled with X-ray scattering, we have directly examined the salt sensitivity of the intermolecular forces between helices in condensed protamine–DNA arrays. Thermodynamic forces are measured from the dependence of DNA helical interaxial spacings on external salt concentration or the osmotic pressure applied by neutral polymer solutions in equilibrium with the condensed phase. Force curves of salmon protamine–DNA condensates are highly dependent on salt species and concentration, indicating salt binding to protamine–DNA complexes. This dependence of the forces on salt species follows the Hofmeister series for anions. Chaotropic anions bind more tightly to protamine–DNA arrays than kosmotropic anions, thus more greatly disrupting the attractive thermodynamic forces. Variations with cation type are small compared with those observed for anions. Further, osmotic stress is used to estimate the number of ions bound in the condensed phase through a Gibbs–Duhem relationship. We estimate that at equilibrium, ∼1 Br– is bound per protamine molecule at 200 mM NaBr concentration. Remarkably, this one bound anion results in a change of ∼12% in the surface-to-surface distance between DNA helices. Potential biological implications of this attractive force salt sensitivity are discussed.

Transport processes within biological polymer networks, including mucus and the extracellular matrix, play an important role in the human body, where they serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate diffusive processes through finely tuned particle-network interactions. In this work, we present experimental and theoretical studies to examine the role of electrostatics on the basic mechanisms governing the diffusion of charged probe molecules inside model polymer networks. Translational diffusion coefficients are determined by fluorescence correlation spectroscopy measurements for probe molecules in uncharged as well as cationic and anionic polymer solutions. We show that particle transport in the charged hydrogels is highly asymmetric, with diffusion slowed down much more by electrostatic attraction than by repulsion, and that the filtering capability of the gel is sensitive to the solution ionic strength. Brownian dynamics simulations of a simple model are used to examine key parameters, including interaction strength and interaction range within the model networks. Simulations, which are in quantitative agreement with our experiments, reveal the charge asymmetry to be due to the sticking of particles at the vertices of the oppositely charged polymer networks.

Understanding the strength and specificity of interactions among biologically important macromolecules that control cellular functions requires quantitative knowledge of intermolecular forces. Controlled DNA condensation and assembly are particularly critical for biology, with separate repulsive and attractive intermolecular forces determining the extent of DNA compaction. How these forces depend on the charge of the condensing ion has not been determined, but such knowledge is fundamental for understanding the basis of DNA-DNA interactions. Here, we measure DNA force-distance curves for a homologous set of arginine peptides. All forces are well fit as the sum of two exponentials with 2.4- and 4.8-Å decay lengths. The shorter-decay-length force is always repulsive, with an amplitude that varies slightly with length or charge. The longer-decay-length force varies strongly with cation charge, changing from repulsion with Arg1 to attraction with Arg2. Force curves for a series of homologous polyamines and the heterogeneous protein protamine are quite similar, demonstrating the universality of these forces for DNA assembly. Repulsive amplitudes of the shorter-decay-length force are species-dependent but nearly independent of charge within each species. A striking observation was that the attractive force amplitudes for all samples collapse to a single curve, varying linearly with the inverse of the cation charge.