Quantifying the Effect of Surface Ligands on Dendron–DNA Interactions: Insights into Multivalency through a Combined Experimental and Theoretical Approach

Abstract

We report the synthesis, DNA binding ability and preliminary gene delivery profiles of dendrons with different amine surface groups, 1,3-diaminopropane (DAP), N,N-di-(3-aminopropyl)-N-(methyl)amine (DAPMA) and spermine (SPM). By using a combination of ethidium bromide displacement, gel electrophoresis and transfection assays, it is shown that the dendrons with SPM groups are the most effective DNA binders, while the DAPMA-functionalised dendrons were the most effective systems for gene delivery (although the gene delivery profiles were still modest). In order to provide deeper insight into the experimental data, we performed a molecular dynamics simulation of the interactions between the dendrons and DNA. The results of these simulations demonstrated that, in general terms, the enthalpic contribution to binding was roughly proportional to the dendron surface charge, but that dendrons with DAP (and DAPMA) surface amines had significant entropic costs of binding to DNA. In the case of DAP, this is a consequence of the fact that the entire dendron structure has to be organised in order for each individual monoamine charge to make effective contact with DNA. For SPM, however, each surface ligand is already a multivalent triamine, therefore, each individual charge has a much lower entropic cost of binding. For DAPMA, we observed that strong binding of the hindered tertiary amine to the DNA double helix led to ligand back-folding and significant geometric distortion of DNA. Although this weakens the overall binding, we suggest that this distortion might be an explanation for the experimentally observed enhanced gene delivery, in which DNA compaction is an important step. Overall, this paper demonstrates how structure-activity relationships can be developed for multivalent dendritic ligands and provides insights into the thermodynamics of multivalent interactions.

Double-degradable responsive self-assembled multivalent arrays – temporary nanoscale recognition between dendrons and DNA

“…Importantly, in the absence of any hydrophobic modification, the G2 dendron 65 is incapable of effective DNA binding (data not shown) -and as such, SAMul plays a key role in all of the binding discussed. For the disulfide-linked G2 dendrons, the system with less hydrophobic modification is a more effective DNA binder -this is in agreement with the experimental and simulated zeta 75 potential results (Tables 1 and 2) which indicated that the hydrophobic/hydrophilic balance of Chol-SS-G2 is such that it has a higher surface charge density than Chol 2 -SS-G2. However, it should also be noted that Chol-G2 is better than the degradable dendrons in the EthBr assay, and comparable to the best in gel 80 electrophoresis.…”

“…It was therefore clear from these MS studies that over a 24 hour timescale, all three dendrons degrade via ester hydrolysis and that for Chol 2 -SS-G2 disulfide degradation, enhanced by DTT could also be detected. In combination, these assays demonstrate that rapid disulfide cleavage in the presence of DTT leads to triggered disassembly 75 and loss of SAMul binding of DNA. The products, which have released their grip on DNA, are then able to slowly degrade further into smaller fragments through an ester hydrolysis mechanism, which does not operate if DNA is still bound to the dendrons.…”

Molecular modeling and in vivo imaging can identify successful flexible triazine dendrimer-based siRNA delivery systems

“…To study the multivalent molecular recognition that characterizes the complexation, the binding between siRNA and dendrimers in a 1:1 ratio was modeled according to a validated strategy reported for the binding of dendrons and dendrimers with DNA [26, 27] and siRNA [28]. The structures of F2-2 , F3 and F4–2 were composed of different residues according to previous studies on similar dendrimers [22].…”

Synthesis and characterization of pH-responsive diblock copolymers with cadaverine side groups

“…Polyamines such as putrescine, spermidine, and spermine as well as their derivatives have attracted considerable interest due to their biological functions and pharmacological properties [30][31][32][33][34][35]. Recently, gene delivery, especially that using nonviral synthetic vectors which were based on polyamine block, has attracted considerable interest [36][37][38][39][40][41][42]. The polyamine homopolymer behaves as a weak polybase at higher pH values, whereas at lower pH H. Wang : X. Ren : H. Zhang : Y. Tan values, the amine groups are protonated, and the polymer behaves as a cationic polyelectrolyte.…”