Local rigidification and possible coacervation of the Escherichia coli DNA by cationic nylon-3 polymers

Synthetic, cationic random nylon-3 polymers (3-peptides) show promise as inexpensive antimicrobial agents less susceptible to proteolysis than normal peptides. We have used superresolution, single-cell, time-lapse fluorescence microscopy to compare the effects on live Escherichia coli cells of four such polymers and the natural antimicrobial peptides LL-37 and cecropin A. The longer, densely charged monomethyl-cyclohexyl (MM-CH) copolymer and MM homopolymer rapidly traverse the outer membrane and the cytoplasmic membrane. Over the next similar to 5 min, they locally rigidify the chromosomal DNA and slow the diffusive motion of ribosomal species to a degree comparable to LL-37. The shorter dimethyl-dimethylcyclopentyl (DM-DMCP) and dimethyl-dimethylcyclohexyl (DM-DMCH) copolymers, and cecropin A are significantly less effective at rigidifying DNA. Diffusion of the DNA-binding protein HU and of ribosomal species is hindered as well. The results suggest that charge density and contour length are important parameters governing these antimicrobial effects. The data corroborate a model in which agents having sufficient cationic charge distributed across molecular contour lengths comparable to local DNA-DNA interstrand spacings (similar to 6 nm) form a dense network of multivalent, electrostatic "pseudo-cross-links" that cause the local rigidification. In addition, at times longer than similar to 30 min, we observe that the MM-CH copolymer and the MM homopolymer (but not the other four agents) cause gradual coalescence of the two nucleoid lobes into a single dense lobe localized at one end of the cell. We speculate that this process involves coacervation of the DNA by the cationic polymer, and may be related to the liquid droplet coacervates observed in eukaryotic cells.