Binding efficacy and kinetics of chitosan with DNA duplex: The effects of deacetylation degree and nucleotide sequences

Abstract

The binding process of DNA duplex with various types of chitosan polymers were studied at atomic level through molecular dynamics simulations. The interaction kinetics and binding strength, complex morphology and DNA structure evolution were systematically accessed. The binding efficacy of chitosan to DNA reduces (both in complexation speed and binding strength) when deacetylation degree is decreased, because protonated amine groups on chitosan backbone are more prone to bind with DNA, especially the phosphate oxygen, through coulomb interaction. The Watson Crick hydrogen bonds of A-T base pairs are more easily to break because chitosan is capable to form competitive hydrogen bonds with them. It is surprising to find that the G-C nucleotides have highly restrained kinetic motion than that of A-T nucleotides, which would be important for DNA-chitosan complexation and condensation to happen at the microscopic level. From our current results, the degree of chitosan deacetylation is found to play a certain role in regulating the DNA-chitosan complexation process, but is not as important as being believed before. Other types of chemical functionalization that can tune the chitosan’s hydrophobicity should deserve more attentions in the experiment.