Change in flexibility of DNA with binding ligands

Abstract

The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force spectroscopy technique shows different interaction modes by measuring the mechanical properties of DNA bound with small ligands. When a ds-DNA molecule is overstretched in the presence of ligands, it undergoes a co-operative structural transition based on the externally applied force, the mode of binding of the ligands, the binding constant of the ligands to the DNA, the concentration of the ligands and the ionic strength of the supporting medium. This leads to the changes in the regions- upto 60 pN, cooperative structural transition region and the overstretched region, compared to that of the FEC in the absence of any binding ligand. The cooperative structural transitions were studied by the extended and twistable worm-like chain model. Here we have depicted these changes in persistence length and the elastic modulus constant as a function of binding constant and the concentration of the bound ligands, which vary with time. Therefore, besides ionic strength, interacting proteins and content of AT and GC base pairs, the ligand binding or intercalation with the ligands is an important parameter which changes the stiffness of DNA.