Mechanical Properties of High-G.C Content DNA with A-Type Base-Stacking

The sequence of a DNA molecule is known to influence its secondary structure and flexibility. Using a combination of bulk and single-molecule techniques, we measure the structural and mechanical properties of two DNAs which differ in both sequence and base-stacking arrangement in aqueous buffer, as revealed by circular dichroism: one with 50% G.C content and B-form and the other with 70% G.C content and A-form. Atomic force microscopy measurements reveal that the local A-form structure of the high-G.C DNA does not lead to a global contour-length decrease with respect to that of the molecule in B-form although it affects its persistence length. In the presence of force, however, the stiffness of high-G.C content DNA is similar to that of balanced-G.C DNA as magnetic and optical tweezers measured typical values for the persistence length of both DNA substrates. This indicates that sequence-induced local distortions from the B-form are compromised under tension. Finally, high-G.C DNA is significantly harder to stretch than 50%-G.C DNA as manifested by a larger stretch modulus. Our results show that a local, basepair configuration of DNA induced by high-G.C content influences the stretching elasticity of the polymer but that it does not affect the global, double-helix arrangement.