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

Abstract

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.

Condensation Prevails over B-A Transition in the Structure of DNA at Low Humidity

“…However, we did not find any signature of the B-A transition, which should appear as a definite and reproducible change in extension of the molecules. These data strengthen the idea that the overall contour length is not affected by the specific base-stacking arrangement (47), here induced by low humidity, and that condensation prevails over the B-A transition in the global conformation of DNA. The fact that a cooperative B-A shortening was obtained with aggregated molecules under stress (12,(54)(55)(56)(57), and not at the singlemolecule level (this work and (47)), suggests that interhelical interactions may stabilize a global contraction of the molecule promoted by a B-A transition at the basepair level.…”

“…S1, A and B, in the Supporting Material). Our previous experiments with linearized piJ702 DNA (70% G$C) showed A-form CD spectra in aqueous solution due to its high content of G$C basepairs (47). As expected, the A-type CD signal of this DNA is maintained in bufferethanol mixtures of decreasing water activity, because the addition of ethanol increases the stabilization of the A-type base-stacking (see Fig.…”

“…Phasing of A$T dinucleotides was shown to affect the persistence length and rigidity of DNA (53) and our previous experiments based on CD spectra showed that DNA with high G$C content can adopt an A-type base-stacking arrangement. Our work (47), based on measurements of the contour length, showed that high-G$C-content DNA maintains the overall B-form but that the structural differences arising from the nucleotide content affect the persistence length of the molecule at zero force and the stretch modulus at high forces. However, it is not known whether high-G$C-content DNA has a tendency to change its extension in dehydration conditions.…”

“…Constant-force experiments were carried out with magnetic tweezers. The description of these methods is detailed in the accompanying article (47). All experiments were carried out at room temperature, 23 5 1 C.…”

DNA structure and function

“…Not only does the A → B transition affect direct readout, it also changes the physicochemical properties of the polymer. An A‐type double helix is, on average, stiffer than a B‐type double helix and consequently distortion of A‐DNA to a particular bent configuration is energetically less favourable than for the corresponding distortion in B‐DNA . Such differences would be expected to favour B‐DNA as the preferred substrate for packaging involving tight DNA bending.…”