Direct Measurements of Base Stacking Interactions in DNA by Single-Molecule Atomic-Force Spectroscopy

We investigate the elasticity of two types of single-stranded synthetic DNA homopolydeoxynucletides, poly(dA) and poly(dT), by AFM-based single-molecule force spectroscopy. We find that poly(dT) exhibits the expected entropic elasticity behavior, while poly(dA) unexpectedly displays two overstretching transitions in the force-extension relationship. We suggest that these transitions, which occur at $\sim 23\mathrm{pN}$ and $\sim 113\mathrm{pN}$, directly capture, for the first time, the mechanical signature of base-stacking interactions among adenines in DNA, in the absence of base pairing.

Figure 1

Schematic of single-molecule atomic-force microscopy measurements of ssDNA molecules (the figure is not to scale).

Figure 2

(a) three typical force-extension measurement curves for poly(dA), (b) magnified view of the force curve in (a) corresponding to the longest molecule and the comparison between the stretching trace (green, online; gray, in print) and the relaxing trace (black). The inset plot shows the overlapping of six recorded force-extension curves of poly(dA) on a normalized extension basis. These recordings were obtained in different experiments on different poly(dA) molecules.

Figure 3

(a) three typical force-extension measurement curves for poly(dT), (b) comparison between poly(dA) and poly(dT) on a normalized extension basis. We assume that at a force of 600 pN, ssDNA is fully stretched, and the distance between two neighboring phosphates is 0.7 nm.