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

Abstract

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.