Electrostatic forces at helix-coil boundaries in DNA

Abstract

The T_m of internal loop-forming (dA · dT)_N domains in pBR322 DNA has been measured over a tenfold range of [Na⁺]. The slopes S_N = dT_m/d log[Na⁺] are linear and decrease in magnitude with decreasing loop size N, signaling a reduction in Na⁺ released during the transition of these domains to the coil state. Values of S_N decrese linearly with increasing N⁻¹ in accordance with the expectation of a simple model for the occurrence of a gradient of long-range electrostatic forces at helix–coil boundaries, and extrapolate almost precisely to the value of S_∞ observed for (dA · dT)_∞. These results indicate (1) less counterion is released per phosphate residue from the finite loop than from the infinitesized loop, and (2) the difference in binding is constant for each boundary formed and independent of the size of the loop within the range examined: ∼ 350 base pair (bp) > N > 71 bp. The slope of the dependence of S_N on N⁻¹ indicates the region of higher charge density at the boundary extends at least 18 Å into the coil and probably 40–50 Å before dropping to a value characteristic of the unperturbed coil. The free energy for excess counterion binding at boundaries can be expressed by When the loop entropy function in a statistical mechanical algorithm for the dissociation of DNA is weighted by this quantity, calculated T_m are seen to vary by only ±0.09°C from observed.