Effects of stacking on the configurations and elasticity of single-stranded nucleic acids

Stacking interactions in single-stranded nucleic acids give rise to configurations of an annealed rod-coil multiblock copolymer. Theoretical analysis identifies the following resulting signatures for long homopolynucleotides: a nonmonotonic dependence of size on temperature, the corresponding effects on cyclization and a plateau in the extension force law. Explicit numerical results for polydeoxyadenylate [poly(dA)] and polyriboadenylate [poly(rU)] are presented.

Figure 1

Plots of $⟨R^2⟩∕Na=2l_p$ vs $T$ for poly(dA), with $l_p$ given by Eq. (3), exhibit a minimum at $T_{\min }=307\mathrm{K}$ for $\lambda =3.5\mathrm{nm}$ (solid line), $T_{\min }=327\mathrm{K}$ for $\lambda =0.6\mathrm{nm}$ (dashed line) in comparison with $⟨R^2⟩∕Na$ vs $T$ when $l_p=\kappa ∕kT$ (dotted-dashed line). $\kappa$ was set by equating $l_p$ at $T_{\min }$ for $\lambda =3.5\mathrm{nm}$. The inset depicts the same plots for poly (rU).

Figure 2

Plots of $f$ vs $R∕Na$ for poly(dA) at $T=25°\mathrm{C}$ as obtained from the stacking model Eq. (5) with $\lambda =3.5\mathrm{nm}$ (—–), from the freely jointed chain model with $l_p$ given by Eq. (3) (xxxx) and with $l_p=3.5\mathrm{nm}$ (oooo). Insets: (a) depicts the same plots for poly(rU) at $10°\mathrm{C}$. (b) Schematic picture of ssDNA with stacked blocks.