Persistency of single-stranded DNA: The interplay between base sequences and base stacking

The chain persistency of single-stranded (ss) DNA at a high-salt limit mainly arises from the so-called base-stacking interaction between consecutive bases along the strand. Stacking is appreciable for purine-purine (e.g., A-A) and purine-pyrimidine stacks (e.g., A-T), but it is weak for pyrimidine stacks (i.e., T-T, T-C, and C-C). We study how base stacking can stiffen the strand by classifying bases into two subclasses: stacking pairs (i.e., purine-purine and purine-pyrimidine) and non-stacking (i.e., pyrimidine-pyrimidine) pairs. With this simplification, we develop an exactly solvable model for calculating the stacking-induced persistence length ℓstack of heterogeneous ssDNA. It is shown that ℓstack is mainly determined by the occurrence rate of purines; intrinsic correlations in real DNA sequences barely influence ℓstack. Our approach leads to a reasonable estimate of ℓstack≈2b-3b (under typical conditions), where b is the inter-base distance.