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

Author

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  • Sain, Anirban
  • Chen, Jeff Z.Y.
  • Ha, Bae-Yeun

Abstract

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.

Suggested Citation

  • Sain, Anirban & Chen, Jeff Z.Y. & Ha, Bae-Yeun, 2006. "Persistency of single-stranded DNA: The interplay between base sequences and base stacking," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 369(2), pages 679-687.
    • Handle: RePEc:eee:phsmap:v:369:y:2006:i:2:p:679-687
    DOI: 10.1016/j.physa.2006.01.084
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