Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?

Details Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter? Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?

2001-01-18

arxiv.org/abs/cond-mat/0101286v1

J. Chem. Phys. 114, 8694-8700 (2001). AIP Copyright

Physics

Condensed Matter

Soft Condensed Matter

8 pages using Revtex

Scientific paper

10.1063/1.1368401

Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and base-pair stacking interactions, and a threshold external force is needed to pull the hairpinned structure into a random coiled one. The base-pair stacking interaction in the ssDNA chain makes this hairpin-coil conversion a discontinuous (first-order) phase transition process characterized by a force plateau in the force-extension curve, while lowering this potential below some critical level turns this transition into continuous (second-order) type, no matter how strong the base-pairing interaction is. The phase diagram (including hairpin-I, -II, and random coil) is discussed as a function of stacking potential and external force. These results are in quantitative agreement with recent experimental observations of different ssDNA sequences, and they reveal the necessity to consider the base-pair stacking interactions in order to understand the structural formation of RNA, a polymer designed by nature itself. The theoretical method used may be extended to study the long-range interaction along double-stranded DNA caused by the topological constraint of fixed linking number.

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