Role of helicity in DNA hairping folding dynamics
| Autor: | Li, Huaping, Kabakcioglu, Alkan |
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| Rok vydání: | 2018 |
| Předmět: | |
| Zdroj: | Phys. Rev. Lett. 121, 138101 (2018) |
| Druh dokumentu: | Working Paper |
| DOI: | 10.1103/PhysRevLett.121.138101 |
| Popis: | We study hairpin folding dynamics by means of extensive computer simulations, with particular attention paid to the influence of helicity on the folding time $\tau$. We find that the dynamical exponent $\alpha$ of the anomalous scaling $\tau \sim N^\alpha$ for a hairpin with length N changes from 1.6 ($1+\nu$) to 1.2 ($2\nu$) in three dimensions, when duplex helicity is removed. The relation $\alpha = 2\nu$ in rotationless hairpin folding is further verified in two dimensions ($\nu = 0.75$), and for a ghost-chain ($\nu = 0.5$). This, to our knowledge, is the first observation of the theoretical lower bound on $\alpha$, which was predicted earlier on the basis of energy conservation for polymer translocation through a pore. Our findings suggest that the folding dynamics in long helical chains is governed by the duplex dynamics, contrasting the earlier understanding based on the stem-flower picture of unpaired segments. We propose a scaling argument for $\alpha = 1+\nu$ in helical chains, assuming that duplex relaxation required for orientational positioning of the next pair of bases is the rate-limiting process. Comment: 4 pages, 5 figures, submitted for publication |
| Databáze: | arXiv |
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