Persistency of single-stranded DNA: The interplay between base sequences and base stacking
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Title |
Persistency of single-stranded DNA: The interplay between base sequences and base stacking
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Creator |
SAIN, ANIRBAN
CHEN, JEFF ZY BAE-YEUN HA |
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Subject |
aromatic compounds
molecular dynamics statistical mechanics solubility |
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Description |
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.
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Publisher |
Elsevier
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Date |
2009-03-23T05:14:47Z
2011-11-25T20:16:28Z 2011-12-26T13:08:15Z 2011-12-27T05:56:15Z 2009-03-23T05:14:47Z 2011-11-25T20:16:28Z 2011-12-26T13:08:15Z 2011-12-27T05:56:15Z 2006 |
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Type |
Article
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Identifier |
Physica A: Statistical Mechanics and its Applications 369(2), 679-687
0378-4371 http://dx.doi.org/10.1016/j.physa.2006.01.084 http://hdl.handle.net/10054/1080 http://dspace.library.iitb.ac.in/xmlui/handle/10054/1080 |
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Language |
en
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