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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
 
Creator SAIN, ANIRBAN
CHEN, JEFF ZY
BAE-YEUN HA
 
Subject aromatic compounds
molecular dynamics
statistical mechanics
solubility
 
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.
 
Publisher Elsevier
 
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
 
Type Article
 
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
 
Language en