Feng-Hua Wang and Yuan-Yan Wu are contributed equally to this work.
Salt contribution to the flexibility of single-stranded nucleic acid of finite length
Article first published online: 25 MAR 2013
Copyright © 2012 Wiley Periodicals, Inc.
Volume 99, Issue 6, pages 370–381, June 2013
How to Cite
Wang, F.-H., Wu, Y.-Y. and Tan, Z.-J. (2013), Salt contribution to the flexibility of single-stranded nucleic acid of finite length. Biopolymers, 99: 370–381. doi: 10.1002/bip.22189
This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at email@example.com
- Issue published online: 25 MAR 2013
- Article first published online: 25 MAR 2013
- Accepted manuscript online: 26 NOV 2012 07:05AM EST
- Manuscript Accepted: 18 NOV 2012
- Manuscript Received: 8 OCT 2012
- National Science Foundation of China. Grant Number: 10844007, 11074191 and 11175132
- Program for New Century Excellent Talents. Grant Number: NCET 08-0408
- Fundamental Research Funds for the Central Universities. Grant Number: 1103007
- National Key Scientific Program (973)-Nanoscience and Nanotechnology. Grant Number: 2011CB933600
- Scientific Research Foundation for Returned Overseas Chinese Scholars, State Education Ministry Contract grant sponsor: Interdisciplinary and postgraduate programs (under the “Fundamental Research Funds for the Central Universities”)
- ss nucleic acid;
- persistence length
Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this article, the salt effects on the flexibility of single-stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse-grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual-bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and both trivalent/small divalent ions can induce more compact state than a random relaxation state. We found that monovalent, divalent, and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion-exclusion-volume effect to ion Coulomb correlations. In addition, the predicted Na+ and Mg2+-dependent persistence length lp’s of ss nucleic acid are in accordance with the available experimental data, and through systematic calculations, we obtained the empirical formulas for lp as a function of [Na+], [Mg2+] and chain length. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 370–381, 2013.