A coarse-grained MARTINI-like force field for DNA unzipping in nanopores
Authors:
- Anna Stachiewicz,
- Andrzej Molski
Abstract
In nanopore force spectroscopy (NFS) a charged polymer is threaded through a channel of molecular dimensions. When an electric field is applied across the insulating membrane, the ionic current through the nanopore reports on polymer translocation, unzipping, dissociation, and so forth. We present a new model that can be applied in molecular dynamics simulations of NFS. Although simplified, it does reproduce experimental trends and all-atom simulations. The scaled conductivities in bulk solution are consistent with experimental results for NaCl for a wide range of electrolyte concentrations and temperatures. The dependence of the ionic current through a nanopore on the applied voltage is symmetric and, in the voltage range used in experiments (up to 2 V), linear and in good agreement with experimental data. The thermal stability and geometry of DNA is well represented. The model was applied to simulations of DNA hairpin unzipping in nanopores. The results are in good agreement with all-atom simulations: the scaled translocation times and unzipping sequence are similar.
- Record ID
- UAM7438a14df9074d728f4ba18a8dab2482
- Author
- Journal series
- Journal of Computational Chemistry, ISSN 0192-8651, [1096-987X]
- Issue year
- 2015
- Vol
- 36
- Pages
- 947-956
- ASJC Classification
- ;
- DOI
- DOI:10.1002/jcc.23874 Opening in a new tab
- Language
- (en) English
- Score (nominal)
- 35
- Score source
- journalList
- Score
- Publication indicators
- = 6; = 6; : 2015 = 1.368; : 2015 (2 years) = 3.648 - 2015 (5 years) =4.648
- Uniform Resource Identifier
- https://researchportal.amu.edu.pl/info/article/UAM7438a14df9074d728f4ba18a8dab2482/
- URN
urn:amu-prod:UAM7438a14df9074d728f4ba18a8dab2482
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or PerishOpening in a new tab system.