Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 121, Issue 33, Pages 7761-7770Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpcb.7b03793
Keywords
-
Categories
Funding
- Singapore Ministry of Education Academic Research Fund (AcRF) [MOE2014-T2-1-123 (ARC51/14), MOE2012-T3-1-001]
- Swedish Research Council
Ask authors/readers for more resources
It is well established that the presence of the trivalent cobalt(III)-hexammine cation (CoHex(3+)) at submillimolar concentrations leads to bundling (condensation) of double stranded DNA molecules, which is caused by DNA DNA attraction induced by the multivalent counterions. However, the detailed mechanism of this process is still not fully understood. Furthermore, in all-atom molecular dynamics (MD) simulations, spontaneous aggregation of several DNA oligonucleotides in the presence of CoHex(3+) has previously not been, demonstrated. In order to obtain a rigorous description of CoHex(3+)-nucleic acid interactions and CoHex(3+)-induced DNA condensation to be used in MD siniulations, we have derived optimized force field parameters of the CoHex(3+) ion. They were obtained from Car Parrinello molecular dynamics simulation of a single CoHex3+ ion in the presence of 126 water molecules. The new set,of force field parameters reproduces the experimentally known transition of DNA from B- to A-form; and qualitatively describes changes of DNA and RNA persistence lengths. We then carried out a 2 mu s long atomistic simulation of four DNA oligomers each consisting of 36 base pairs in the presence of CoHex(3+). We demonstrate that, in this system, DNA molecules display attractive interactions and aggregate into bundle-like structures. This behavior depends critically on the details of the CoHex(3+) interaction with DNA. A control simulation with a similar setup but in the presence of Mg2+ does not induce DNA DNA attraction, which is also in agreement with experiment.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available