Molecular dynamics simulation of multivalent ion mediated DNA attraction

Abstract

All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e. multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.

4 pages, 5 figures, to be published in Physical Review Letters

References in corpus (2)

• Wigner crystal model of counterion induced bundle formation of rod-like polyelectrolytes
• Charge Fluctuation Forces Between Stiff Polyelectrolytes in Salt Solution: Pairwise Summability Re-examined

Cited by in corpus (7)

• Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel
• Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA
• Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
• Ion assisted structural collapse of a single stranded DNA: a molecular dynamics approach
• Multi-shell model of ion-induced nucleic acid condensation
• Distribution of counterions and interaction between two similarly charged dielectric slabs: Roles of charge discreteness and dielectric inhomogeneity
• Structural Analysis of DNA molecule in a confined shell