Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules

Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542.
Physical Review Letters (Impact Factor: 7.73). 03/2008; 100(11):118301. DOI: 10.1103/PhysRevLett.100.118301
Source: PubMed

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.

Download full-text


Available from: Johan R C van der Maarel, Dec 15, 2012
1 Follower
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: In this paper we aim to create an experimental and numerical model of nano and micro filaments suspended in a confined Poiseuille flow. The experimental data obtained for short nanofibres will help to elucidate fundamental questions concerning mobility and deformation of biological macromolecules due to hydrodynamic stresses from the surrounding fluid motion. Nanofibres used in the experiments are obtained by electrospinning polymer solutions. Their typical dimensions are 100–1000 μm (length) and 0.1–1 μm (diameter). The nanofibre dynamics is followed experimentally under a fluorescence microscope. A precise multipole expansion method of solving the Stokes equations, and its numerical implementation are used to construct a bead-spring model of a filament moving in a Poiseuille flow between two infinite parallel walls. Simulations show typical behaviour of elongated macromolecules. Depending on the parameters, folding and unfolding sequences of a flexible filament are observed, or a rotational and translation motion of a shape-preserving filament. An important result of our experiments is that nanofibres do not significantly change their shape while interacting with a micro-flow. It appeared that their rotational motion is better reproduced by the shape-preserving Stokesian bead model with all pairs of beads connected by springs, omitting explicit bending forces.
    International Journal of Heat and Fluid Flow 12/2010; DOI:10.1016/j.ijheatfluidflow.2010.02.021 · 1.78 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range of 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with the scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.
    The Journal of Chemical Physics 07/2008; 128(22):225109. DOI:10.1063/1.2937441 · 3.12 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Lyotropic chromonic liquid crystals (LCLCs) are formed by molecules with ionic groups at the periphery that associate into stacks through noncovalent self-assembly while in water. The very existence of the nematic (N) phase in the typical LCLC, the dye Sunset Yellow (SSY) is a puzzle, as the correlation length associated with the stacking, as measured in the X-ray experiments, is too short to explain the orientational order by the Onsager model. We propose that the aggregates can be more complex than simple rods and contain "stacking faults" such as junctions with a shift of neighboring molecules, 3-fold junctions, etc. We study how ionic additives, such as salts of different valency and pH-altering agents, alter the N phase of SSY purified by recrystallization. The additives induce two general trends: (a) stabilization of the N phase, caused by the mono and divalent salts (such as NaCl), and evidenced by the increase of the N-to-I transition temperature and the correlation length; (b) suppression of the N phase manifested in the decrease of the N-to-I transition temperature and in separation of the N phase into a more densely packed N phase or the columnar (C) phase, coexisting with a less condensed I phase. The scenario (b) can be triggered by simply increasing pH (adding NaOH). The effects produced by tetravalent spermine fall mostly into the category (b), but the detail depends on whether this additive is in its salt form or a free base form. The base form causes changes through changes in pH and possible excluded volume effects whereas the salt form might disrupt the structure of SSY aggregates.
    The Journal of Physical Chemistry B 01/2009; 112(51):16307-19. DOI:10.1021/jp804767z · 3.38 Impact Factor