Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics Simulations

DNA structure and properties sensitively depend on its environment, in particular on the ion atmosphere. One of the most fundamental properties of DNA is its helicity and here we investigate how it changes with concentration and identity of the surrounding ions. To resolve how metal cations influence the helical twist, we have combined magnetic tweezer experiments and extensive all-atom molecular dynamics simulations. Two interconnected trends are observed for monovalent alkali and divalent alkaline earth cations. First, DNA twist increases with increasing ion concentration. Secondly, for a given salt concentration, DNA twist strongly depends on cation identity. Metal cations with high charge density (such as Li+ or Ca2+) are most efficient at inducing DNA twist and lead to overwinding. By contrast, metals with intermediate charge density (such as Na+ or Ba2+) reduce the twist and underwind the helix compared to higher density ions. Our molecular dynamics simulations reveal that preferential binding of the metals to the DNA backbone and the nucleobases has opposing effects on DNA twist and provide a microscopic explanation of the observed ion specificity. The comprehensive view gained from our combined approach provides a foundation to understand and predict metal-induced structural changes in nature or in DNA nanotechnology.

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Molecular Dynamics Simulations of Water and Ion Structures Near Charged Surfaces

Volume 11: Micro and Nano Systems, Parts A and B ◽

10.1115/imece2007-42536 ◽

2007 ◽

Author(s):

Dongyan Xu ◽

Deyu Li ◽

Yongsheng Leng

Keyword(s):

Molecular Dynamics ◽

Surface Charge ◽

Molecular Dynamics Simulations ◽

Single Molecule ◽

Research Field ◽

Water Molecules ◽

Wall Region ◽

Surface Charges ◽

Ion Distribution ◽

Dynamics Simulations

Extensive research has been devoted to nanofluidics in the past decade because of its potential applications in single molecule sensing and manipulations. Fundamental studies have attracted significant attention in this research field since the success of nanofluidic devices depends on a thorough understanding of the fluidic, ionic, and molecular behavior in highly confined nano-environments. In this paper, we report on molecular dynamics simulations of the effect of surface charge densities on the ion distribution and the water density profile close to a charged surface. We demonstrate that surface charges not only interact with mobile ions in the electrolyte, but also interact with water molecules due to their polarizability, and hence influence the orientation of water molecules in the near wall region. For the first time, we show that as the surface charge density increases, the water molecules within ∼ 5 Å of the {100} silicon surface will evolve from one layer into two layers. Meanwhile, the orientation of the water molecules is more aligned instead of randomly distributed. This layering effect may have important implications on electroosmotic flow through nanochannels and heat transfer across the solid-liquid interface.

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