Molecular dynamics studies of ion distributions for DNA duplexes and DNA clusters: Salt effects and connection to DNA melting

Article Abstract:

An extensive molecular dynamics simulation of the ion distributions for DNA duplexes and DNA clusters using the Amber force field with implicit water is presented. The distribution of ions and the electrostatic energy of ions around an isolated DNA duplex and clusters of DNA duplexes in different salt (NaCl) concentrations over the range 0.2-1.0 mol/L are determined on the basis of the simulation results.

Molecular dynamics, Electrostatics

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A model for simulating dynamics of DNA denaturation

Article Abstract:

DNA melting is an important feature of a new class of biological sensors that is developed recently by Mirkin and co-workers. The results of our calculations suggest that this model is able to describe realistically many aspects of DNA melting, including melting temperatures and ranges and the dependence of melting temperatures on DNA base composition.

Hydrogen bonding, Chemistry, Physical and theoretical, Physical chemistry, Dynamics, Dynamics (Mechanics), Structure

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Structures of DNA-linked nanoparticle aggregates

Article Abstract:

The room-temperature structure of DNA-linked gold nanoparticle aggregates in examined using a combination of experiment and theory. The experiments take extinction spectroscopy measurements and dynamic light scattering measurements of aggregates made using 60 and 80 nm gold particles and 30-base pair DNA.

All Other Basic Inorganic Chemical Manufacturing, Industrial inorganic chemicals, not elsewhere classified, Gold Compounds, Spectra

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