Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection t
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Molecular Dynamics Studies of Ion Distributions around DNA Duplexes and Duplex Dimers: Salt Effects and the Connection to Cooperative DNA Melting Hai Long and George C. Schatz Department of Chemistry, Northwestern University, Evanston IL 60208-3113 We present extensive molecular dynamics simulations of DNA duplexes and duplex dimers based on the Amber force field to determine the distribution of ions as a function of salt (NaCl) concentration over the range 0.2-1.0M. Periodic boundary conditions are used to model an infinite DNA chain, and particle mesh Ewald summation is used to describe long range electrostatic interactions. We have used these simulations to determine the ion distributions associated with a 10 base pair duplex, and we find that the positive and negative ion distributions are identical for distances greater than a radius Rcounter which is on the order of 25 Å from the DNA axis, and which decreases as the bulk salt concentration is varied. Based on the calculated Rcounter, we determine the local counterion concentration as a function of bulk salt concentration. Similar studies of DNA duplex dimers separated by 30-40 Å leads to a determination of the local counterion concentration around these dimers. Here we find that dimerization leads to greatly enhanced counterion concentrations. If this information is combined with the measured results concerning the dependence of DNA melting temperature on bulk salt concentration, we find that dimerization leads to a several degree increase in melting temperature, with the increase being 10oC for a dimer separation of 30 Å. This result provides justification for a recently developed cooperative melting model of DNA duplex aggregates. Introduction Recent measurements of the melting behavior of DNA-linked gold nanoparticle aggregates[1] have demonstrated that melting transitions in the aggregates are significantly narrower than those for the same DNA duplexes in solution. In a typical experiment in which 30 bp DNA is used to link 15 nm gold nanoparticles to produce aggregates containing thousands of nanoparticles (see Figure 1 for a schematic of this), the melting width (for 0.3 M NaCl concentration) is 3oC, which is to be compared with a width of 20o for melting of the same DNA in solution.[2] Even smaller widths (1o) are found for aggregates involving larger nanoparticles. This result has important consequences for DNA detection using colorimetric methods,[3] as the melting temperature often varies by a few degrees in the presence of single base pair mismatches, insertions or deletions. As a result, a simple stringency wash can be developed to distinguish complementary DNA using gold nanoparticle aggregates under circumstances where free solution DNA detection (based on fluorescence) doesn’t work.[4] The origin of the narrower melting transitions has remained unsolved until very recently, when a thermodynamic model for melting of the gold nanoparticle aggregates was developed.[2] In this model, which is schematically illustrated in Figure 2, it is assu
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