Excluded Volume Effects in Gene Stretching

We investigate the effects excluded volume on the stretching of a single DNA in solution. We find that for small force F, the extension h is not linear in F but proportion to F^{\chi}, with \chi=(1-\nu)/\nu, where \nu is the well-known universal correlation length exponent. A freely joint chain model with the segment length chosen to reproduce the small extension behavior gives excellent fit to the experimental data of \lambda-Phage DNA over the whole experimental range. We show that excluded volume effects are stronger in two dimensions and also derive results in two dimensions which are different from the three dimensional results. This suggests experiments to be performed in these lower dimensions.Comment: 17 pages, four figure

Discrete Persistent Chain Model for Protein Binding on DNA

We describe and solve a discrete persistent chain model of protein binding on DNA, involving an extra sigma_i s at a site i of the DNA. This variable takes the value 1 or 0 depending on whether the site is occupied by a protein or not. In addition, if the site is occupied by a protein, there is an extra energy cost epsilon. For small force, we obtain analytic expressions for the force-extension curve and the fraction of bound protein on the DNA.For higher forces, the model can be solved numerically to obtain force extension curves and the average fraction of bound proteins as a function of applied force. Our model can be used to analyze experimental force extension curves of protein binding on DNA, and hence deduce the number of bound proteins in the case of non-specific binding.Comment: 14 pages, 5 figure