Fig. 3.

Distinguishing between similar genomes: the target strain E. coli O157 Sakai and the nontarget strain E. coli bl21-de3 (wild type). (A) Results of our Langevin dynamics simulations for the average degree of binding (number of blob–surface contacts $n_c$), for the target and nontarget genomic DNA. The solid lines show results for the top-scoring 20-nt probe, which is designed to maximize the difference function $\mathrm{\Delta }S=S_{Sakai}-S_{bl21-de3}$. The dashed lines show results for the published 70-nt “probe B” (38), which targets the rfbE gene specific to E. coli O157. For the published probe, the genomic DNA has been fragmented into 400-nt pieces to mimic standard DNA microarray conditions while for our 20-nt probe we assume unfragmented genomic DNA. (B) The effect of genome fragmentation at surface probe density $\rho =0.03/r_b^2$, for our top-scoring 20-nt probe. As in our other simulations, $l_b=400,T=50{}^{○}\mathrm{C}$, and a genome–surface contact was defined as a DNA blob being located within 2$r_b=20$ nm of the surface.