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Illustration of our model. Single-stranded genomic DNA is represented as a chain of blobs, connected by harmonic springs. Each blob represents -nt bases. The interactions among the blobs, and between each blob and the probe DNA-coated surface, are sequence specific and are calculated from the SantaLucia interaction free energies (34, 35) (see SI Appendix for a full description). The oxDNA model is used to represent the configuration of the single-stranded DNA chain (40).
