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. 2005 Jun 24;1(1):e7. doi: 10.1371/journal.pcbi.0010007

Figure 1. Comparison of Stress-Induced Duplex Destabilization Calculations with Assessments of Thermodynamic Stability.

Figure 1

(A) The SIDD profile showing the G(x) values computed for a 3-kbp region (525701–528700) on Chromosome X of yeast at superhelix density σ = −0.055.

(B) The SIDD profile of a 38-bp deletion mutant of the same region [28], at the same superhelicity. The deletion is at positions 526489–526526, indicated by the red arrow. This deletion causes drastic changes of SIDD properties throughout the region, even 2 kbp away. This is an effect of the global coupling induced by the superhelical stresses.

(C) Thermodynamic stability profiles of the same regions as computed by WEB-THERMODYN [12,13], both before (black) and after (red) the deletion. The only effect of this deletion, whose location is indicated by the red arrow, is to displace the downstream profile by 38 bp. However, as shown in (B), the SIDD profile is profoundly altered throughout the region.