Are shown in Fig. 1. Just beyond the onset of transition where jsj is still tiny, the superhelical free of charge power on the untransformed state also is somewhat modest. Beneath these circumstance the energy relief afforded by transition is significantly less than it is actually at extra extreme superhelicities. So in this regime the magnitude on the transition power may be the dominant aspect in determining which regions transform. That is why the shorter but energetically significantly less costly Insert 1 may be the initial to transform, as shown within the figure. As jsj increases the superhelical no cost power becomes quadratically larger. Now transitions at longer sequences grow to be more desirable since they relieve far more superhelical pressure energy. Under these circumstances the difference in transition totally free energy as a result of ZZ-junctions becomes significantly less important than the advantage afforded by transforming a substantially longer segment. Because of this a coupled transition-reversion occasion occurs around s {0:04, in which transition of Insert 2 is coupled to the reversion of Insert 1 back to B-form. In the range jsj0:038{0:048 it is energetically too costly for both segments to transform to Z-DNA simultaneously, so such states occur infrequently at equilibrium. Transition of the long Insert 2 has caused substantial relaxation,which decreases the residual superhelicity felt by Insert 1 below the value that would drive it to transform. So at these stress levels the probability of transformation of Insert 1 drops to near zero. As jsj increases beyond the point where Insert 2 has a high probability of being entirely in Zform, the additional stress accumulates as negative residual superhelicity. When this reaches a sufficient level Insert 1 again transforms to Z-DNA. Beyond s {0:055 both inserts have high probabilities of simultaneously being in PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/20149905 Z-form. One sees that there are specific intervals of superhelicity within which 1) neither insert transforms, 2) the first transforms but not the second, 3) the second transforms but not the first, or 4) both inserts transform simultaneously. The transition in this example experiences every logical possibility. When Z-Hunt is applied to this sequence it assigns Z-score of 112|106 to Insert 1, and 3:5|106 to Insert 2. The above analysis shows that when the competition between sites is considered there are circumstances when a region with a lower Z-score mayStress BGP-15 Induced B-Z TransitionsFigure 1. The competition is shown between two segments inserted at separated locations in a (T)5000 circular plasmid. Insert 1 is (CG)10 , and insert 2 is (CG)30 with six Z-Z junctions. The probabilities of each segment flipping entirely to Z-form are shown as a function of negative superhelical density, here plotted as jsj. doi:10.1371/journal.pcbi.1001051.gtransform while one with a higher Z-score does not. The analysis of individual sites in isolation simply does not capture the complexity of behavior that can occur in stress-driven transitions.B-Z Transitions in Sample DNA SequencesWe have analyzed the B-Z transition properties of three circular DNAs – the pBR322 plasmid, and the wX174 bacteriophage and Bdellovibrio phage wMH2K genomes. Fig. 2 shows the B-Z transition probability profiles of these sequences calculated at superhelical density s {0:06. In each case the B-Z transition is substantially confined to a small number of sites where it is energetically most favorable, although there are several additional locations that have smaller, but still significant, transiti.
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