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The rationale for working with once more the straight hairpin, was to verify if the Zn fingers have the opportunity to spot a pristine SSB, at the very least In this particular conversation method.

This combined Zn1-Zn2-DNA configuration is thus our greatest candidate for even further equilibration at finite temperature and force. After 1 μs of MD simulation, the trajectory is clustered and consultant configurations were extracted.

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one. The extremely peculiar hairpin conformation in the DNA structure permits a sizable conformational variability under thermal fluctuations, when compared with straight, long DNA harboring an identical SSB at its Centre. although the straight DNA can experience broad curvatures, particularly when its length approaches and surpasses the persistence length (\(\gtrsim\)50 nm), the atomic construction surrounding the SSB stays somewhat unaffected.