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Interference between Triplex and Protein Binding to Distal Sites on Supercoiled DNA

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JournalBiophysical Journal
DateAccepted/In press - 16 Dec 2016
DateE-pub ahead of print - 17 Jan 2017
DatePublished (current) - 7 Feb 2017
Volume112
Number of pages9
Pages (from-to)523-531
Early online date17/01/17
Original languageEnglish

Abstract

have explored the interdependence of the binding of a DNA triplex and a repressor protein to distal recognition sites on supercoiled DNA minicircles using MD simulations. We observe that the interaction between the two ligands through
their influence on their DNA template is determined by a subtle interplay of DNA mechanics and electrostatics, that the changes in flexibility induced by ligand binding play an important role and that supercoiling can instigate additional ligand-DNA contacts that would not be possible in simple linear DNA sequences.

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