Abstract
We 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.
Highlights
While the structural information available for protein-DNA interactions at the atomistic level has mostly been obtained for linear short DNA fragments, in vivo protein-DNA interactions occur in a variety of complex structural topologies like DNA loops or hierarchical chromatin
For the highly writhed DLk 1⁄4 À2 topoisomer, the bound 434 repressor was located at the crossover, where polar residues on the protein surface could provide electrostatic screening (Fig. 1 d)
Our molecular dynamics (MD) simulations have shown that the binding of two distant ligands to supercoiled DNA is determined by a subtle interplay of DNA mechanics and electrostatics at the local level, which is capable of introducing global topological changes within the whole minicircle, establishing a mechanism to transfer conformational information beyond the simple 1D order of regulatory elements placed sequentially on the DNA double helix
Summary
While the structural information available for protein-DNA interactions at the atomistic level has mostly been obtained for linear short DNA fragments, in vivo protein-DNA interactions occur in a variety of complex structural topologies like DNA loops or hierarchical chromatin. The overor underwinding of DNA emerges from several cellular processes that induce torsional stress either by sequentially separating the two strands (transcription and replication) [2] or by wrapping DNA around proteins (such as in the nucleosome [3] and by interaction with DNA gyrase [4,5]). The latter, together with the use of ATP, usually serve to maintain an homeostatically underwound state in eukaryotes [6] and prokaryotes [7], respectively. The formation of triplex DNA has been demonstrated to be more efficient for negatively supercoiled DNA, and this property has been subsequently successfully exploited to develop an assay for reporting topoisomerase activity [14]
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