Abstract
Most DNA-binding proteins alter the conformation of the double helix and many induce topological structures such as loops or wraps by binding to two or more sites along the DNA. While such topologies may efficiently regulate initiation at a promoter, they may also be roadblocks for an incoming RNA polymerase (RNAP) transcribing a different gene. The lac repressor protein bound to a weak binding site was shown to turn into a strong roadblock when securing a loop of 400 bp. The question remains if other proteins could similarly become strong roadblocks when mediating different types of topological structures.
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