DNA deformability in sequence-dependent capture of E. coli gyrase.

To understand how gyrase interacts with DNA and selects a site of action, we created an ad hoc shape-based recognition methodology to ascertain the DNA sequence from cryoEM density maps as a string of purines and pyrimidines, which matched to the DNA minicircle sequence in our two previous cryoEM structures of negatively supercoiled DNA bound to E. coli gyrase. For one structure, the Gate- or G-segment sequence contains base-pair steps that are among the most flexible in the minicircle, facilitating the bend. The sequence flanking this G-segment is highly inflexible, preventing wrapping the β-pinwheel of gyrase. In the other structure, a flexible DNA minicircle sequence wraps a β-pinwheel of gyrase and the G-segment contains base-pair steps of average deformability. This work highlights how DNA sequence and deformability impact gyrase. It also demonstrates the utility of both identifying DNA sequences from cryoEM structures and assessing base-pair step deformability.