Psoralen binding across the Escherichia coli chromosome

We used trimethylpsoralen intercalation to map supercoiling across the E. coli chromosome. We treated E. coli cells with trimethylpsoralen and exposed them to UV light. Psoralen enters cells, intercalates between DNA base pairs, and crosslinks the two strands of DNA at a rate proportional to the local superhelical density. We then fragmented DNA and hybridized crosslinked and non-crosslinked DNA fragments separately to tiling microarrays. In total 14 samples; 6 for wild-type in stationary phase (3 replicates x 2 samples as there are crosslinked and non-crosslinked samples for each replicate); 4 for wild-type in mid-exponential phase (2 replicates x 2 samples); 4 for the delta hupAB mutant in stationary phase (2 replicates x 2 samples)