  As the chief informational molecule of life, DNA is subject to extensive
physical manipulations. The energy required to deform double-helical DNA
depends on sequence, and this mechanical code of DNA influences gene
regulation, such as through nucleosome positioning. Here we examine the
sequence-dependent flexibility of DNA in bacterial transcription
factor-mediated looping, a context for which the role of sequence remains
poorly understood. Using a suite of synthetic constructs repressed by the Lac
repressor and two well-known sequences that show large flexibility differences
in vitro, we make precise statistical mechanical predictions as to how DNA
sequence influences loop formation and test these predictions using in vivo
transcription and in vitro single-molecule assays. Surprisingly,
sequence-dependent flexibility does not affect in vivo gene regulation. By
theoretically and experimentally quantifying the relative contributions of
sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal
that bending by HU dominates DNA mechanics and masks intrinsic
sequence-dependent flexibility. Such a quantitative understanding of how
mechanical regulatory information is encoded in the genome will be a key step
towards a predictive understanding of gene regulation at single-base pair
resolution.
