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Although DNA is often bent in vivo, it is unclear how DNA-bending forcesmodulate DNA-protein binding affinity. Here, we report how a range ofDNA-bending forces modulates the binding of the Integration Host Factor (IHF)protein to various DNAs. Using solution fluorimetry and electrophoreticmobility shift assays, we measured the affinity of IHF for DNAs with differentbending forces and sequence mutations. Bending force was adjusted by varyingthe fraction of double-stranded DNA in a circular substrate, or by changing theoverall size of the circle (1). DNA constructs contained a pair of ForsterResonance Energy Transfer dyes that served as probes for affinity assays, andread out bending forces measured by optical force sensors (2). Small bendingforces significantly increased binding affinity; this effect saturated beyond~3 pN. Surprisingly, when DNA sequences that bound IHF only weakly weremechanically bent by circularization, they bound IHF more tightly than thelinear "high-affinity" binding sequence. These findings demonstrate that smallbending forces can greatly augment binding at sites that deviate from aprotein's consensus binding sequence. Since cellular DNA is subject tomechanical deformation and condensation, affinities of architectural proteinsdetermined in vitro using short linear DNAs may not reflect in vivo affinities.

Mechanical conversion of low-affinity Integration Host Factor binding sites into high-affinity sites