Flexibility of DNA in complex with proteins deduced from the distribution of bending angles observed by scanning force microscopy

Flexibility and dynamics of DNA are important for DNA-binding and recognition by proteins. Here the flexibility of DNA is calculated from the distribution of DNA-bending angles of single DNA molecules as observed by scanning force microscopy by applying an equation that links the force constant of DNA-bending (f) to the variance of the distribution of bending angles (sigma): f=RT/sigma(2). Using published data, f is calculated to be 3-5 J/degree(2) for free DNA. Thus, bending DNA by 20 degrees requires approx. 0.5-1 kJ/mol. This result shows that DNA is very flexible and readily can be bent by thermal motion. DNA-flexibility is not altered in some protein-DNA complexes (HhaI methyltransferase, EcoRV restriction endonuclease). In contrast, DNA-binding by EcoRI endonuclease increases DNA-flexibility and binding by EcoRI methyltransferase restricts the flexibility of DNA. During the transition of the RNA polymerase-sigma(54)-DNA complex from the closed to the open form and of cro repressor from a non-specific to a specific binding mode the flexibility of the DNA is strongly reduced.