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 reco gnition by proteins. Here the flexibility of DNA is calculated from th e distribution of DNA-bending angles of single DNA molecules as observ ed 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 i s 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 i s very flexible and readily can be bent by thermal motion. DNA-flexibi lity is not altered in some protein-DNA complexes (HhaI methyltransfer ase, EcoRV restriction endonuclease). In contrast, DNA-binding by EcoR I endonuclease increases DNA-flexibility and binding by EcoRI methyltr ansferase restricts the flexibility of DNA. During the transition of t he RNA polymerase-sigma(54)-DNA complex from the closed to the open fo rm and of cro repressor from a non-specific to a specific binding mode the flexibility of the DNA is strongly reduced. (C) 1998 Elsevier Sci ence B.V. All rights reserved.