  Genomic DNA is constantly subjected to various mechanical stresses arising
from its biological functions and cell packaging. If the local mechanical
properties of DNA change under torsional and tensional stress, the activity of
DNA-modifying proteins and transcription factors can be affected and regulated
allosterically. To check this possibility, appropriate steady forces and
torques were applied in the course of all-atom molecular dynamics simulations
of DNA with AT- and GC-alternating sequences. It is found that the stretching
rigidity grows with tension as well as twisting. The torsional rigidity is not
affected by stretching, but it varies with twisting very strongly, and
differently for the two sequences. Surprisingly, for AT-alternating DNA it
passes through a minimum with the average twist close to the experimental value
in solution. For this fragment, but not for the GC-alternating sequence, the
bending rigidity noticeably changes with both twisting and stretching. The
results have important biological implications and shed light upon earlier
experimental observations.
