A DNA nick, defined as a discontinuity
in a double-stranded
DNA
molecule where the phosphodiester bond between adjacent nucleotides
of one strand is absent due to enzyme action, serves as an effective
mechanism to alleviate stress in supercoiled DNA. This stress release
is essential for the smooth operation of transcriptional machinery.
However, the underlying mechanisms and their impact on protein search
dynamics, which are crucial for initiating transcription, remain unclear.
Through extensive computer simulations, we unravel the molecular picture,
demonstrating that intramolecular stress release due to a DNA nick
is driven by a combination of writhing and twisting motions, depending
on the nick’s position. This stress release is quantitatively
manifested as a step-like increase in the linking number. Furthermore,
we elucidate that the nicked supercoiled minicircles exhibit enhanced
torsional dynamics, promoting rapid conformational changes and frequent
shifts in the identities of juxtaposed DNA sites on the plectoneme.
The dynamics of the juxtaposition sites facilitates communication
between protein and DNA, resulting in faster protein diffusion compared
with native DNA with the same topology. Our findings highlight the
mechanistic intricacies and underscore the importance of DNA nicks
in facilitating transcription elongation by actively managing torsional
stress during DNA unwinding by the RNA polymerase.