posted on 2021-11-18, 14:35authored bySehui Bae, Jun Soo Kim
Sharp bending and wrapping of DNA
around proteins and nanoparticles
(NPs) has been of extensive research interest. Here, we present the
potential of mean force (PMF) for wrapping a DNA double helix around
a cationic NP using coarse-grained models of a double-stranded DNA
and a cationic NP. Starting from a NP wrapped around by DNA, the PMF
was calculated along the distance between the center of the NP and
one end of the DNA molecule. A relationship between the distance and
the extent of DNA wrapping is used to calculate the PMF as a function
of DNA wrapping around a NP. In particular, the PMF was compared for
two DNA sequences of (AT)25/(AT)25 and (AC)25/(GT)25, for which the persistence lengths are
different by ∼10 nm. The simulation results provide solid evidence
of the thermodynamic preference for complex formation of a cationic
NP with more flexible DNA over the less flexible DNA. Furthermore,
we estimated the elastic energy of DNA bending, which was in good
order-of-magnitude agreement with the theoretical prediction of elastic
rods. This work suggests that the variation of sequence-dependent
DNA flexibility can be utilized in DNA nanotechnologies, in which
the position and dynamics of NPs are regulated on large-scale DNA
structures, or the structural transformation of DNA is triggered by
the sequence-dependent binding of NPs.