posted on 2021-07-15, 18:35authored bySehui Bae, Inrok Oh, Jejoong Yoo, Jun Soo Kim
We present extensive
molecular dynamics simulations of a cationic
nanoparticle and a double-stranded DNA molecule to discuss the effect
of DNA flexibility on the complex formation of a cationic nanoparticle
with double-stranded DNA. Martini coarse-grained models were employed
to describe double-stranded DNA molecules with two different flexibilities
and cationic nanoparticles with three different electric charges.
As the electric charge of a cationic nanoparticle increases, the degree
of DNA bending increases, eventually leading to the wrapping of DNA
around the nanoparticle at high electric charges. However, a small
increase in the persistence length of DNA by 10 nm requires a cationic
nanoparticle with a markedly increased electric charge to bend and
wrap DNA around. Thus, a more flexible DNA molecule bends and wraps
around a cationic nanoparticle with an intermediate electric charge,
whereas a less flexible DNA molecule binds to a nanoparticle with
the same electric charge without notable bending. This work provides
solid evidence that a small difference in DNA flexibility (as small
as 10 nm in persistence length) has a substantial influence on the
complex formation of DNA with proteins from a biological perspective
and suggests that the variation of sequence-dependent DNA flexibility
can be utilized in DNA nanotechnology as a new tool to manipulate
the structure of DNA molecules mediated by nanoparticle binding.