10.1021/acsnano.7b00236.s003
Zonglin Gu
Zonglin
Gu
Lin Zhao
Lin
Zhao
Shengtang Liu
Shengtang
Liu
Guangxin Duan
Guangxin
Duan
Jose Manuel Perez-Aguilar
Jose Manuel
Perez-Aguilar
Judong Luo
Judong
Luo
Weifeng Li
Weifeng
Li
Ruhong Zhou
Ruhong
Zhou
Orientational
Binding of DNA Guided by the C<sub>2</sub>N Template
American Chemical Society
2017
dsDNA migration
results show
template-guided nanostructures
binding patterns
biomolecular coating
dsDNA terminal base pairs
solvation shell water clusters
C 2 N Template
DNA Guided
quantum calculations
binding mode
umbrella sampling technique
nanoscale dewetting
C 2 N substrate
benzene rings
nitrogenized graphene
C 2 N monolayer
charge distributions
Orientational Binding
steric hindrance
orientational binding
C 2 N
C 2 N surface
nanomaterial surfaces
2017-03-13 00:00:00
Journal contribution
https://acs.figshare.com/articles/journal_contribution/Orientational_Binding_of_DNA_Guided_by_the_C_sub_2_sub_N_Template/4763518
A detailed understanding
of the interactions between biomolecules
and nanomaterial surfaces is critical for the development of biomedical
applications of these nanomaterials. Here, we characterized the binding
patterns and dynamics of a double stranded DNA (dsDNA) segment on
the recently synthesized nitrogenized graphene (C<sub>2</sub>N) with
both theoretical (including classical and quantum calculations) and
experimental approaches. Our results show that the dsDNA repeatedly
exhibits a strong preference in its binding mode on the C<sub>2</sub>N substrate, displaying an upright orientation that is independent
of its initial configurations. Interestingly, once bound to the C<sub>2</sub>N monolayer, the transverse mobility of the dsDNA is highly
restricted. Further energetic and structural analyses reveal that
the strength and position of the binding is guided by the favorable
π–π stacking between the dsDNA terminal base pairs
and the benzene rings on the C<sub>2</sub>N surface, accompanied by
a simultaneous strong nanoscale dewetting that provides additional
driving forces. The periodic atomic charge distributions on C<sub>2</sub>N (from its unique porous structure) also cause the formation
of local highly dense first solvation shell water clusters, which
act as further steric hindrance for the dsDNA migration. Furthermore,
free energy profiling calculated by the umbrella sampling technique
quantitatively supports these observations. When compared to graphene,
C<sub>2</sub>N is found to show a milder attraction to dsDNA, which
is confirmed by experiments. This orientational binding of DNA on
the C<sub>2</sub>N substrate might shed light on the design of template-guided
nanostructures where their functions can be tuned by specialized biomolecular
coating.