Markita P. Landry, Lela Vukovic, Sebastian Kruss, Gili Bisker, Alexandra M.
Landry, Shahrin Islam, Rishabh Jain, Klaus Schulten, and Michael S. Strano.
Comparative dynamics and sequence dependence of DNA and RNA
binding to single walled carbon nanotubes.
Journal of Physical Chemistry C, 119:10048-10058, 2015.
(PMC: PMC4440682)
LAND2015
Noncovalent polymer-single wall carbon nanotube (SWCNT) conjugates
have gained
recent interest due to their prevalent use as electrochemical and optical
sensors, SWCNT-
based therapeutics, and for SWCNT purification methods. However, little
is known about
the effects of polymer-SWCNT molecular interactions on functional
properties of these
conjugates. In this work, we show that SWCNT complexed with related
polynucleotide
polymers (DNA, RNA) have dramatically different fluorescence stability.
Surprisingly, we
find a difference of nearly 2500-fold in fluorescence emission between
the most
fluorescently stable DNA-SWCNT complex, C DNA-SWCNT,
compared to the least
fluorescently stable complex, (AT)A(GU)G DNA-RNA hybrid-
SWCNT. We further
reveal the existence of three regimes in which SWCNT fluorescence
varies nonmonotonically with SWCNT concentration. We utilize molecular
dynamics simulations to
elucidate the conformation and atomic details of SWCNT-corona phase
interactions. Our
results show that variations in polynucleotide sequence or sugar
backbone can lead to
large changes in the conformational stability of the polymer SWCNT
corona and the SWCNT
optical response. Finally, we demonstrate the effect of the coronae on
the response of a
recently developed dopamine nanosensor, based on (GT) DNA-
and (GU)
RNA-SWCNT complexes. Our results clarify several features of the
sequence dependence of
corona phases produced by polynucleotides adsorbed to single walled
carbon nanotubes,
and the implications for molecular recognition in such phases.
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