Coarse-Grained Modeling and Simulations of Thermoresponsive …
49
Fig. 5 Melting curves of flexible and neutral ONA with sequence d(GGGGCCCC) at 6 μM ONA
concentration for a ε PP = 1ε and b ε PP = 5ε. Melting curves of semi-flexible and negatively
charged ONA with sequence d(GGGGCCCC) at 6 μM ONA concentration for c ε PP = 1ε and
d ε PP = 5ε. Circles and down triangles represent ONAs conjugated to 40-mer (P 40 ) and 100-mer
(P 100 ), respectively. Black up triangles represent the case of unconjugated ONAs. Representative
snapshots of the ONA-polymer aggregates at a particular T * is also shown. Polymer is represented
in tan while G and C are represented in cyan and pink, respectively. The legend for a also holds for
b, c and d. Reproduced from Ref. [67] with permission from John Wiley and Sons
curves for both polymer lengths studied (Fig. 5a). This is consistent with published
results of Ghobadi and Jayaraman [20] where the polymer is solvophilic in nature
modeled with WCA interactions between polymer beads. Since ε
P P
= 1ε is a weak
interaction parameter, the solvent quality can be considered as similar to the good
solvent quality. This shows that the presence of a solvophilic polymer does not alter
the entropic/enthalpic driving forces enough to change the ONA duplex stability. As
ε
P P increases from ε
PP
= 1ε to ε
PP
= 5ε, the melting curves of ONAs conjugated
with 40-mer and 100-mer polymers are shifted to higher temperatures as compared to
unconjugated ONAs. The increase in thermal stability of neutral and flexible ONAs
upon conjugation to weakly solvophobic polymers is due to the formation of polymer
aggregates which stabilize the linked ONA duplexes even at higher temperatures. A
representative snapshot of ONA duplexes on top of polymer aggregate is shown in
the inset of Fig. 5b.
Next, we present the results for negatively charged and semi-flexible ONAs (e.g.,
DNA) which are conjugated to solvophobic polymer (Fig. 5c, d). At ε
PP
= 1ε, similar
to neutral and flexible ONAs, we do not observe any effect of polymer conjugation
49
Fig. 5 Melting curves of flexible and neutral ONA with sequence d(GGGGCCCC) at 6 μM ONA
concentration for a ε PP = 1ε and b ε PP = 5ε. Melting curves of semi-flexible and negatively
charged ONA with sequence d(GGGGCCCC) at 6 μM ONA concentration for c ε PP = 1ε and
d ε PP = 5ε. Circles and down triangles represent ONAs conjugated to 40-mer (P 40 ) and 100-mer
(P 100 ), respectively. Black up triangles represent the case of unconjugated ONAs. Representative
snapshots of the ONA-polymer aggregates at a particular T * is also shown. Polymer is represented
in tan while G and C are represented in cyan and pink, respectively. The legend for a also holds for
b, c and d. Reproduced from Ref. [67] with permission from John Wiley and Sons
curves for both polymer lengths studied (Fig. 5a). This is consistent with published
results of Ghobadi and Jayaraman [20] where the polymer is solvophilic in nature
modeled with WCA interactions between polymer beads. Since ε
P P
= 1ε is a weak
interaction parameter, the solvent quality can be considered as similar to the good
solvent quality. This shows that the presence of a solvophilic polymer does not alter
the entropic/enthalpic driving forces enough to change the ONA duplex stability. As
ε
P P increases from ε
PP
= 1ε to ε
PP
= 5ε, the melting curves of ONAs conjugated
with 40-mer and 100-mer polymers are shifted to higher temperatures as compared to
unconjugated ONAs. The increase in thermal stability of neutral and flexible ONAs
upon conjugation to weakly solvophobic polymers is due to the formation of polymer
aggregates which stabilize the linked ONA duplexes even at higher temperatures. A
representative snapshot of ONA duplexes on top of polymer aggregate is shown in
the inset of Fig. 5b.
Next, we present the results for negatively charged and semi-flexible ONAs (e.g.,
DNA) which are conjugated to solvophobic polymer (Fig. 5c, d). At ε
PP
= 1ε, similar
to neutral and flexible ONAs, we do not observe any effect of polymer conjugation