Endohedral Confinement of a DNA Dodecamer onto Pristine Carbon
Nanotubes and the Stability of the Canonical B Form
Fernando J. A. L. Cruz, Juan J. de Pablo and José P. B. Mota
Supplemental Material
FIG. SI1 – Dickerson DNA dodecamer employed in the calculations. Representation of the B-DNA
Dickerson dodecamer[1] with the sequence 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)3': (left) longitudinal view and (right) perspective along the double-strand internal volume. PO43 ions
are depicted as yellow (P) and red (O) tetrahedra and the deoxyribose rings as grey pentagons
connecting an individual nucleobase to the corresponding strand. For a clearer view of the double helix
internal volume, nucleobases are coloured according to the chemical nature of the corresponding rings,
namely red (A), pink (C), green (G), and light blue (T). Note that the whole DNA molecule is
atomistically detailed in the calculations, and thus each individual atom has a corresponding partial
electrostatic charge.
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FIG. SI2 – Energetic profiles. A) van der Waals interactions with the solid. The strong energetic
stabilization of the double-strand upon confinement, EDNA/SWCNT = – 442 ± 0.3 kJ/mol, is mainly due to
the purines contribution (E(A,G)/SWCNT = – 262.3 ± 0.2 kJ/mol), whose interaction with graphitic-like
solids are enhanced[2] compared with the pyrimidine moieties (E(T,C)/SWCNT = – 179.7 ± 0.1 kJ/mol):
black) DNA/SWCNT, green) (A,G)/SWCNT, purple) (T,C)/SWCNT. B) Nucleobase pairs interaction
energies. The inter-strand energetic stability of the double-helix arises essentially from the strong
pairing between complimentary G and C nucleotides, which result in pairs that are ca. 2.7 times more
stable than the corresponding AT pairs, Etot(GC) = 291.9 kJ/mol , Etot(AT) = 110.2 kJ/mol: dark blue)
van der Waals A/T, light blue) electrostatic A/T, dark red) van der Waals G/C and light red)
electrostatic G/C. C) Time averaged energies of interaction between DNA and H2O/Ions (Na+, Cl–).
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FIG. SI 3 – Two-dimensional maps of DNA@(51,0) SWCNT number density. The existence of a
cylindrical exclusion volume close to the nanopore walls, where molecular density ® 0, is the direct
consequence of direct repulsion between the heavily charged phosphate groups and the hydrophobic
(electrically neutral) solid walls. The dashed lines indicate the boundaries of the (51,0) single-walled
carbon nanotube.
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FIG. SI4 – Geometrical definition of nucleobase molecular plane. Three atoms (red dots) are
considered to define the molecular plane (red lines) used in the intrastrand stacking calculations: in the
pyrimidine moieties (T, C) it has one vertex located on the atom connecting the nucleobase and the
sugar, whilst in the purine molecules (A, G) the molecular plane spans both rings.
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FIG. SI5 – Convergence profiles of the metadynamics order parameters. Each line corresponds to a
1
4 ns integration time of equation 2 performed for each order parameter, F i   
4
 j 4 ns
 V  ,t dt , and the
i
j
open dots are the relative free energy minima identified by the four snapshots depicted in the three–
dimensional landscape, F 1 , 2  (Fig. 2). The convergence analysis was performed over the last 40 ns
of simulation time and therefore 10 differently coloured lines are depicted according to: green) 30–38
ns, pink) 38–42 ns, red) 42–58 ns, blue) 62–66 ns, black) 66–70 ns. Note that the overall F 1  and
F 2  lines, obtained in ∆t = 40–70ns and also depicted in black, overlap the final 4 ns timewindow
(66–70 ns). It becomes clear that the free-energy profiles are essentially converged to the corresponding
minima after ca. 60 ns, with only minor contributions being added to the free-energy from this time
onwards; the energetic landscape recorded in Fig. 2 is an accurate representation of the
thermodynamical free-energy changes associated with the confinement process.
[1]
[2]
H. R. Drew et al., Proc. Nat. Acad. Sci. 78, 2179 (1981).
F. J. A. L. Cruz, J. J. de Pablo, and J. P. B. Mota, RSC Advances 4, 1310 (2014).
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