Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs by Scanning Tunneling Microscopy and Computational Modeling

Abstract

We present a combined approach that relies on computational simulations and scanning tunneling microscopy (STM) measurements to reveal morphological properties and stability criteria of carbon nanotube-DNA (CNT-DNA) constructs. Application of STM allows direct observation of very stable CNT-DNA hybrid structures with the well-defined DNA wrapping angle of 63.4° and a coiling period of 3.3 nm. Using force field simulations, we determine how the DNA-CNT binding energy depends on the sequence and binding geometry of a single strand DNA. This dependence allows us to quantitatively characterize the stability of a hybrid structure with an optimal π-stacking between DNA nucleotides and the tube surface and better interpret STM data. Our simulations clearly demonstrate the existence of a very stable DNA binding geometry for (6,5) CNT as evidenced by the presence of a well-defined minimum in the binding energy as a function of an angle between DNA strand and the nanotube chiral vector. This novel approach demonstrates the feasibility of CNT-DNA geometry studies with subnanometer resolution and paves the way towards complete characterization of the structural and electronic properties of drug-delivering systems based on DNA-CNT hybrids as a function of DNA sequence and a nanotube chirality.

Figure 1

Raman spectra of the prepared DNA-CNT solution. (a) The wide frequency window showing all vibronic bands. (b) The frequency range associated with RBM bands of nanotubes.

Figure 2

STM data and theoretical interpretation: (a) 21 × 21 nm STM topographic image of CNT-DNA hybrids on Si(110) substrate acquired at I _t = 10 pA and U _b = 3 V at 50 K; (b) height profile along Section A; (c) statistical distribution of characteristic lengths of periodic modulations extracted from height profiles along the Section A. (d) Optimized structures of (6,5) tube wrapped in GAGAAGAGAGCAGAAGGAGA-oligomer. For the simulated geometry, the average period of DNA helices along the tube is  A = 3.0–3.3 nm and the wrapping angle is α ~ 63°, which are in good agreement with an STM experiment.

Figure 3

Optimized geometries of the (6,5) tube with adsorbed C-mers obtained from different initial wrapping configurations. First column shows the averaged final wrapping angle α of the DNA. Second and third columns correspond to hybrid configurations constructed from the 3 and 4 repeat units long (6,5) nanotube and DNA consisting of 25 (C-25-mer) and 29 (C-29-mer) cytosine bases, respectively. The bottom panel shows 31 and 42 C-mers wrapped along (6,5) tube of 4 units in length.

Figure 4

Variation of the binding energy of the CNT-DNA hybrids with the DNA wrapping angle. The solid lines correspond to hybrid configurations with fixed ends, that is, where the end bases of the DNA molecule are fixed and all other atoms of the hybrid system are free to move during geometry optimization. Dashed lines represent the optimized hybrid structure where all the atoms are allowed to move during optimization. The red line corresponds to the hybrid constructed out of 3 unit-long (6,5) tube (3u) and DNA strand consisting of 25 guanine bases (G-25); the black line represents the same tube but with 25-mer cythosine bases (C-25); the dark green line represents (6,5) tube of 4 repeat units in length (4u) with adsorbed 23-mer cythosine bases (C-23). The light green dashed line corresponds to configurations constructed from the (6,5) nanotube of 4 repeat units in length (4u) and 29-mer cythosine bases (C-29).