Certain single-stranded DNA (ssDNA) sequences are known to recognize their partner single-walled carbon nanotube (CNT). Here, we report on activation energies for the removal of several ssDNA sequences from a few CNT species by a surfactant molecule. We find that DNA sequences systematically have higher activation energy on their CNT recognition partner than on non-partner species. For example, the DNA sequence (TAT)4 has much lower activation energy on the (9,1) CNT than on its partner (6,5) CNT, whereas the DNA sequence (CCA)10 binds strongly to its partner (9,1) CNT compared to (6,5) CNT. The (6,5) and (9,1) CNTs have the same diameter but different electronic properties, suggesting that the activation energy difference is related to electronic properties. The activation energies of increasing lengths of closely related sequences from the 11-mer (TAT)3TA to the 21-mer (TAT)7 on three different CNT species (9,1), (6,5), and (8,3) were measured. For the shorter sequences, the activation energy on the CNT varies periodically with the sequence.

Single- and double-stranded DNA are increasingly being paired with surfaces and nanoparticles for numerous applications, such as sensing, imaging, and drug delivery. Unlike the majority of DNA structures in bulk that are stabilized by canonical Watson-Crick pairing between Ade-Thy and Gua-Cyt, those adsorbed on surfaces are often stabilized by noncanonical base pairing, quartet formation, and base-surface stacking. Not much is known about these kinds of interactions. To build an understanding of the role of non-Watson-Crick pairing on DNA behavior near surfaces, one requires basic information on DNA base pair stacking and hydrogen-bonding interactions. All-atom molecular simulations of DNA bases in two cases--in bulk water and strongly adsorbed on a graphite surface--are conducted to study the relative strengths of stacking and hydrogen bond interactions for each of the 10 possible combinations of base pairs. The key information obtained from these simulations is the free energy as a function of distance between two bases in a pair. We find that stacking interactions exert the dominant influence on the stability of DNA base pairs in bulk water as expected. The strength of stability for these stacking interactions is found to decrease in the order Gua-Gua > Ade-Gua > Ade-Ade > Gua-Thy > Gua-Cyt > Ade-Thy > Ade-Cyt > Thy-Thy > Cyt-Thy > Cyt-Cyt. On the other hand, mutual interactions of surface-adsorbed base pairs are stabilized mostly by hydrogen-bonding interactions in the order Gua-Cyt > Ade-Gua > Ade-Thy > Ade-Ade > Cyt-Thy > Gua-Gua > Cyt-Cyt > Ade-Cyt > Thy-Thy > Gua-Thy. Interestingly, several non-Watson-Crick base pairings, which are commonly ignored, have similar stabilization free energies due to interbase hydrogen bonding as Watson-Crick pairs. This clearly highlights the importance of non-Watson-Crick base pairing in the development of secondary structures of oligonucleotides near surfaces.

Single-walled carbon nanotubes (SWCNTs) coated with single-stranded DNA can be effectively separated into various chiralities using an aqueous two-phase (ATP) system. Partitioning is driven by small differences in the dissolution characteristics of the hybrid between the two phases. Thus, in addition to being a separation technique, the ATP system potentially also offers a way to quantify and rank the dissolution properties of the solute (here the DNA/SWCNT hybrids), such as the solvation free energy and solubility. In this study, we propose two different approaches to quantitatively analyze the ATP partitioning of DNA/SWCNT hybrids. First, we present a model that extracts the relative solvation free energy of various DNA/SWCNT hybrids by using an expansion relative to a standard state. Second, we extract a solubility parameter by analyzing the partitioning of hybrids in the ATP system. The two approaches are found to be consistent, providing some confidence in each as a method of quantifying differences in the solubility of various DNA/SWCNT hybrids.

Hybrids of single-stranded DNA and single-walled carbon nanotubes (SWCNTs) have proven to be very successful in separating various chiralities and, recently, enantiomers of carbon nanotubes using aqueous two-phase separation. This technique sorts objects based on small differences in hydration energy, which is related to corresponding small differences in structure. Separation by handedness requires that a given ssDNA sequence adopt different structures on the two SWCNT enantiomers. Here we study the physical basis of such selectivity using a coarse-grained model to compute the energetics of ssDNA wrapped around an SWCNT. Our model suggests that difference by handedness of the SWCNT requires spontaneous twist of the ssDNA backbone. We also show that differences depend sensitively on the choice of DNA sequence.

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