Molecular-Basis of Single-Walled Carbon Nanotube Recognition by Single-Stranded DNA

Hybrids of biological molecules and single-walled carbon nanotubes (SWCNT) have proven useful for SWCNT sorting and are enabling several biomedical applications in sensing, imaging, and drug delivery. In the DNA-SWCNT system, certain short (10–20mer) sequences of single-stranded DNA recognize specific SWCNT, allowing the latter to be sorted from a chirality diverse mixture. However, little is known about the DNA secondary structures that underlie their recognition of SWCNTs. Using replica exchange molecular dynamics (REMD) of multiple strands on a single SWCNT, we report that DNA forms ordered structures on SWCNTs that are strongly DNA sequence and SWCNT dependent. DNA sequence (TAT)₄ on its recognition partner, the (6,5) SWCNT, forms an ordered right-handed helically wrapped barrel, stabilized by intrastrand, self-stitching hydrogen bonds and interstrand hydrogen bonding. The same sequence on the larger diameter (8,7)-SWCNT forms a different and less-stable structure, demonstrating SWCNT selectivity. In contrast, homopolymer (T)₁₂, with weaker tendency for intrastrand hydrogen bonding, forms a distinctly left-handed wrap on the (6,5)-SWCNT, demonstrating DNA sequence specificity. Experimental measurements show that (TAT)₄ selectively disperses smaller diameter SWCNTs more efficiently than (T)₁₂, establishing a relationship between recognition motifs and binding strength. The developing understanding of DNA secondary structure on nanomaterials can shed light on a number of issues involving hybrids of nanomaterials and biological molecules, including nanomedicine, health-effects of nanomaterials, and nanomaterial processing.