Guanine-Specific Chemical Reaction Reveals ssDNA Interactions on Carbon Nanotube Surfaces

Abstract

Understanding the conformations of physisorbed single-stranded DNA (ssDNA) oligos on single-wall carbon nanotube (SWCNT) surfaces is important for advancing basic nanoscience and for developing applications in biomedicine and quantum information processing. Here we report evidence that the ssDNA strands are partly desorbed from the nanotube surface under common conditions. SWCNT suspensions were prepared in eight ssDNA oligos, each containing 1 guanine and 30 thymine bases but differing in the position of the guanine within the strand. Singlet oxygen exposure then covalently functionalized the guanine to the SWCNT surface, red-shifting the nanotube fluorescence by an amount reflecting the guanine spatial density at the surface. Spectral shifts were greatest for central guanine positions and smallest for end positions. In conjunction with steered molecular dynamics simulations, the results suggest that steric interference between neighboring ssDNA strands on an individual nanotube causes significant dislocation or desorption of the strand ends while central regions remain better wrapped around the nanotube. This effect decreases with decreasing concentrations of free ssDNA.

Compositional Analysis of ssDNA-Coated Single-Wall Carbon Nanotubes through UV Absorption Spectroscopy

“…A variety of scientific and engineering applications, including sorting SWCNTs by structure, require raw samples to be disaggregated and dispersed into stable liquid suspensions with SWCNT surfaces coated by surfactants or polymers. Short strands of single-stranded DNA (ssDNA) have emerged as one of the most important coating types. − …”

“…Although a typical snapshot (see Figure S10) illustrates that ∼33% of the SWCNT atoms within the average DNA axial length of a DNA strand remain uncovered, the computation modeled only a single DNA strand. It therefore could not simulate interactions among strands that would lead to higher surface coverage, such as axial DNA compression or overlapped helical wrapping motifs that cover exposed regions. More extensive computations that include a range of ( n , m ) species may clarify the role of such effects in this and similar systems.…”

Signatures of Chemical Dopants in Simulated Resonance Raman Spectroscopy of Carbon Nanotubes

“…The mode at 300 cm -1 also shows the same trends as the 600-cm -1 mode but with smaller intensity. These two modes at 300 and 600 cm -1 originate from the sp 3 -defect located at the center of the SWCNT and demonstrate that these intermediate energy frequencies (200 -700 cm -1 ) are enhanced in the experimental resonant Raman spectra due to sp 3 -lattice defects. However, the mode near 800 cm -1 seems to be edge-dominated.…”

“…Chemical control of surface modification in single-walled carbon nanotubes (SWCNTs) has recently taken a leap forward after developing new synthetic routes to functionalize SWCNTs with single-strand DNA (ssDNA) [1][2][3] wrapping, photochemistry utilizing singlet and triplet state pathways, 4,5 as well as well-established chemistries using diazonium salts, hypochlorite, and ozone functionalizations. [6][7][8][9] In all these cases, chemical doping creates a low-lying defect-associated E11 * exciton state below the fundamental E11 exciton band of SWCNT that has improved optical properties and tunability.…”

“…[6][7][8][9] In all these cases, chemical doping creates a low-lying defect-associated E11 * exciton state below the fundamental E11 exciton band of SWCNT that has improved optical properties and tunability. For example, in case of ssDNA wrapping, it is hypothesized that the guanine nucleotide base uniquely reacts with the SWCNT surface to form a sp 3 -or sp 2 -hybridiztion defect with complete control over the spacing between the adjacent defects and hence their interdefect interactions and exciton delocalization properties. When utilizing photochemical routes, the photoexcited triplet pathway, in the absence of triplet-quenching oxygen species, has been shown to produce experimentally new atomistic configurations of defects expanding diversity of bonding configurations on the SWCNT lattice.…”