Takuya Hayashida

Surface morphology of hybrids of double-stranded DNA and single-walled carbon nanotubes studied by atomic force microscopy

We examined the formation of hybrids of double-stranded DNA (dsDNA) and single-walled carbon nanotubes (SWNTs), which has not been well investigated yet. In particular, the adsorption of dsDNA onto SWNT produced by chemical vapor deposition (CVD) was examined for the first time. When small amount of dsDNA was mixed with CVD SWNT, well dispersed hybrids with smooth surfaces were observed by atomic force microscopy (AFM). Through a comparison of dsDNA, single-stranded DNA (ssDNA), CVD SWNT, and high-pressure carbon monoxide process (HiPco) SWNT, we found that the surface morphology of the hybrids was independent of the DNA type. Even when sonicated salmon testes DNA, which has a random sequence and length, was employed, smooth surfaces were obtained on the dsDNA-CVD hybrids as well as on the ssDNA-CVD hybrids. The ratio of monodispersed SWNT and bundled SWNT in a dispersion solution was also not affected by the DNA type. In contrast, the quantity of the fabricated hybrids was affected by the types of DNA especially when HiPco SWNT was used. Our results indicated that characteristic features of the dsDNA-CVD hybrids and provide an enhanced understanding of the adsorption mechanism of dsDNA onto SWNTs.

Controlling the adsorption and desorption of double-stranded DNA on functionalized carbon nanotube surface

We demonstrated controlled adsorption and desorption of double-stranded DNA (dsDNA) on single-walled carbon nanotube (SWNT) surface functionalized with polyethyleneglycol (PEG SWNT). First, when dsDNA molecules were mixed with the PEG SWNT solution, the DNA molecules spontaneously adsorbed onto the PEG SWNT surface and formed dsDNA-PEG SWNT conjugates without sonication. Next, we succeeded in detaching the dsDNA adsorbed on PEG SWNT by annealing at 95°C for 30 min. These results were confirmed using atomic force microscopy, agarose gel electrophoresis, and micro-Raman spectroscopy. In contrast, when we used the usual SWNT produced by the high-pressure carbon monoxide method (HiPco SWNT), the DNA molecules were fragmented during the adsorption process as sonication was necessary for the hybridization of DNA-SWNT conjugates. Furthermore, detachment of DNA molecules from HiPco SWNT by annealing was impossible. Our method may be useful for developing DNA devices using SWNTs as substrates when it is combined with previously established various biochemical techniques.

Selective binding of single-stranded DNA-binding proteins onto DNA molecules adsorbed on single-walled carbon nanotubes

Single-stranded DNA-binding (SSB) proteins were treated with hybrids of DNA and single-walled carbon nanotubes (SWNTs) to examine the biological function of the DNA molecules adsorbed on the SWNT surface. When single-stranded DNA (ssDNA) was used for the hybridization, significant binding of the SSB molecules to the ssDNA-SWNT hybrids was observed by using atomic force microscopy (AFM) and agarose gel electrophoresis. When double-stranded DNA (dsDNA) was used, the SSB molecules did not bind to the dsDNA-SWNT hybrids in most of the conditions that we evaluated. A specifically modified electrophoresis procedure was used to monitor the locations of the DNA, SSB, and SWNT molecules. Our results clearly showed that ssDNA/dsDNA molecules on the SWNT surfaces retained their single-stranded/double-stranded structures.

Atomic Force Microscopy of DNA-wrapped Single-walled Carbon Nanotubes in Aqueous Solution

We evaluated hybrids of DNA and single-walled carbon nanotubes (SWNTs) in aqueous solution and in air using atomic force microscopy (AFM). Although intensive AFM observations of these hybrids were previously carried out for samples in air, this is the first report on AFM observations of these hybrids in solution. As expected, diameters of DNA-SWNT hybrids dramatically increased in tris(hydroxymethyl)aminomethane-ethylenediaminetetraacetic acid (TE) buffer solution. The data suggest that DNA molecules maintain their structures even on the SWNT surfaces. Furthermore, we simultaneously observed single DNA-SWNT hybrids using three different AFM modes in air and in the TE buffer solution. Height value of the hybrids was largest in the solution, and lowest for the mode that repulsive force is expected in air. For the bare SWNT molecules, height differences among the three AFM modes were much lower than those of the DNA-SWNT hybrids. DNA molecules adsorbed on SWNT surfaces flexibly changed their morphology as well as DNA molecules on flat surfaces such as mica. This is hopeful results for biological applications of DNA-SWNT hybrids. In addition, our results revealed the importance of the single-molecule approach to evaluate DNA structures on SWNT surfaces.

Atomic force microscopy imaging of dialyzed single-walled carbon nanotubes dispersed with sodium dodecyl sulfate

The existence of excess sodium dodecyl sulfate (SDS) molecules in a single-walled carbon nanotube (SWNT) solution dispersed by hybridization with SDS leads to unstable atomic force microscopy (AFM) imaging. In this study, we demonstrate sequential dialysis against pure water in order to remove excess SDS molecules from an SDS-SWNT hybrid dispersion. A 1:102 volume ratio of SDS-SWNT dispersion to water in the dialysis was found to be effective in realizing stable AFM observations of the SDS-SWNT hybrids despite imperfect filtering of SDS via dialysis. On the other hand, the SDS-SWNT hybrids were stable even when this volume ratio was 1:106. Further, the SDS-SWNT hybrids were present in the solution even when the dialyzed samples were stored for 14 days. Our results reveal that dialysis under optimal conditions enables improved handling of SDS-SWNT hybrids, particularly for stable AFM observations.

Structures of hybrids of DNA and carbon nanotubes in air and in liquids

We investigated single-walled carbon nanotubes (SWNT) and DNA-SWNT hybrids by atomic force microscopy (AFM). From the AFM observation of several different types of SWNTs and DNA-SWNT hybrids in air, we found several specific differences in morphology among the samples. Longer SWNT molecules were observed when the SWNT was dispersed using a bath type sonicator. When a probe type sonicator was used, the SWNT became short obviously. The phenomenon was common in all of our experiments, thus, the phenomenon was independent on the types SWNTs. SWNT functionalized with polyethyleneglycol (PEG SWNT), amino group (NH2 SWNT), and carboxyl group (COOH SWNT) showed individual specific features in AFM images. Although NH2 SWNT is typically soluble in organic solvents, uniform distribution was observed when DNA molecules were mixed with NH2 SWNT. Finally, we observed DNA-SWNT hybrids by AFM in liquids for the first time. DNA-SWNT hybrids were significantly swollen in the aqueous solution even though the sample was dried once. This is helpful information for considering biological applications of the DNA-SWNT hybrids.