DNA-SWNT Hybrids Research Articles

Interactions of Secondary DNA and Initial DNA on Single-Walled Carbon Nanotube Surfaces Studied by Photoluminescence, Atomic Force Microscopy, and Electrophoresis

We examined the interactions of initial single-stranded DNA (ssDNA) and secondary ssDNA molecules on single-walled carbon nanotubes (SWNTs). Thymine 30-mers (T30) and 30-mers from a partial sequence of φx174 DNA (φ30) were used to prepare the DNA-SWNT hybrids. First, the hybrids were annealed at various temperatures without secondary DNA to evaluate the stability of the hybrids. As a result, aggregates of SWNTs were formed in the T30-SWNT hybrids, even at 54°C, although the φ30-SWNT hybrids were stable up to 84°C. Second, we added secondary DNA molecules during the annealing procedure. We reacted adenine 30-mers (A30) with the T30-SWNT hybrids and characterized the samples by combining agarose gel electrophoresis with/without ethidium bromide and atomic force microscopy (AFM) as well as near-infrared photoluminescence (PL) spectroscopy. Cross-links appeared to form among the SWNTs because of nonspecific hybridization of T30 and A30. PL measurements revealed clear shifts in the PL emission wavelength of SWNTs. However, when complementary φ30 DNA (cφ30) was reacted with φ30-SWNT hybrids, there was no significant difference in the PL spectra after the reaction, although electrophoresis suggested the hybridization of the cφ30 and φ30 DNA molecules. Our results suggest that the hybridization manner of DNA molecules with unnatural sequences greatly differs from that of natural DNA molecules.

Novel Strategy for the Investigation on Chirality Selection of Single-Walled Carbon Nanotubes with DNA by Electrochemical Characterization.

There is a correlation between specific bases of DNA molecules and the chirality of single-walled carbon nanotubes (SWNTs), which contributes the recognition ability of DNA toward partner species of chiral SWNTs. A novel strategy of electrochemical characterization is reported here for the investigation on chirality selection of (7,6) and (6,5) SWNTs with various DNA sequences, and it is found that both DNA strand length and sequence composition significantly affected the interaction of chiral SWNTs with DNA. Then (7,6) and (6,5) SWNTs were distinguished from each other with DNA sequences chosen by electrochemical methods, which demonstrated an effective and excellent feasibility for the strategy and presented a new insight into DNA-SWNT applications. This strategy can also be applied to more chiral SWNTs and DNA sequence recognition and may serve as a prescreening method for the recognition and separation of single-chirality SWNTs, which would be a new contribution to the further development of DNA-SWNT hybrids.

Observation of Adsorption Process of Single Stranded DNA to Single-Walled Carbon Nanotubes Surfaces by Fluorescence Quenching

Single walled carbon nanotubes (SWNTs) are one of the promising nanomaterials for various applications in nanotechnology. In biomedical fields, hybrids of DNA and SWNT (DNA-SWNT hybrids) are expected to be attractive nanodevices for drug delivery and DNA sensors. For preparing DNA-SWNT hybrids, mixture of SWNT and DNA solutions are prepared via sonication. Although DNA-SWNT hybridization techniques have been established, the diverse sonication conditions in every paper may affect structures of DNA-SWNT hybrids. Here we report a method of monitoring adsorption process of DNA to SWNT surfaces using fluorescent labeled single-stranded DNA (Fluor-ssDNA). It is known that fluorescent emission of fluorescent dyes is quenched when the dye is adsorbed on SWNT surfaces. Using this unique quenching phenomenon, we evaluated adsorption process of Fluor-ssDNA on SWNT surfaces. In the experiments, 0.25 mg of SWNT powder, 50 uL of Fluor-ssDNA solution (1.0 mg/mL in tris (hydroxymethyl aminomethane buffer solution, 200mM, pH 7.5)), and 450 uL of the buffer were mixed, and then sonicated under three different sonication conditions as follows: probe type with amplitude 60% of 130 W (P60), probe type with amplitude 20% of 130 W (P20), and bath type with 80 W (B80). In order to monitor the adsorption process, samples were characterized by fluorescent spectroscopy and atomic force microscopy. In the case of P60, fluorescent intensity of Fluor-ssDNA decreased 98% within 2 min. This suggests that most of Fluor-ssDNA rapidly adsorbed on SWNT surfaces. However, AFM images demonstrated that it took more time to form mono-dispersed DNA-SWNT hybrids. In the case of P20 and B80, 30 min was needed for 98% quenching. In addition, reproducibility of the B80 data was much higher than that of P20. This is an advantage of bath type sonicator.

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.

Intense photoluminescence from dried double-stranded DNA and single-walled carbon nanotube hybrid

Semiconducting single-walled carbon nanotubes (SWNTs) show near-infrared photoluminescence (PL) when they are individually isolated. This was an obstacle to use photonic properties of SWNTs on a solid surface. We show that SWNTs wrapped with DNA maintain intense PL under the dry conditions. SWNTs are well isolated individually by DNA even when the DNA-SWNT hybrids are agglomerated. This finding opens up application of SWNTs to photonic devices.

Structures of Hybrids of DNA and Carbon Nanotubes Observed by Atomic Force Microscopy 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. First, longer SWNT molecules were observed when the SWNT was dispersed using a bath type sonicator. When a probe type sonicator was employed, much shorter SWNT molecules were observed in all of our experiments using several different SWNTs. The result suggests that effects of the type of sonicator on SWNT length were significant in contrast to that of the type of SWNTs. Second, SWNT functionalized with polyethyleneglycol (PEG SWNT), amino group (NH 2 SWNT), and carboxyl group (COOH SWNT) individually showed specific features in AFM images. Although NH 2 SWNT is typically soluble in organic solvents, uniform distribution was observed when DNA molecules were mixed with NH 2 SWNT. Finally, we observed DNASWNT 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.

1P122 一本鎖DNA結合蛋白質のDNA-SWNT複合体への選択的な吸着(05A.核酸:構造・物性,ポスター,日本生物物理学会年会第51回(2013年度))

1P122 一本鎖DNA結合蛋白質のDNA-SWNT複合体への選択的な吸着(05A.核酸:構造・物性,ポスター,日本生物物理学会年会第51回(2013年度))

Electronic Properties of Nonideal Nanotube Materials: Helical Symmetry Breaking in DNA Hybrids

Helical wrapping of single-strand DNA around single-wall nanotubes (SWNTs) results in the symmetry breaking and modification of the nanotube band structure. Empirical tight-binding theory was employed to investigate this symmetry breaking and modulation of the electronic and optical properties of a SWNT in the field of an ionized DNA. The model allows the computation of the polarization component of the hybrid's energy of cohesion, with a typical value of 0.5 eV per DNA base. A screening parameter that quantifies the response of the SWNT electrons to the DNA perturbation was obtained. SWNT symmetry breaking shows up in the optical absorption for light polarized across the SWNT axis. In addition, circular dichroism is predicted for DNA-SWNT hybrids, even when the nanotube itself is achiral. These optical effects may be used for experimental determination of the DNA wrapping.

Atomic force microscopic study on DNA-wrapping for different diameter single-wall carbon nanotubes

DNA-wrapped single-wall carbon nanotubes (DNA-SWNT hybrids) prepared from different diameter HiPco- and Arc-SWNTs were investigated by atomic force microscopy. The mean diameter of DNA-HiPco-SWNT hybrids is 1.94 nm that is consistent with one HiPco-SWNT (~ 0.9 nm) wrapped by DNA (~ 1 nm). On the other hand, the mean diameter of DNA-Arc-SWNT hybrids is 3.74 nm that can correspond to one Arc-SWNT (~ 1.4 nm) wrapped by several layers of DNA. It is suggested that the DNA-wrapping mechanism for large diameter Arc-SWNTs is different from that for small diameter HiPco-SWNTs.

Double-Stranded DNA Single-Walled Carbon Nanotube Hybrids for Optical Hydrogen Peroxide and Glucose Sensing

The unique optical properties of semiconducting single-walled carbon nanotubes (SWNTs) are exquisitely sensitive to variations in the surrounding environments. Here, we have studied the redox chemistry of SWNTs encased with double-stranded deoxyribonucleic acid (DNA) reacted with either hydrogen peroxide H2O2 or glucose in the presence of the glucose oxidase enzyme. The DNA-SWNT hybrids are prepared in aqueous solution by sonication that cuts the DNA into short fragments of 100−300 base pairs which efficiently wrap individual nanotubes. The DNA-SWNT hybrids are optically sensitive to H2O2 and glucose, and the hybrid surface can be regenerated by dialytically removing the hydrogen peroxide. This study reinforces the potential of DNA-SWNT hybrids for use in immunoassays and glucose sensing.

Raman study of DNA-wrapped single-wall carbon nanotube hybrids under various humidity conditions

DNA-wrapped single-wall carbon nanotubes (DNA-SWNT hybrids) under various humidity conditions were investigated by Raman spectroscopy. The G band, especially Breit–Wigner–Fano (BWF) line, in the Raman spectra of DNA-SWNT hybrids strongly depends on the relative humidity. In the high humidity range above 55%, the BWF coupling increases with decreasing humidity. On the contrary, in the low humidity range below 55%, the BWF coupling decreases with decreasing humidity. The origin of such humidity dependence is discussed in the light of the behavior of the absorption of the water vapor on DNA in air.