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

Distinguishing Antioxidant Molecules with Near-Infrared Photoluminescence of DNA-Wrapped Single-Walled Carbon Nanotubes

In this study, two biomolecule solutions were distinguished using the capacity difference in the near-infrared photoluminescence (PL) of single-walled carbon nanotubes (SWNTs). Biosensing techniques using sensitive responses of SWNTs have been intensively studied. When a small amount of an oxidant or reductant solution was injected into the SWNT suspensions, the PL intensity of the SWNTs is significantly changed. However, distinguishing between different molecules remains challenging. In this study, we comparably injected saponin and banana solutions, which are known antioxidant chemicals, into an SWNT suspension. The SWNTs were solubilized by wrapping them with DNA molecules. The results show that 69.1 and 155.2% increases of PL intensities of SWNTs were observed after injection of 20 and 59 μg/mL saponin solutions, respectively. Subsequently, the increase in PL was saturated. With the banana solution, 18.1 and 175.4% increases in PL intensities were observed with 20 and 59 μg/mL banana solutions, respectively. Based on these results, the two antioxidant molecules could be distinguished based on the different PL responses of the SWNTs. In addition, the much higher saturated PL intensities observed with the banana solution suggests that the banana solution increased the capacity of the PL increase for the same SWNT suspension. These results provide helpful information for establishing biosensing applications of SWNTs, particularly for distinguishing chemicals.

Optical Response Characteristics of Single-Walled Carbon Nanotube Chirality Exposed to Oxidants with Different Oxidizing Power

Semiconductor single-walled carbon nanotubes (SWNTs) have unique characteristics owing to differences in the three-dimensional structure (chirality) expressed by the chiral index (n,m), and many studies on the redox characteristics of chirality have been reported. In this study, we investigated the relationship between the chirality of SWNTs and the oxidizing power of oxidants by measuring the near-infrared (NIR) absorption spectra of two double-stranded DNA-SWNT complexes with the addition of three oxidants with different oxidizing powers. A dispersion was prepared by mixing 0.5 mg of SWNT powder with 1 mg/mL of DNA solution. Different concentrations of hydrogen peroxide (H₂O₂), potassium hexachloroidylate (IV) (K₂IrCl₆), or potassium permanganate (KMnO₄) were added to the dispersion to induce oxidation. Thereafter, a catechin solution was added to observe if the absorbance of the oxidized dispersion was restored by the reducing action of the catechin. We found that the difference in the oxidizing power had a significant effect on the detection sensitivity of the chiralities of the SWNTs. Furthermore, we revealed a detectable range of oxidants with different oxidizing powers for each chirality.

Restriction Enzyme Analysis of Double-Stranded DNA on Pristine Single-Walled Carbon Nanotubes

Nanoprobes such as single-walled carbon nanotubes (SWCNTs) are capable of label-free detection that benefits from intrinsic and photostable near-infrared fluorescence. Despite the growing number of SWCNT-based applications, uncertainty surrounding the nature of double-stranded DNA (dsDNA) immobilization on pristine SWCNTs has limited their use as optical sensors for probing DNA-protein interactions. To address this limitation, we study enzyme activity on unmodified dsDNA strands immobilized on pristine SWCNTs. Restriction enzyme activity on various dsDNA sequences was used to verify the retention of the dsDNA's native conformation on the nanotube surface and to quantitatively compare the degree of dsDNA accessibility. We report a 2.8-fold enhancement in initial enzyme activity in the presence of surfactants. Förster resonance electron transfer (FRET) analysis attributes this enhancement to increased dsDNA displacement from the SWCNT surface. Furthermore, the accessibility of native dsDNA was found to vary with DNA configuration and the spacing between the restriction site and the nanotube surface, with a minimum spacing of four base pairs (bp) from the anchoring site needed to preserve enzyme activity. Molecular dynamics (MD) simulations verify that the anchored dsDNA remains within the vicinity of the SWCNT, revealing an unprecedented bimodal displacement of the bp nearest to SWCNT surface. Together, these findings illustrate the successful immobilization of native dsDNA on pristine SWCNTs, offering a new near-infrared platform for exploring vital DNA processes.

Differences in the response of the near-infrared absorbance spectra of single-walled carbon nanotubes; Effects of chirality and wrapping polymers

We detected antioxidant activity of catechin, one of the main components of tea, using SWNTs surface coated with two different biomolecules. Compared to coating with DNA already reported, it can hardly be detected when coated with carboxymethyl cellulose. For nanobiosensing using SWNTs, its sensitivity is not determined only by SWNTs, we found that biomolecules covering the surface are extremely important. In this experiment, we measured the near-infrared absorption spectra of SWNTs coated separately with two different water-soluble polymers; DNA (double-stranded DNA-SWNT complexes) and carboxymethyl cellulose (CMC, CMC-SWNT complexes), and uncovered the differences in their antioxidant properties against the flavonoid catechin. Each dispersion was oxidized with H₂O₂ at 0.03% (final concentration), following which catechin solutions were added to reduce the samples. Our results showed that the magnitude of the change in the absorbance spectra for dsDNA-SWNT complexes in response to oxidation and reduction was superior to that for CMC-SWNT complexes. The CMC-SWNT complexes exhibited almost no change in their spectra even though the same SWNT powder (produced by the high-pressure carbon monoxide (HiPco) method) was used. On the other hand, when (6, 5)-enriched SWNT powder produced by the ComoCat method was used, no significant change in the absorbance was observed, even though (6, 5)-enriched SWNTs are frequently used for nanobiosensing. Our results revealed that both the SWNT chirality and type of polymer for wrapping SWNTs are important factors for establishing nanobiosensing methods utilizing SWNTs.

A fundamental study of photoluminescence modulation from DNA-wrapped single-walled carbon nanotubes

In this study, we investigated the interaction of base sequence-assigned single-stranded DNA (ssDNA) molecules with the surfaces of single-walled carbon nanotube (SWNT)-thymine (T30)/cytosine (C30) hybrids (T30/C30-SWNT), by measuring the modulation of near-infrared (NIR) photoluminescence (PL). Significant PL shifts were observed when T30/C30-SWNTs were reacted with 30-mers of adenine (A30)/guanine (G30). In contrast, when non-complementary ssDNA was used, no significant energy shift was observed in the PL modulation except when T30-SWNTs were reacted with G30. Furthermore, atomic force microscopy (AFM) measurements revealed that the average heights of the T30-SWNTs and C30-SWNTs, after reaction with A30 were 2 ± 0.6 and 1.1 ± 0.3 nm, respectively. This result was in good agreement with the results of PL measurements. Our data reveal that DNA hybridization could be detected by measuring PL from SWNTs, without the use of fluorescent molecules. This leads to the possibility of developing nanotube-based photoelectric conversion or optical switch devices driven by organic molecules.

Scanning Techniques for Nanobioconjugates of Carbon Nanotubes

Nanobioconjugates using carbon nanotubes (CNTs) are attractive and promising hybrid materials. Various biological applications using the CNT nanobioconjugates, for example, drug delivery systems and nanobiosensors, have been proposed by many authors. Scanning techniques such as scanning electron microscopy (SEM) and scanning probe microscopy (SPM) have advantages to characterize the CNT nanobioconjugates under various conditions, for example, isolated conjugates, conjugates in thin films, and conjugates in living cells. In this review article, almost 300 papers are categorized based on types of CNT applications, and various scanning data are introduced to illuminate merits of scanning techniques.

Using a fluorescence quenching method to detect DNA adsorption onto single-walled carbon nanotube surfaces

Surface modification of single-walled carbon nanotubes (SWNTs) with DNA molecules has attracted much attention in recent years to increase SWNT solubility and make various SWNT-based nanobiodevices. Therefore, there is a critical need to quantify the interaction between DNA molecules and SWNT surfaces, particularly the intermediate structures during DNA adsorption. In this study, we demonstrate the ability to detect the adsorption of DNA oligomers on SWNT surfaces by fluorescence spectroscopy. Fluorescein-labelled, 30mer, thymine oligonucleotides (F-T30) were employed as a fluorescent probe to study the interaction of DNA with SWNTs. A clear quenching effect was observed when F-T30 was adsorbed onto SWNT surfaces. Using this method, the amount of DNA adsorbed onto the SWNT surfaces was measured under different sonication conditions to correlate adsorption efficiency with sonication strength and duration. When a bath-type sonicator was used, mild adsorption of F-T30 on SWNT surfaces was observed. Furthermore, a two-step adsorption was observed in this condition. In contrast, we observed rapid adsorption of F-T30 to SWNT surfaces at the higher sonication amplitude (60% maximal) using a probe-type sonicator, while only slight adsorption of DNA molecules was observed at the lower amplitude (20% maximal). Our data revealed that the quenching effect can be used to evaluate DNA adsorption onto SWNT surfaces. In addition, atomic force microscopy (AFM) and photoacoustic spectroscopy (PAS) were conducted to provide complementary information on the DNA-SWNT nanoconjugates.

Conjugates between photosystem I and a carbon nanotube for a photoresponse device

Photosystem I (PS I) is a large pigment-protein complex embedded in the thylakoid membranes that performs light-driven electron transfer across the thylakoid membrane. Carbon nanotubes exhibit excellent electrical conductivities and excellent strength and stiffness. In this study, we generated PSI-carbon nanotube conjugates dispersed in a solution aimed at application in artificial photosynthesis. PS I complexes in which a carbon nanotube binding peptide was introduced into the middle of the PsaE subunit were conjugated on a single-walled carbon nanotube, orienting the electron acceptor side to the nanotube. Spectral and photoluminescence analysis showed that the PS I is bound to a single-walled carbon nanotube, which was confirmed by transmission electron microscopy. Photocurrent observation proved that the photoexcited electron originated from PSI and transferred to the carbon nanotube with light irradiation, which also confirmed its orientated conjugation. The PS I-carbon nanotube conjugate will be a useful nano-optoelectronic device for the development of artificial systems.

Adsorption of DNA binding proteins to functionalized carbon nanotube surfaces with and without DNA wrapping

We examined the adsorption of DNA binding proteins on functionalized, single-walled carbon nanotubes (SWNTs). When SWNTs were functionalized with polyethylene glycol (PEG-SWNT), moderate adsorption of protein molecules was observed. In contrast, nanotubes functionalized with CONH₂ groups (CONH₂-SWNT) exhibited very strong interactions between the CONH₂-SWNT and DNA binding proteins. Instead, when these SWNT surfaces were wrapped with DNA molecules (thymine 30-mers), protein binding was a little decreased. Our results revealed that DNA wrapped PEG-SWNT was one of the most promising candidates to realize DNA nanodevices involving protein reactions on DNA-SWNT surfaces. In addition, the DNA binding protein RecA was more adhesive than single-stranded DNA binding proteins to the functionalized SWNT surfaces.

Probe Microscopic Studies of DNA Molecules on Carbon Nanotubes

Hybrids of DNA and carbon nanotubes (CNTs) are promising nanobioconjugates for nanobiosensors, carriers for drug delivery, and other biological applications. In this review, nanoscopic characterization of DNA-CNT hybrids, in particular, characterization by scanning probe microscopy (SPM), is summarized. In many studies, topographical imaging by atomic force microscopy has been performed. However, some researchers have demonstrated advanced SPM operations in order to maximize its unique and valuable functions. Such sophisticated approaches are attractive and will have a significant impact on future studies of DNA-CNT hybrids.

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.

Physisorption of DNA molecules on chemically modified single-walled carbon nanotubes with and without sonication

We investigated the physisorption phenomenon of single-stranded DNA (ssDNA) molecules onto two types of commercially available chemically functionalized single-walled carbon nanotubes (SWNTs) by atomic force microscopy (AFM) and agarose gel electrophoresis. We found that DNA molecules can adsorb on the water-soluble SWNT surfaces without sonication, although sonication treatment has been used for hybridization of DNA and SWNTs in many previous studies. Using our method, damage of DNA molecules by sonication can be avoided. On the other hand, the amount of DNA molecules adsorbed on SWNT surfaces increased when the samples were sonicated. This fact suggests that the sonication is effective not only at debundling of SWNTs, but also at assisting DNA adsorption. Furthermore, DNA adsorption was affected by the types of functionalized SWNTs. In the case of SWNTs functionalized with polyethylene glycol (PEG-SWNT), physisorption of ssDNA molecules was confirmed only by agarose-gel electrophoresis. In contrast, amino-terminated SWNTs (NH2-SWNTs) showed a change in the height distribution profile based on AFM observations. These results suggest that DNA molecules tended to adsorb to NH2-SWNT surfaces, although DNA molecules can also adsorb on PEG-SWNT surfaces. Our results revealed fundamental information for developing nanobiodevices using hybrids of DNA and SWNTs.

Protein Adsorption on Hybrids of Thermoresponsive Polymers and Single-Walled Carbon Nanotubes

Poly(N-isopropylacrylamide) (PNIPAAm) is one of the most popular thermoresponsive polymers. Adsorption of RecA proteins onto hybrids of PNIPAAm and single-walled carbon nanotubes (SWNTs) was observed in the presence and absence of DNA molecules. Although RecA molecules were adsorbed efficiently onto the hybrid surfaces at 37°C, even in the absence of DNA molecules, the adsorption of RecA was inhibited at 4°C. These results suggest that the thermoresponsive functions of PNIPAAm were effective, even on the SWNT surfaces, which supports the possibility of developing nanobiodevices using PNIPAAm-SWNT hybrids. However, although RecA is a DNA binding protein, there was no significant difference in the adsorption of RecA onto PNIPAAm-SWNT surfaces with and without DNA molecules. This study provides fundamental information for potential biological applications of PNIPAAm-SWNT hybrids.

Hybrids of Nucleic Acids and Carbon Nanotubes for Nanobiotechnology

Recent progress in the combination of nucleic acids and carbon nanotubes (CNTs) has been briefly reviewed here. Since discovering the hybridization phenomenon of DNA molecules and CNTs in 2003, a large amount of fundamental and applied research has been carried out. Among thousands of papers published since 2003, approximately 240 papers focused on biological applications were selected and categorized based on the types of nucleic acids used, but not the types of CNTs. This survey revealed that the hybridization phenomenon is strongly affected by various factors, such as DNA sequences, and for this reason, fundamental studies on the hybridization phenomenon are important. Additionally, many research groups have proposed numerous practical applications, such as nanobiosensors. The goal of this review is to provide perspective on biological applications using hybrids of nucleic acids and CNTs.