Ordered DNA Wrapping Switches on Luminescence in Single-Walled Nanotube Dispersions

Mapping the Morphology of DNA on Carbon Nanotubes in Solution Using X-ray Scattering Interferometry

Single-walled carbon nanotubes (SWCNTs) with adsorbed single-stranded DNA (ssDNA) are applied as sensors to investigate biological systems, with potential applications ranging from clinical diagnostics to agricultural biotechnology. Unique ssDNA sequences render SWCNTs selectively responsive to target analytes such as (GT)n-SWCNTs recognizing the neuromodulator, dopamine. It remains unclear how the ssDNA conformation on the SWCNT surface contributes to functionality, as observations have been limited to computational models or experiments under dehydrated conditions that differ substantially from the aqueous biological environments in which the nanosensors are applied. We demonstrate a direct mode of measuring in-solution ssDNA geometries on SWCNTs via X-ray scattering interferometry (XSI), which leverages the interference pattern produced by AuNP tags conjugated to ssDNA on the SWCNT surface. We employ XSI to quantify distinct surface-adsorbed morphologies for two (GT)n ssDNA oligomer lengths (n = 6, 15) that are used on SWCNTs in the context of dopamine sensing and measure the ssDNA conformational changes as a function of ionic strength and during dopamine interaction. We show that the shorter oligomer, (GT)6, adopts a more periodically ordered ring structure along the SWCNT axis (inter-ssDNA distance of 8.6 ± 0.3 nm), compared to the longer (GT)15 oligomer (most probable 5'-to-5' distance of 14.3 ± 1.1 nm). During molecular recognition, XSI reveals that dopamine elicits simultaneous axial elongation and radial constriction of adsorbed ssDNA on the SWCNT surface. Our approach using XSI to probe solution-phase morphologies of polymer-functionalized SWCNTs can be applied to yield insights into sensing mechanisms and inform future design strategies for nanoparticle-based sensors.

Computer Aided Development of Nucleic Acid Applications in Nanotechnologies

Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.

Approximate Corona Phase Hamiltonian for Individual Cylindrical Nanoparticle-Polymer Interactions

Nanoparticle surfaces, such as cylindrical nanowires and carbon nanotubes, are commonly coated with adsorbed polymer corona phases to impart solution stabilization and to control molecular interactions. These adsorbed polymer molecules (biological or otherwise), also known as the corona phase, are critical to engineering particle and molecular interactions. However, the prediction of its structure and the corresponding properties remains an unresolved problem in polymer physics. In this work, we construct a Hamiltonian describing the adsorption of an otherwise linear polymer to the surface of a cylindrical nanorod in the form of an integral equation summing up the energetic contributions corresponding to polymer bending, confinement, solvation, and electrostatics. We introduce an approximate functional that allows for the solution of the minimum energy configuration in the strongly bound limit. The functional is shown to predict the pitch and surface area of observed helical corona phases in the literature based on the surface binding energy and persistence length alone. This approximate functional also predicts and quantitatively describes the recently observed ionic strength-mediated phase transitions of charged polymer corona at carbon nanotube surfaces. The Hamiltonian and the approximate functional provide the first theoretical link between the polymer's mechanical and chemical properties and the resulting adsorbed phase configuration and therefore should find widespread utility in predicting corona phase structures around anisotropic nanoparticles.

Adsorption of Polyadenylic acid on graphene oxide: experiments and computer modeling

In this work, we study the adsorption of poly(rA) on graphene oxide (GO) using AFM and UV absorption spectroscopies. A transformation of the homopolynucleotide structure on the GO surface is observed. It is found that an energetically favorable conformation of poly(rA) on GO is achieved after a considerable amount of time (days). It is revealed that GO can induce formation of self-structures of single-stranded poly(rA) including a duplex at pH 7. The phenomenon is analyzed by polymer melting measurements and observed by AFM. Details of the noncovalent interaction of poly(rA) with graphene are also investigated using molecular dynamics simulations. The adsorption of (rA)₁₀ oligonucleotide on graphene is compared with the graphene adsorption of (rC)₁₀. DFT calculations are used to determine equilibrium structures and the corresponding interaction energies of the adenine-GO complexes with different numbers of the oxygen-containing groups. The IR intensities and vibrational frequencies of free and adsorbed adenines on the GO surface are calculated. The obtained spectral transformations are caused by the interaction of adenine with GO.

Dispersion quality of single-walled carbon nanotubes reveals the recognition sequence of DNA

The specific recognition between DNA and single-walled carbon nanotubes (SWCNTs) has enabled wide applications, especially in the chiral sorting of SWCNTs. However, the molecular recognition mechanism has not been fully understood. In our work, various DNA-SWCNT dispersions were prepared by the ultrasonic dispersion method, and characterized by UV absorption spectroscopy, fluorescence emission spectroscopy, zeta potential measurement, SDBS exchange kinetics and computer simulation. The effect of DNA sequence on the structure and properties of hybrid molecules was analyzed. Data analysis showed that DNA with specific recognition had better dispersion quality of the corresponding SWCNT, which means that higher content of monodispersed SWCNTs was obtained. The high-quality dispersion of the DNA-SWCNT pair was attributed to the stronger binding between DNA and SWCNT, resulting in a tighter conformation of DNA on the SWCNT surface and a larger zeta potential of DNA-SWCNT hybrids. Consequently, DNA-SWCNT dispersions of the recognition pair exhibited better stability against salt and stronger fluorescence emission intensity. However, the correlation between specific recognition and DNA coverage on SWCNT was not observed. This work gives more insight into the recognition mechanism between DNA and SWCNTs.

Experimental Evidence of Single-Stranded DNA Adsorption on Multiwalled Carbon Nanotubes

Noncovalent DNA functionalization is one of the most used routes for the easy dispersion of carbon nanotubes (CNTs) yielding DNA-CNTs complexes with promising applications. Definition of the structure of adsorbed DNA is crucial, but the organization of polymer at the carbon interface is far from being understood. In comparison to single-walled nanotubes, not much effort has been devoted to assessing the structure of the adsorbed DNA on multiwalled carbon nanotubes (MWCNTs), where their metallic nature, large size, and polydispersity represent serious obstacles for both experimental and theoretical studies. As a contribution to fill this lack in these aspects, we investigated DNA-MWCNT complexes by dielectric spectroscopy (DS) which is sensitive to even small changes in the charge distribution at charged interfaces and was largely employed in studying the electric and conformational properties of polyelectrolytes, such as DNA, in aqueous solutions and at interfaces. The dielectric relaxation in the MHz range is the signature of DNA adsorption on CNTs and sheds light on its conformational properties. A detailed analysis of the conductivity of the DNA-MWCNT suspensions unequivocally proves that DNA is adsorbed in a single-stranded conformation while excess DNA reassociates without interfering with the stability of the complexes.

Templating colloidal sieves for tuning nanotube surface interactions and optical sensor responses

Surfactants offer a tunable approach for modulating the exposed surface area of a nanoparticle. They further present a scalable and cost-effective means for suspending single-walled carbon nanotubes (SWCNTs), which have demonstrated practical use as fluorescence sensors. Though surfactant suspensions show record quantum yields for SWCNTs in aqueous solutions, they lack the selectivity that is vital for optical sensing. We present a new method for controlling the selectivity of optical SWCNT sensors through colloidal templating of the exposed surface area. Colloidal nanotube sensors were obtained using various concentrations of sodium cholate, and their performances were compared to DNA-SWCNT optical sensors. Sensor responses were measured against a library of bioanalytes, including neurotransmitters, amino acids, and sugars. We report an intensity response towards dopamine and serotonin for all sodium cholate-suspended SWCNT concentrations. We further identify a selective, 14.1 nm and 10.3 nm wavelength red-shifting response to serotonin for SWCNTs suspended in 1.5 and 0.5 mM sodium cholate, respectively. Through controlled, adsorption-based tuning of the nanotube surface, this study demonstrates the applicability of sub-critical colloidal suspensions to achieve selectivities exceeding those previously reported for DNA-SWCNT sensors.

Optoelectrical and mechanical properties of multiwall carbon nanotube-integrated DNA thin films

Thin films made of deoxyribonucleic acid (DNA), dissolved in an aqueous solution, and cetyltrimethyl-ammonium-modified DNA (CDNA), dissolved in an organic solvent, utilising multiwall carbon nanotubes (MWCNTs) are not yet well-understood for use in optoelectronic device and sensor applications. In this study, we fabricate MWCNT-integrated DNA and CDNA thin films using the drop-casting method. We also characterise the optical properties (i.e. absorption spectra, Fourier-transform infrared spectra, Raman spectra, photoluminescence, and time-of-flight secondary ion mass spectrometry) to study spectral absorption, interaction, functional group, chirality, and compositional moiety and its distribution of MWCNTs in DNA and CDNA thin films. The electrical property for conductance and the mechanical characterisations of hardness, modulus and elasticity for stability are also discussed. Lastly, to show the feasibility of directional alignment of MWCNTs in DNA thin films, we perform an alignment experiment with MWCNTs in DNA via brushing and shearing methods, and we evaluate the results using polarised optical microscopy. Our simple methodology to align ingredients in DNA and CDNA thin films leveraging various optical, electrical and mechanical properties, provides great potential for the development of efficient devices and sensors.

Long Carbon Nanotubes Functionalized with DNA and Implications for Spintronics

Helical molecules such as DNA have recently been found to behave as an efficient source and detector of spin-polarized charge carriers. This phenomenon, often dubbed as chirality-induced spin selectivity or CISS, could be used to significantly improve the performance of spintronic devices, which utilize carrier spins (rather than charge) to realize electronic and sensing functions. Recently, it has been reported that carbon nanotubes, helically wrapped with DNA, can also act as an efficient source and detector of spin-polarized carriers, by virtue of spin-orbit coupling originating from the helical potential. It has been postulated that spin polarization should increase with the length of the wrapped tubes. However, in literature, most fabrication processes yield tubes with submicron lengths, which can produce ∼70% spin polarization. In an effort to enhance this effect further, here, we report a fabrication process that can yield DNA-wrapped nanotubes of length ∼1-4 microns. Detailed characterization of these devices, using atomic force microscopy, Raman, UV-vis, and temperature-dependent transport, has been presented. Initial transport measurements indicate the presence of strong magnetoresistance in these tubes, which could be attributed to spin-dependent effects. Systematic fabrication of long DNA-wrapped nanotubes, which has hitherto not been reported, is expected to enable further investigation into the spin-dependent properties of these ultimate one-dimensional nanoscale hybrids and may have a significant impact on nanoscale spintronics.

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.

Debundling, Dispersion, and Stability of Multiwalled Carbon Nanotubes Driven by Molecularly Designed Electron Acceptors

Carbon nanotubes (CNTs) have attracted significant attention because of their outstanding physical and chemical properties, and yet, their high natural tendency to form bundles, ropes, or aggregates, as a consequence of their strong π-π interactions, limits their solvent processing and further applications. Efficient processing solvents, mostly amide-based, that partially compensate for these strong inter-CNT π-π interactions have been widely reported. However, the yield of debundled/dispersed CNTs and the stability of subsequent dispersions in these solvents remain key challenges. Moreover, there are major concerns related to the large-scale use of conventional solvents, as they are fossil fuel based and intrinsically highly toxic, hence the need to identify environmentally friendly and safer alternatives. Herein, we address these challenges by using a ternary system composed of multiwalled CNTs (MWCNTs), tailored electron-deficient acceptors, and an organic solvent. Not only do the electron-deficient acceptors interrupt the inter-CNTs π-π interactions, thereby enabling the subsequent debundling and dispersion of MWCNTs aggregates in the solvent, they also act as stabilizers, after dispersion, by inhibiting inter-CNT π-π interactions and re-agglomeration. The use of electron acceptors increases the yield by a factor of 165 in N-methyl 2-pyrrolidone, improves the long-term stability of the debundled and dispersed MWCNTs, and reduces the energy input to only 30 min of mild bath sonication, compared with prolonged high-energy sonication reported in the literature. We also report for the first time, the use in MWCNT processing of a "green" biosolvent, dihydrolevoglucosenone, as an environmentally friendly and nontoxic alternative to the more conventional amide-based solvents.

Reversible dispersion and release of carbon nanotubes via cooperative clamping interactions with hydrogen-bonded nanorings

Due to their outstanding electronic and mechanical properties, single-walled carbon nanotubes (SWCNTs) are promising nanomaterials for the future generation of optoelectronic devices and composites. However, their scarce solubility limits their application in many technologies that demand solution-processing of high-purity SWCNT samples. Although some non-covalent functionalization approaches have demonstrated their utility in extracting SWCNTs into different media, many of them produce short-lived dispersions or ultimately suffer from contamination by the dispersing agent. Here, we introduce an unprecedented strategy that relies on a cooperative clamping process. When mixing (6,5)SWCNTs with a dinucleoside monomer that is able to self-assemble in nanorings via Watson-Crick base-pairing, a synergistic relationship is established. On one hand, the H-bonded rings are able to associate intimately with SWCNTs by embracing the tube sidewalls, which allows for an efficient SWCNT debundling and for the production of long-lasting SWCNT dispersions of high optical quality along a broad concentration range. On the other, nanoring stability is enhanced in the presence of SWCNTs, which are suitable guests for the ring cavity and contribute to the establishment of multiple cooperative noncovalent interactions. The inhibition of these reversible interactions, by just adding, for instance, a competing solvent for hydrogen-bonding, proved to be a simple and effective method to recover the pristine nanomaterial with no trace of the dispersing agent.

Monitoring the antioxidant effects of catechin using single-walled carbon nanotubes: Comparative analysis by near-infrared absorption and near-infrared photoluminescence

We measured the optical responses of single-walled carbon nanotubes (SWNTs) after adding Japanese green tea or catechin. SWNTs were covered with DNA in aqueous solution, and tea or catechin solution was added to the DNA-SWNT suspension. The antioxidant effects of tea and catechin were detected as changes in the near-infrared (NIR) absorption (ABS) and NIR-photoluminescence (PL) spectra of the SWNTs. Commercial Japanese tea, diluted 100 times and containing 15μg/mL catechin, was sufficient for recovering NIR-ABS and NIR-PL spectra when the DNA-SWNT suspension was pre-treated with 0.03% hydrogen peroxide(H₂O₂). Similar results were obtained with 15μg/mL of pure catechin solution. SWNTs with specific chirality were sensitive to the NIR-ABS and NIR-PL changes. The (10, 5)/(8, 7) and (9, 4) SWNTs showed the highest recovery in NIR-ABS and NIR-PL, respectively. NIR-PL recovery was higher than that of NIR-ABS for (10, 5)/(8, 7) and (9, 4). Spectral changes could be monitored thoroughly at pH 8.0, contrary to pH 6.0 and 7.3. However, the most dynamic recovery of NIR-ABS and NIR-PL was observed at pH 6.0. Furthermore, time-lapse measurements revealed that recovery was faster with tea or catechin addition than H₂O₂-induced oxidation.

DNA-Assisted Dispersion of Carbon Nanotubes and Comparison with Other Dispersing Agents

Separation and sorting of pristine carbon nanotubes (CNTs) from bundle geometry is a very challenging task due to the insoluble and nondispersive nature of CNTs in aqueous medium. Recently, many studies have been performed to address this problem using various organic and inorganic solutions, surfactant molecules, and biomolecules as dispersing agents. Recent experimental studies have reported the DNA to be highly efficient in dispersing CNTs from bundle geometry. However, there is no microscopic study and also quantitative estimation of the dispersion efficiency of the DNA. Using all-atom molecular dynamics simulation, we study the structure and stability of single-stranded DNA (ssDNA)-single-walled carbon nanotube (SWNT) (6,5) complex. To quantify the dispersion efficiency of various DNA sequences, we perform potential of mean forces (PMF) calculation between two bare SWNTs as well ssDNA-wrapped CNTs for different base sequences. From the PMF calculation, we find the PMF between two bare (6,5) SWNTs to be approximately -29 kcal/mol. For the ssDNA-wrapped SWNTs, the PMF reduces significantly and becomes repulsive. In the presence of ssDNA of different polynucleotide bases (A, T, G, and C), we present a microscopic picture of the ssDNA-SWNT (6,5) complex and also a quantitative estimate of the interaction strength between nanotubes from PMF calculation. From PMF, we show the sequence of dispersion efficiency for four different nucleic bases to be T > A > C > G. We have also presented a comparison of the dispersion efficiencies of ssDNA, flavin mononucleotide surfactant, and poly(amidoamine) (PAMAM) dendrimer by comparing their respective PMF values.

DNA-Carbon Nanotube Complexation Affinity and Photoluminescence Modulation Are Independent

Short single-stranded DNA (ssDNA) has emerged as the natural polymer of choice for noncovalently functionalizing photoluminescent single-walled carbon nanotubes. In addition, specific empirically identified DNA sequences can be used to separate single species (chiralities) of nanotubes, with an exceptionally high purity. Currently, only limited general principles exist for designing DNA-nanotube hybrids amenable to separation processes, due in part to an incomplete understanding of the fundamental interactions between a DNA sequence and a specific nanotube structure, whereas even less is known in the design of nanotube-based sensors with determined optical properties. We therefore developed a combined experimental and analysis platform on the basis of time-resolved near-infrared fluorescence spectroscopy to extract the complete set of photoluminescence parameters that characterizes DNA-nanotube hybrids. Here, we systematically investigated the affinity of the d(GT)_n oligonucleotide family for structurally defined carbon nanotubes by measuring photoluminescence response of the nanotube upon oligonucleotide displacement. We found, surprisingly, that the rate of displacement of the oligonucleotides is independent of the coverage on the nanotube, as inferred through the intrinsic optical properties of the hybrid. The kinetics of intensity modulation is essentially a single-exponential, and the time constants, which quantify the stability of DNA binding, span an order of magnitude. Surprisingly, these time constants do not depend on the intrinsic optical parameters within the hybrids, suggesting that the DNA-nanotube stability is not due to increased nanotube surface coverage by DNA. Further, a principal component analysis of the excitation and emission shifts along with intensity enhancement at equilibrium accurately identified the (8,6) nanotube as the partner chirality to (GT)₆ ssDNA. When combined, the chirality-resolved equilibrium and kinetics data can guide the development of the DNA-nanotube pairs, with tunable stability and optical modulation. Additionally, this high-throughput optical platform could function as a primary screen for mapping the DNA-chirality recognition phase space.

Dendrimer assisted dispersion of carbon nanotubes: a molecular dynamics study

Various unique physical, chemical, mechanical and electronic properties of carbon nanotubes (CNTs) make them very useful materials for diverse potential application in many fields. Experimentally synthesized CNTs are generally found in bundle geometry with a mixture of different chiralities and present a unique challenge to separate them. In this paper we have proposed the PAMAM dendrimer to be an ideal candidate for this separation. To estimate the efficiency of the dendrimer for the dispersion of CNTs from the bundle geometry, we have calculated potential of mean forces (PMF). Our PMF study of two dendrimer-wrapped CNTs shows lesser binding affinity compared to the two bare CNTs. PMF study shows that the binding affinity decreases for non-protonated dendrimer, and for the protonated case the interaction is fully repulsive in nature. For both the non-protonated as well as protonated cases, the PMF increases gradually with increasing dendrimer generations from 2 to 4 compared to the bare PMF. We have performed PMF calculations with (6,5) and (6,6) chirality to study the chirality dependence of PMF. Our study shows that the PMFs between two (6,5) and two (6,6) CNTs respectively are ∼-29 kcal mol^-1 and ∼-27 kcal mol^-1. Calculated PMF for protonated dendrimer-wrapped chiral CNTs is more compared to the protonated dendrimer-wrapped armchair CNTs for all the generations studied. However, for non-protonated dendrimer-wrapped CNTs, such chirality dependence is not very prominent. Our study suggests that the dispersion efficiency of the protonated dendrimer is more compared to the non-protonated dendrimer and can be used as an effective dispersing agent for the dispersion of CNTs from the bundle geometry.

Carbon Nanomaterials and DNA: from Molecular Recognition to Applications

DNA is polymorphic. Increasing evidence has indicated that many biologically important processes are related to DNA's conformational transition and assembly states. In particular, noncanonical DNA structures, such as the right-handed A-form, the left-handed Z-form, the triplex, the G-quadruplex, the i-motif, and so forth, have been specific targets for the diagnosis and therapy of human diseases. Meanwhile, they have been widely used in the construction of smart DNA nanomaterials and nanoarchitectures. As rising stars in materials science, the family of carbon nanomaterials (CNMs), including two-dimensional graphene, one-dimensional carbon nanotubes (CNTs), and zero-dimensional graphene or carbon quantum dots (GQDs or CQDs), interact with DNA and are able to regulate the conformational transitions of DNA. The interaction of DNA with CNMs not only opens new opportunities for specific molecular recognition, but it also expands the promising applications of CNMs from materials science to biotechnology and biomedicine. In this Account, we focus on our contributions to the field of interactions between CNMs and DNA in which we have explored their promising applications in nanodevices, sensing, materials synthesis, and biomedicine. For one-dimensional CNTs, two-dimensional graphene, and zero-dimensional GQDs and CQDs, the basic principles, binding modes, and applications of the interactions between CNMs and DNA are reviewed. We aim to give prominence to the important status of CNMs in the field of molecular recognition for DNA. First, we summarized our discovery of the interactions between single-walled carbon nanotubes (SWNTs) with duplex, triplex, and human telomeric i-motif DNA and their interesting applications. For example, SWNTs are the first chemical agents that can selectively stabilize human telomeric i-motif DNA and induce its formation under physiological conditions. On the basis of this principle, two types of nanodevices were designed. One was used for highly sensitive detection of ppm levels of SWNTs in cells, and the other monitored i-motif DNA formation. Further studies indicated that SWNTs could inhibit telomerase activity in living cells and cause telomere dysfunction, providing new insight into the biological effects of SWNTs. Then, some applications that are based on the interactions between graphene and DNA are also summarized. Combined with other nanomaterials, such as metal and upconversion nanoparticles, several hybrid nanomaterials were successfully constructed, and a series of DNA logic gates were successfully developed. Afterwards, the newcomer of the carbon nanomaterials family, carbon quantum dots (CQDs), were found to be capable of modulating right-handed B-form DNA to left-handed Z-form DNA. These were further used to design FRET logic gates that were based on the CQD-derived DNA conformational transition. Taking into account the remaining challenges and promising aspects, CNM-based DNA nanotechnology and its biomedical applications will attract more attention and produce new breakthroughs in the near future.

Carbon nanomaterials: multi-functional agents for biomedical fluorescence and Raman imaging

Carbon based nanomaterials have emerged over the last few years as important agents for biomedical fluorescence and Raman imaging applications. These spectroscopic techniques utilize either fluorescently labelled carbon nanomaterials or the intrinsic photophysical properties of the carbon nanomaterial. In this review article we present the utilization and performance of several classes of carbon nanomaterials, namely carbon nanotubes, carbon nanohorns, carbon nanoonions, nanodiamonds and different graphene derivatives, which are currently employed for in vitro as well as in vivo imaging in biology and medicine. A variety of different approaches, imaging agents and techniques are examined and the specific properties of the various carbon based imaging agents are discussed. Some theranostic carbon nanomaterials, which combine diagnostic features (i.e. imaging) with cell specific targeting and therapeutic approaches (i.e. drug delivery or photothermal therapy), are also included in this overview.

Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes

Noncovalent polymer-single walled carbon nanotube (SWCNT) conjugates have gained recent interest due to their prevalent use as electrochemical and optical sensors, SWCNT-based therapeutics, and for SWCNT separation. However, little is known about the effects of polymer-SWCNT molecular interactions on functional properties of these conjugates. In this work, we show that SWCNT complexed with related polynucleotide polymers (DNA, RNA) have dramatically different fluorescence stability. Surprisingly, we find a difference of nearly 2500-fold in fluorescence emission between the most fluorescently stable DNA-SWCNT complex, C30 DNA-SWCNT, compared to the least fluorescently stable complex, (AT)7A-(GU)7G DNA-RNA hybrid-SWCNT. We further reveal the existence of three regimes in which SWCNT fluorescence varies nonmonotonically with SWCNT concentration. We utilize molecular dynamics simulations to elucidate the conformation and atomic details of SWCNT-corona phase interactions. Our results show that variations in polynucleotide sequence or sugar backbone can lead to large changes in the conformational stability of the polymer SWCNT corona and the SWCNT optical response. Finally, we demonstrate the effect of the coronae on the response of a recently developed dopamine nanosensor, based on (GT)15 DNA- and (GU)15 RNA-SWCNT complexes. Our results clarify several features of the sequence dependence of corona phases produced by polynucleotides adsorbed to single walled carbon nanotubes, and the implications for molecular recognition in such phases.

Non-covalent polymer wrapping of carbon nanotubes and the role of wrapped polymers as functional dispersants

Carbon nanotubes (CNTs) have been recognized as a promising material in a wide range of applications from biotechnology to energy-related devices. However, the poor solubility in aqueous and organic solvents hindered the applications of CNTs. As studies have progressed, the methodology for CNT dispersion was established. In this methodology, the key issue is to covalently or non-covalently functionalize the surfaces of the CNTs with a dispersant. Among the various types of dispersions, polymer wrapping through non-covalent interactions is attractive in terms of the stability and homogeneity of the functionalization. Recently, by taking advantage of their stability, the wrapped-polymers have been utilized to support and/or reinforce the unique functionality of the CNTs, leading to the development of high-performance devices. In this review, various polymer wrapping approaches, together with the applications of the polymer-wrapped CNTs, are summarized.

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.

DNA-Assisted Solubilization of Carbon Nanotubes and Construction of DNA-MWCNT Cross-Linked Hybrid Hydrogels

A simple method for preparation of DNA-carbon nanotubes hybrid hydrogel based on a two-step procedure including: (i) solubilization of multi-walled carbon nanotubes (MWCNT) in aqueous solution of DNA, and (ii) chemical cross-linking between solubilized MWCNT via adsorbed DNA and free DNA by ethylene glycol diglycidyl ether is reported. We show that there exists a critical concentration of MWCNT below which a homogeneous dispersion of MWCNT in hybrid hydrogel can be achieved, while at higher concentrations of MWCNT the aggregation of MWCNT inside hydrogel occurs. The strengthening effect of carbon nanotube in the process of hydrogel shrinking in solutions with high salt concentration was demonstrated and significant passivation of MWCNT adsorption properties towards low-molecular-weight aromatic binders due to DNA adsorption on MWCNT surface was revealed.

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.

Surfactant concentration dependent spectral effects of oxygen and depletion interactions in sodium dodecyl sulfate dispersions of carbon nanotubes

Quenching of optical absorbance spectra for carbon nanotubes (CNTs) dispersed in sodium dodecyl sulfate (SDS) has been observed to be more pronounced at higher concentrations of the surfactant. The protonation-based quenching behavior displays wavelength dependence, affecting larger diameter nanotube species preferentially. Although absorbance may be recovered by hydroxide addition, pH measurements suggest that hydrolysis of SDS does not play a major role in the short term quenching behavior at high SDS concentrations. The degree of quenching is observed to correlate well with an increase in attractive depletion as SDS concentration is increased, while the extent of depletion is found to depend heavily on the concentration of preparation in comparison to the final SDS concentration. Attractive depletion in SDS is also found to be preferential for CNTs of larger diameter. It is proposed that depletion enhances the quenching effect due to close association of CNT-SDS complexes providing higher SDS densities on the CNT surface, leading to further oxidation. In addition, the quenching behavior in SDS is found to strongly suppress the optical and Raman signal from metallic nanotube species even at high pH. Displacement of SDS by sodium deoxycholate as a secondary surfactant is able to reverse the effects of protonation of metallic species, whereas hydroxide addition is only partially effective.

Binding between DNA and carbon nanotubes strongly depends upon sequence and chirality

Certain single-stranded DNA (ssDNA) sequences are known to recognize their partner single-walled carbon nanotube (CNT). Here, we report on activation energies for the removal of several ssDNA sequences from a few CNT species by a surfactant molecule. We find that DNA sequences systematically have higher activation energy on their CNT recognition partner than on non-partner species. For example, the DNA sequence (TAT)4 has much lower activation energy on the (9,1) CNT than on its partner (6,5) CNT, whereas the DNA sequence (CCA)10 binds strongly to its partner (9,1) CNT compared to (6,5) CNT. The (6,5) and (9,1) CNTs have the same diameter but different electronic properties, suggesting that the activation energy difference is related to electronic properties. The activation energies of increasing lengths of closely related sequences from the 11-mer (TAT)3TA to the 21-mer (TAT)7 on three different CNT species (9,1), (6,5), and (8,3) were measured. For the shorter sequences, the activation energy on the CNT varies periodically with the sequence.

Molecular modeling in structural nano-toxicology: interactions of nano-particles with nano-machinery of cells

Over the past two decades, nanotechnology has emerged as a key player in various disciplines of science and technology. Some of the most exciting applications are in the field of biomedicine - for theranostics (for combined diagnostic and therapeutic purposes) as well as for exploration of biological systems. A detailed understanding of the molecular interactions between nanoparticles and biological nano-machinery - macromolecules, membranes, and intracellular organelles - is crucial for obtaining adequate information on mechanisms of action of nanomaterials as well as a perspective on the long term effects of these materials and their possible toxicological outcomes. This review focuses on the use of structure-based computational molecular modeling as a tool to understand and to predict the interactions between nanomaterials and nano-biosystems. We review major approaches and provide examples of computational analysis of the structural principles behind such interactions. A rationale on how nanoparticles of different sizes, shape, structure and chemical properties can affect the organization and functions of nano-machinery of cells is also presented.

pH- and solute-dependent adsorption of single-wall carbon nanotubes onto hydrogels: mechanistic insights into the metal/semiconductor separation

The gel separation of single-wall carbon nanotubes (SWCNTs) suspended in sodium dodecyl sulfate (SDS) is expected to be one of the most successful methods of large-scale and high-purity separation. Understanding the mechanism of the gel separation helps improve the quality and quantity of separation and reveals the colloidal behaviors of SWCNTs, which reflects their band structures. In this study, we characterize the pH- and solute-dependent adsorption of SWCNTs onto agarose and Sephacryl hydrogels and provide a mechanistic model of the metal/semiconductor separation. The adsorbability of SWCNTs is substantially reduced under acidic pH conditions. Importantly, the pH dependence differs between metallic and semiconducting species; therefore, the adsorbability is related to the band-structure-dependent oxidation of the SWCNTs. Oxidation confers positive charges on SWCNTs, and these charges enhance the electrostatic interactions of the SWCNTs with SDS, thereby leading to the condensation of SDS on the SWCNTs. This increase in SDS density reduces the interactions between the SWCNTs and hydrogels. Under highly basic conditions, such as pH ∼12.5, or in the presence of salts, the adsorption is dissociative because of the condensation of SDS on the SWCNTs through electrostatic screening by counterions. Desorption of the SWCNTs from the hydrogels due to the addition of urea implies a hydrophobic interface between SDS-dispersed SWCNTs and the hydrogels. These results suggest that the metal/semiconductor separation can be explained by the alteration of the interaction between SDS-dispersed SWCNTs and the hydrogels through changes in the conformation of SDS on the SWCNTs depending on the SWCNTs' band structures.

Nanotubes complexed with DNA and proteins for resistive-pulse sensing

We use a resistive-pulse technique to analyze molecular hybrids of single-wall carbon nanotubes (SWNTs) wrapped in either single-stranded DNA or protein. Electric fields confined in a glass capillary nanopore allow us to probe the physical size and surface properties of molecular hybrids at the single-molecule level. We find that the translocation duration of a macromolecular hybrid is determined by its hydrodynamic size and solution mobility. The event current reveals the effects of ion exclusion by the rod-shaped hybrids and possible effects due to temporary polarization of the SWNT core. Our results pave the way to direct sensing of small DNA or protein molecules in a large unmodified solid-state nanopore by using nanofilaments as carriers.

Effect of Polymer Molecular Weight and Solution Parameters on Selective Dispersion of Single-Walled Carbon Nanotubes

The selective dispersion of single-walled carbon nanotube species (n,m) with conjugated polymers such as poly(9,9-dioctylfluorene) (PFO) and poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) in organic solvents depends not only on the type of solvent but also on the molecular weight of the polymer. We find an increasing amount of nanotubes and altered selectivities for dispersions with higher molecular weight polymers. Including the effects of different aromatic solvents, we propose that solution viscosity is one of the factors influencing the apparent selectivity by changing the reaggregation rate of the single-walled carbon nanotubes (SWNT). The type of solvent, polymer molecular weight, concentration, and viscosity should thus be taken into account when screening for new polymers for selective SWNT dispersion.

Peculiarities of homooligonucleotides wrapping around carbon nanotubes: molecular dynamics modeling

Spontaneous adsorption of homooligonucleotides dC(25), dT(25), dG(25), and dA(25) on the surface of the carbon nanotube (16,0) has been simulated by the molecular dynamics method. It was demonstrated that the rate of pyrimidine oligonucleotide wrapping around the nanotube is higher than that of purine ones which do not form a complete pitch even after the maximum simulation time (50 ns). This behavior can be explained by a stronger self-stacking between the purines than pyrimidines, which prevents the reorientation of the polymer required for the acquisition of a more energetically favored conformation on the nanotube. Estimations obtained from modeling allowed to establish the oligonucleotide row which demonstrates decreasing interaction energies between oligonucleotides and the carbon nanotube: d(T)(25) > d(C)(25) > d(A)(25) ≈ d(G)(25). It was shown that the temperature growth increases the rate of oligonucleotides to reach the maximum binding energy mainly due to the destruction of nitrogen base self-stacking. Ribonucleic oligonucleotides r(C)(25), r(A)(25), and r(G)(25) do not make a pitch around the nanotube for 50 ns. The presence of the additional hydroxyl group in ribose restricts the conformational flexibility of ribonucleic oligonucleotides in comparison with their deoxy analogues and this reduces the possibility of rapid occupation of the stable conformation on the nanotube surface.

Recognition ability of DNA for carbon nanotubes correlates with their binding affinity

The ability to sort mixtures of carbon nanotubes (CNTs) based on chirality has recently been demonstrated using special short DNA sequences that recognize certain matching CNTs of specific chirality. In this work, we report on a study of the relationship between recognition sequences and the strength of their binding to the recognized CNT. We have chosen the (6,5) CNT and its corresponding DNA recognition sequences for investigation in this study. Binding strength is quantified by studying the kinetics of DNA replacement by a surfactant, which is monitored by following shifts in the absorption spectrum. We find that recognition ability correlates strongly with binding strength thus measured; addition or subtraction of just one base from the recognition sequence can enhance the kinetics of DNA displacement some 20-fold. The surfactant displaces DNA in two steps: a rapid first stage lasting less than a few seconds, followed by progressive removal lasting tens of minutes. The kinetics of the second stage is analyzed to extract activation energies. Fluorescence studies support the finding that the DNA sequence that recognizes the (6,5)-CNT forms a more stable hybrid than its close relatives.

Stabilization of unstable CGC+ triplex DNA by single-walled carbon nanotubes under physiological conditions

Triplex formation is a promising strategy for realizing artificially controlling of gene expression, reversible assembly of nanomaterials and DNA nanomachine and single-walled nanotubes (SWNTs) have been widely used as gene and drug delivery vector or as 'building blocks' in nano-/microelectronic devices. CGC(+) triplex is not as stable as TAT triplex. The poor stability of CGC(+) triplex limits its use in vitro and in vivo. There is no ligand that has been reported to selectively stabilize CGC(+) triplets rather than TAT. Here, we report that SWNTs can cause d(CT) • d(AG) duplex disproportionation into triplex d(C(+)T) • d(AG) • d(CT) and single-strand d(AG) under physiological conditions. SWNTs can reduce the stringency of conditions for CGC(+) triplex formation studied by UV-vis, CD, DNA melting, light scattering and atomic force microscopy. Further studies indicate that electrostatic interaction is crucial for d(CT) • d(AG) repartition into triplex d(C(+)T) • d(AG) • d(CT). Our findings may facilitate utilization of SWNTs-DNA complex in artificially controlling of gene expression, nanomaterials assembly and biosensing.

'Supramolecular wrapping chemistry' by helix-forming polysaccharides: a powerful strategy for generating diverse polymeric nano-architectures

We have exploited novel supramolecular wrapping techniques by helix-forming polysaccharides, β-1,3-glucans, which have strong tendency to form regular helical structures on versatile nanomaterials in an induced-fit manner. This approach is totally different from that using the conventional interpolymer interactions seen in both natural and synthetic polymeric architectures, and therefore has potential to create novel polymeric architectures with diverse and unexpected functionalities. The wrapping by β-1,3-glucans enforces the entrapped guest polymer to adopt helical or twisted conformations through the convergent interpolymer interactions. On the contrary, the wrapping by chemically modified semi-artificial β-1,3-glucans can bestow the divergent self-assembling abilities on the entrapped guest polymer to create hierarchical polymeric architectures, where the polymer/β-1,3-glucan composite acts as a huge one-dimensional building block. Based on the established wrapping strategy, we have further extended the wrapping techniques toward the creation of three-dimensional polymeric architectures, in which the polymer/β-1,3-glucan composite behaves as a sort of amphiphilic block copolymers. The present wrapping system would open several paths to accelerate the development of the polymeric supramolecular assembly systems, giving the strong stimuli to the frontier of polysaccharide-based functional chemistry.

Carbon nanotubes: measuring dispersion and length

Advanced technological uses of single-walled carbon nanotubes (SWCNTs) rely on the production of single length and chirality populations that are currently only available through liquid-phase post processing. The foundation of all of these processing steps is the attainment of individualized nanotube dispersions in solution. An understanding of the colloidal properties of the dispersed SWCNTs can then be used to design appropriate conditions for separations. In many instances nanotube size, particularly length, is especially active in determining the properties achievable in a given population, and, thus, there is a critical need for measurement technologies for both length distribution and effective separation techniques. In this Progress Report, the current state of the art for measuring dispersion and length populations, including separations, is documented, and examples are used to demonstrate the desirability of addressing these parameters.