DNA-wrapped Single-walled Carbon Nanotubes Research Articles

Predicting Serotonin Detection with DNA-Carbon Nanotube Sensors across Multiple Spectral Wavelengths.

Owing to the value of DNA-wrapped single-walled carbon nanotube (SWNT)-based sensors for chemically specific imaging in biology, we explore machine learning (ML) predictions DNA-SWNT serotonin sensor responsivity as a function of DNA sequence based on the whole SWNT fluorescence spectra. Our analysis reveals the crucial role of DNA sequence in the binding modes of DNA-SWNTs to serotonin, with a smaller influence of SWNT chirality. Regression ML models trained on existing data sets predict the change in the fluorescence emission in response to serotonin, ΔF/F, at over a hundred wavelengths for new DNA-SWNT conjugates, successfully identifying some high- and low-response DNA sequences. Despite successful predictions, we also show that the finite size of the training data set leads to limitations on prediction accuracy. Nevertheless, incorporating entire spectra into ML models enhances prediction robustness and facilitates the discovery of novel DNA-SWNT sensors. Our approaches show promise for identifying new chemical systems with specific sensing response characteristics, marking a valuable advancement in DNA-based system discovery.

Prediction of Mycotoxin Response of DNA-Wrapped Nanotube Sensor with Machine Learning

DNA-wrapped single-walled carbon nanotubes (SWCNTs) have demonstrated great versatility in their use as optical sensors. SWCNTs emit a near-infrared fluorescence that is responsive to even the slightest changes in the nanotube environment, enabling sensors that can respond to single-molecule fluctuations within the vicinity of their surfaces. The fluorescence response and surface interactions of these sensors are determined by the DNA wrapping sequence. However, the lack of information on the relationship between the DNA sequence and its effect on the SWCNT fluorescence remains a bottleneck for designing sequences that are specific to analytes of interest. We have recently demonstrated the use of directed volution to control the fluorescence response of SWCNTs through DNA design. Iterative cycles of DNA mutation, screening, and selection allowed us to evolve sequences that yield DNA-wrapped SWCNT sensors with a desired fluorescence response to mycotoxins.In this work, we apply the screening results of the DNA libraries used in this approach to train machine learning (ML) algorithms. Artificial neural network (ANN) and support vector machine (SVM) methods were used to predict the response of ssDNA-SWCNT sensors to a specific mycotoxin. The reliability of these models was further assessed through cross-validation. The ANN and SVM models with cross-validation were able to accurately classify the various DNA sequences as yielding either a high or low fluorescence response with an accuracy of 73 and 81%, respectively. The models were further used to predict the performance of alternative DNA sequences outside the initial training dataset, using the Hierarchy and k-means++ clustering methods to evaluate the similarity and dissimilarity of each DNA sequence. Compared to the SVM model, the ANN model showed an improved ability to predict high responses for dissimilar DNA sequences. We further applied a combinatorial approach based on SVM and ANN models to design new DNA sequences for improving sensor performance. The success of this approach was validated experimentally, demonstrating the rational design of improved sensors with 95% prediction accuracy.The application of ML algorithms to directed evolution libraries of DNA thus allows one to accurately map the performances of these sensors within a particular sequence space. The computational success of this mapping provides a framework for replacing current empirical approaches with the rational design of DNA sequences for SWCNT sensing. Keywords: Nano Biosensor, DNA-SWCNT, Mycotoxin, Machine learning, Directed evolution method.

(Invited) Recent Progress in Carbon Nanotube Sorting by DNA

DNA-wrapped single-wall carbon nanotubes (DNA-SWCNT) have a number of utilities. Sorting DNA-SWCNTs have been extensively studied by us and others. However, reported sorting procedures are not widely adopted by other labs. In this talk I will report some recent effort we have made in streamlining DNA-SWCNT sorting. It is our hope that the simplified procedure can be more easily adopted by others for various applications.

Prediction of Mycotoxin Response of DNA-Wrapped Nanotube Sensor with Machine Learning

DNA-wrapped single-walled carbon nanotubes (SWCNTs) have demonstrated great versatility in their use as optical sensors. SWCNTs emit a near-infrared fluorescence that is responsive to even the slightest changes in the nanotube environment, enabling sensors that can respond to single-molecule fluctuations within the vicinity of their surfaces. The fluorescence response and surface interactions of these sensors are determined by the DNA wrapping sequence. However, the lack of information on the relationship between the DNA sequence and its effect on the SWCNT fluorescence remains a bottleneck for designing sequences that are specific to analytes of interest. We have recently demonstrated the use of directed evolution to control the fluorescence response of SWCNTs through DNA design. Iterative cycles of DNA mutation, screening, and selection allowed us to evolve sequences that yield DNA-wrapped SWCNT sensors with a desired fluorescence response to mycotoxins.In this work, we apply the screening results of the DNA libraries used in this approach to train machine learning (ML) algorithms. Artificial neural network (ANN) and support vector machine (SVM) methods were used to predict the response of ssDNA-SWCNT sensors to a specific mycotoxin. The reliability of these models was further assessed through cross-validation. The ANN and SVM models with cross-validation were able to accurately classify the various DNA sequences as yielding either a high or low fluorescence response with an accuracy of 73 and 81%, respectively. The models were further used to predict the performance of alternative DNA sequences outside the initial training dataset, using the Hierarchy and k-means ++ clustering methods to evaluate the similarity and dissimilarity of each DNA sequence. Compared to the SVM model, the ANN model showed an improved ability to predict high responses for dissimilar DNA sequences. We further applied a combinatorial approach based on SVM and ANN models to design new DNA sequences for improving sensor performance. The success of this approach was validated experimentally, demonstrating the rational design of improved sensors with 95% prediction accuracy.The application of ML algorithms to directed evolution libraries of DNA thus allows one to accurately map the performances of these sensors within a particular sequence space. The computational success of this mapping provides a framework for replacing current empirical approaches with the rational design of DNA sequences for SWCNT sensing. Keywords: Nano Biosensor, DNA-SWCNT, Mycotoxin, Machine learning, Directed evolution method

Detection of the Inflammatory Cytokine IL-6 in Complex Human Serum Samples Via Rational Nanotube Surface Passivation Screening

In recent years, biosensors have emerged as a tool with strong potential in medical diagnostics. Single-walled carbon nanotube (SWCNT) based optical nanosensors have notably garnered interest due to the unique characteristics of their near-infrared fluorescence emission, including tissue transparency, photostability, and various chiralities with discrete absorption and fluorescence emission bands.The optoelectronic properties of SWCNT are sensitive to the surrounding environment, which makes them suitable for highly selective biosensing. Single-stranded (ss) DNA-wrapped SWCNTs have been reported as optical nanosensors for cancers and metabolic diseases. However, given the complexity of the human protein environment, non-specific interactions occur between SWCNT-based nanosensors and proteins. This inevitably leads to compromised selectivity of SWCNT-based nanosensors unless strategies for prevention are developed and employed.Non-covalent passivation of the ssDNA-SWCNT surface is reported as an excellent strategy to improve nanosensor selectivity in complex biological settings without causing irreversible changes to the optical properties of SWCNTs. Emerging studies have explored and successfully shown passivation using proteins and phospholipids. However, a systematic comparative study of passivating agents has not been done. In this work, we explore and compare the efficacy of select proteins, polymers, and surfactants as passivating agents.We, therefore, sought to evaluate various potential SWCNT surface passivation agents among broad classes of biomolecules and biomaterials. In the category of protein, Bovine serum albumin, dry-fat milk powder, and casein were selected due to their wide application to improve immunoassay selectivity. In the class of polymers, we selected 1 anionic and 2 cationic polymers, namely, polyethylene glycol, poly-ethylene imine, and poly-l-lysine. From surfactants, 2 phospholipids and 1 anionic surfactant: ammonium salt of 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (16:0 PE2000PEG); 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethylene glycol)-2000] (DSPE PEG phospholipids), and sodium dodecylbenzene sulfonate (SDBS) were selected.We analyzed the ability of all passivation agents to screen the non-specific interactions of ssDNA- SWCNTs in the presence of fetal bovine serum using fluorescence spectroscopy. The non-specific interactions between ssDNA-SWCNTs and proteins lead to a reorientation of the dipole moments and charge transfer in the corona phase around ssDNA-SWCNTs, leading to modulation in the center wavelength of the fluorescence as well as absorption peaks. We hence hypothesized that smaller changes in the center wavelength of the fluorescence peaks of passivated ssDNA-SWCNTs in presence of serum, lead to higher screening effect of the passivation agent towards non-specific interactions. We found that the most successful candidates were poly-L-lysine, polyethylene imine, dry-fat milk powder, and casein, in that order. Moreover, the ability to screen the interference was retained over a period of at least 3 hours. We further experimented with the four different mass ratios of passivating agents to ssDNA-SWCNTs and found that the mass ratio 50:1 for passivating agents: ss-DNA SWCNTs was most optimal.We confirmed the strength of passivation using absorption spectroscopy. We hypothesized that stronger surface saturation of the SWCNT-TAT6 is by a passivating agent in buffer conditions leads to a larger shift in the absorption peaks. We found that for the above successful passivation agents, the order of passivation strength followed the same trend as the screening abilities of the successful passivating agents, supporting this mechanistic hypothesis.Then, we evaluated an antibody-conjugated ssDNA-SWCNT nanosensor for the pro-inflammatory cytokine IL-6 with our successful passivation agents. We assessed the ability of the passivation agents to confer selective detection of IL-6 detection in clinical serum samples from patients with atherosclerosis and rheumatoid arthritis, both anticipated to have high IL-6 levels. Samples were compared to healthy human serum sample controls. We validated SWCNT fluorescence response with traditional immunoassays (ELISA).We expect this study to provide rational strategies to screen interferences from non-specific interactions and improve the selectivity of the SWCNT-based optical nanosensors for in vivo applications.

Hybridization of papain molecules and DNA-wrapped single-walled carbon nanotubes evaluated by atomic force microscopy in fluids

Although various conjugates of single-walled carbon nanotubes (SWNTs) and biomolecules, such as nanobiosensors and nanobiodevices, have been reported, the conjugation of papain and SWNTs have not been reported because of the formation of unexpected aggregates. In this study, atomic force microscopy (AFM) in liquid was used to investigate the interactions between papain and DNA-wrapped SWNTs (DNA–SWNTs) at two different pH values (pH 3.0 and 10.5). The direct AFM observation of the mixture of papain and DNA–SWNTs confirmed the aggregation of papain molecules with DNA–SWNTs in the buffer solutions. The numerous and non-uniform adsorption of papain molecules onto DNA–SWNTs was more pronounced at pH 3.0 than that at pH 10.5. Furthermore, thick conjugates appeared when papain and DNA–SWNTs were simultaneously mixed. The near-infrared photoluminescence spectra of the SWNTs drastically changed when the papain molecules were injected into the DNA–SWNT suspension at pH 3.0. Thus, the regulation of electrostatic interactions is a key aspect in preparing optimal conjugates of papain and DNA–SWNTs. Furthermore, although previous papers reported AFM images of dried samples, this study demonstrates the potential of AFM in liquid in evaluating individual bioconjugates of SWNTs.

Numerical Analysis for Light Absorption Spectra of the Base of DNA-Wrapped Single-Walled Carbon Nanotubes

This study numerically demonstrates the light absorption spectra of each base of DNA-wrapped single-walled carbon nanotubes (SWCNTs). Previous experimental and theoretical studies show that the optical properties of these composites are different from the bare SWCNTs. In this work, we investigated the bases of DNA that influence optical properties. To obtain stable molecular states for studying optical properties, molecular dynamics calculations were performed. Additionally, light absorption spectra in the ultraviolet-to-near-infrared region of one type of base-wrapped (e.g., adenine-, thymine-, cytosine-, or guanine-wrapped) SWCNTs were investigated by utilizing the semi-empirical molecular orbital theory using SCIGRESS commercial software. This method can significantly reduce the calculation time compared to the ab initio molecular orbital method, making the handling of composites of bases and SWCNTs possible. We found that the largest peaks appear at a wavelength of around 300 nm for all the composites. Furthermore, we found that the light absorption spectra above 570 nm are strongly influenced by adenine and cytosine. Thus, our computational results provide insight into the optical properties and the effects of base-SWCNTs that are difficult to investigate experimentally under the influence of solvents and various molecules.

Attachment of DNA-Wrapped Single-Walled Carbon Nanotubes (SWNTs) for a Micron-Sized Biosensor.

We fabricated a micron-sized biodevice based on the near-infrared photoluminescence (PL) response of single-walled carbon nanotubes (SWNTs). Various biosensors using the unique optical responses of SWNTs have been proposed by many research groups. Most of these employed either colloidal suspensions of dispersed SWNTs or SWNT films on flat surfaces, such as electrodes. In this study, we attached DNA-wrapped SWNTs (DNA-SWNTs) to frustule (micron-sized nanoporous biosilica) surfaces, which were purified from cultured isolated diatoms. After the injection of an oxidant and a reductant, the SWNTs on the frustules showed prominent PL responses. This suggests that the biodevice functions as a micron-sized redox sensor. Frustules can be easily suspended in aqueous solutions because of their porous structures and can easily be collected as pellets by low-speed centrifugation. Thus, the removal of unbound SWNTs and the recovery of the fabricated DNA-SWNT frustules for reuse were achieved by gentle centrifugation. Our proposal for micron-sized SWNT biodevices would be helpful for various biological applications.

Cell cycle-dependent endocytosis of DNA-wrapped single-walled carbon nanotubes by neural progenitor cells

While exposure of C17.2 neural progenitor cells (NPCs) to nanomolar concentrations of carbon nanotubes (NTs) yields evidence of cellular substructure reorganization and alteration of cell division and differentiation, the mechanisms of NT entry are not understood. This study examines the entry modes of (GT)20 DNA-wrapped single-walled carbon nanotubes (SWCNTs) into NPCs. Several endocytic mechanisms were examined for responsibility in nanomaterial uptake and connections to alterations in cell development via cell-cycle regulation. Chemical cell-cycle arrest agents were used to synchronize NPCs in early G1, late G1/S, and G2/M phases at rates (>80%) aligned with previously documented levels of synchrony for stem cells. Synchronization led to the highest reduction in SWCNT internalization during the G1/S transition of the cell cycle. Concurrently, known inhibitors of endocytosis were used to gain control over established endocytic machineries (receptor-mediated endocytosis (RME), macropinocytosis (MP), and clathrin-independent endocytosis (CIE)), which resulted in a decrease in uptake of SWCNTs across the board in comparison with the control. The outcome implicated RME as the primary mechanism of uptake while suggesting that other endocytic mechanisms, though still fractionally responsible, are not central to SWCNT uptake and can be supplemented by RME when compromised. Thereby, endocytosis of nanomaterials was shown to have a dependency on cell-cycle progression in NPCs.

Spectroscopy analysis of the alignment of nanoassemblies of DNA-wrapped carbon nanotubes in stretched gelatin film

We present the polarized Raman studies and light absorption study of nanoassemblies of DNA-wrapped single-walled carbon nanotubes (SWNTs) incorporated into the gelatin film. Nanoassemblies are formed in aqueous suspension with SWNTs:DNA by positively charged 5,10,15,20-tetrakis-(N-methyl-4-pyridyl) porphyrin (TMPyP4). The gelatin film with embedded nanoassemblies was exposed to a mechanical stretching to about 300% tensile strain for making an alignment along a chosen direction. The analysis of the absorption spectra taken along and normal to the stretching direction revealed the strong polarized dependence. The polarized Raman spectra of the stretched gelatin film showed the angular dependence of the integrated intensity of tangential mode of SWNTs that allowed to estimate the alignment degree. It showed that about 60% of the SWNT nanoassemblies are aligned in the range of ± 15° to the direction of the stretching. The addition of the porphyrin derivative does not impede the orientation of the SWNTs:DNA nanohybrids along the stretching direction. The performed studies of embedded SWNTs:DNA:TMPyP4 nanoassemblies in the flexible gelatin film are intended to show the simple method for obtaining the controlled ordered biocompatible nanotube networks functionalized by the porphyrin derivatives inside a polymer matrix.

Discovery of DNA-Carbon Nanotube Sensors for Serotonin with Machine Learning and Near-infrared Fluorescence Spectroscopy.

DNA-wrapped single walled carbon nanotube (SWNT) conjugates have distinct optical properties leading to their use in biosensing and imaging applications. A critical limitation in the development of DNA-SWNT sensors is the current inability to predict unique DNA sequences that confer a strong analyte-specific optical response to these sensors. Here, near-infrared (nIR) fluorescence response data sets for ∼100 DNA-SWNT conjugates, narrowed down by a selective evolution protocol starting from a pool of ∼1010 unique DNA-SWNT candidates, are used to train machine learning (ML) models to predict DNA sequences with strong optical response to neurotransmitter serotonin. First, classifier models based on convolutional neural networks (CNN) are trained on sequence features to classify DNA ligands as either high response or low response to serotonin. Second, support vector machine (SVM) regression models are trained to predict relative optical response values for DNA sequences. Finally, we demonstrate with validation experiments that integrating the predictions of ensembles of the highest quality neural network classifiers (convolutional or artificial) and SVM regression models leads to the best predictions of both high and low response sequences. With our ML approaches, we discovered five DNA-SWNT sensors with higher fluorescence intensity response to serotonin than obtained previously. Overall, the explored ML approaches, shown to predict useful DNA sequences, can be used for discovery of DNA-based sensors and nanobiotechnologies.

Optical Detection of Stereoselective Interactions with DNA-Wrapped Single-Wall Carbon Nanotubes.

DNA-wrapped carbon nanotubes have been explored increasingly as sensitive near-infrared fluorescence probes for biomolecules. However, notably missing in previous studies is an inquiry on stereoselective interactions between DNA-wrapped carbon nanotubes and biomolecules. Here, enantiopure (+) and (-)(6,5), and (-)(8,3) as well as achiral (11,0) carbon nanotubes wrapped with specific resolving DNA sequences are used to demonstrate their stereoselective detection of amino acid enantiomers. Furthermore, stereoselective sensing abilities are found to be retained by dispersions containing a multitude of chiral nanotube structures. The fluorescence response profiles of six different DNA-wrapped carbon nanotube dispersions to nine standard amino acids, and their enantiomers, demonstrate that DNA-wrapped carbon nanotubes are exquisitely sensitive to the stereoconfiguration and side-chain functionality of amino acids in a manner that is dependent on both DNA sequence and nanotube chirality. Implications of our findings are discussed in the context of developing a machine learning-aided multiplexed biosensing scheme called a molecular perceptron.

Prediction of the Near-Infrared Absorption Spectrum of Single-Walled Carbon Nanotubes Using a Bayesian Regularized Back Propagation Neural Network Model

DNA-wrapped single-walled carbon nanotubes (DNA-SWCNTs) in stable dispersion are expected to be used as biosensors in the future, because they have the property of absorption of light in the near infrared (NIR) region, which is safe for the human body. However, this practical application requires the understanding of the DNA-SWCNTs’ detailed response characteristics. The purpose of this study is to predict, in detail, the response characteristics of the absorption spectra that result when the antioxidant catechin is added to oxidized DNA-SWCNTs, from a small amount of experimental data. Therefore, in the present study, we predicted the characteristics of the absorption spectra of DNA-SWCNTs using the Bayesian regularization backpropagation neural network (BRBPNN) model. The BRBPNN model was trained with the catechin concentration and initial absorption peaks as inputs and the absorption spectra after catechin addition as outputs. The accuracy of the predicted absorption peaks and wavelengths after the addition of catechin, as predicted by the BRBPNN model, was within 1% of the error of the experimental data. By inputting the catechin concentrations under hundreds of conditions into this BRBPNN model, we were able to obtain detailed prediction curves for the absorption peaks. This method has the potential to help to reduce the experimental costs and improve the efficiency of investigating the properties of high-cost materials such as SWCNTs.

Impact of Single-Walled Carbon Nanotubes on Neural Progenitors: From Endocytosis to Differentiation

Carbon nanotubes are often lauded for their utility as delivery agents for drug and gene therapeutics. Their size and tunable functionalization allows them to clear the blood brain barrier and gain access to the central nervous system (CNS). Our previous studies of the effect of (GT)20 DNA-wrapped single walled carbon nanotubes (SWNT) on C17.2 neural progenitor cells (NPCs) have shown that endocytosis of nanomolar concentrations of SWNTs triggers an increase in differentiation yield of NPCs. Biophysical prompts at the extracellular membrane will generate a mechanotransduction-based response in the intracellular space, setting off a signaling cascade and ending in the alteration of cellular fate processes. This biophysical stimulus of the cell can result in biochemical downstream alterations of cell division, proliferation and differentiation. While the later stages of differentiation (14-21 days) of NPCs have been studied, the early induction of differentiation as a result of nanomaterial entry into the cell is not widely understood. This study aims to identify markers associated with early differentiation of NPCs within the first 1-3 days post-nanomaterial internalization. Preceding work on receptor/clathrin-mediated endocytosis (RME) as the primary method of DNA-SWNT entry, lead to detailed pathway analysis and identification of doublecortin (DCX), Notch1/numb, clathrin/AP-2 complex and NeuroD1 to be among the proteins crucial to test for connecting the RME pathway to the onset of NPC differentiation. A mechanistic understanding of the path from endocytosis to neural differentiation, and how nanotubes alter stem cell decision-making machinery, can aid in designing natural differentiation augmentation as a potential therapeutic against neurodegenerative diseases.

Sensing of epigallocatechin gallate and tannic acid based on near infrared optical spectroscopy of DNA-wrapped single-walled carbon nanotube hybrids

The optical responses of DNA-wrapped single-walled carbon nanotubes (DNA-SWNTs) caused by the addition of epigallocatechin gallate (EG) and tannic acid (TA) were investigated. Near infrared absorbance and photoluminescence spectra of pre-oxidized DNA-SWNTs were measured with and without EG and TA. Since both EG and TA have antioxidant abilities, the near infrared spectra changed after the addition of the chemicals. While detection of the antioxidant abilities of EG by DNA-SWNT hybrids has been previously reported, TA was employed for the first time. The changes in the absorbance caused by the addition of TA were found to saturate at 0.33 µM TA, although saturation was not observed even at 3.3 µM with the addition of EG. Oxidation of DNA-SWNT was suppressed by addition of TA or EG. The effects of TA were much greater than those of EG on the absorbance. The photoluminescence did not appear to saturate at 3.3 µM for either EG or TA. photoluminescence had a larger measurement capacity than NIR absorbance. Interestingly, the photoluminescence change caused by EG was much larger than that of TA at 3.3 µM, although the antioxidant property of TA was stronger at 0.33 and 0.033 µM, suggesting that the optical responses were not simple redox reactions. Peak shifts in the absorbance/photoluminescence spectra revealed unique differences according to the chirality of the SWNTs and the types of chemicals used. This suggests that the combination of absorbance/photoluminescence and peak intensity/peak shifts could detect multiple types of chemical information, not only redox reaction. A direct comparison between EG and TA was demonstrated for the first time in this novel study. In addition, sensing of EG and TA by near infrared spectra was made available using not only changes in intensity but also a variety of peak shifts of SWNTs.

Analysis of vibration behavior in single strand DNA-wrapped single-walled carbon nanotubes adhered to lipid membranes

Single strand DNA-wrapped Single-walled carbon nanotubes (ssDNA-SWCNTs) have critical biomedical applications such as drug delivery, bio-imaging and bio-sensing; therefore, the mechanical interaction between ssDNA-SWCNTs and lipid membranes is an important research topic. Several studies have experimentally demonstrated that depending on the length of ssDNA-SWCNTs penetrate the lipid membranes. However, few studies have analyzed the mechanism of the mechanical interaction of this process. In addition, simulation approaches, such as molecule dynamics (MD) with long SWCNTs, are time-consuming. In this study, we examined the mechanical interaction by analyzing the vibration behavior of ssDNA-SWCNTs at difference lengths from 25 to 200 nm adhered to the lipid membranes considering effect of the damping and mass in water. In order to evaluate the vibration behavior between ssDNA-SWCNTs and lipid membranes, the frequency response functions of them was investigated by the modal analysis method. As a result, we found that ssDNA-SWCNTs shorter than 100 nm can efficiently transmit force on the lipid membranes. On the other hand, ssDNA-SWCNTs longer than 100 nm interfere with the efficient transfer of force to the lipid membranes due to the damping resistance in water accompanied by ssDNA vibration on the SWCNTs.

Toward Complete Resolution of DNA/Carbon Nanotube Hybrids by Aqueous Two-Phase Systems.

Sequence-dependent interactions between DNA and single-wall carbon nanotubes (SWCNTs) are shown to provide resolution for the atomic-structure-based sorting of DNA-wrapped SWCNTs. Previous studies have demonstrated that aqueous two-phase (ATP) systems are very effective for sorting DNA-wrapped SWCNTs (DNA-SWCNTs). However, most separations have been carried out with a polyethylene glycol (PEG)/polyacrylamide (PAM) ATP system, which shows severe interfacial trapping for many DNA-SWCNT dispersions, resulting in significant material loss and limiting multistage extraction. Here, we report a study of several new ATP systems for sorting DNA-SWCNTs. We have developed a convenient method to explore these systems without knowledge of the corresponding phase diagram. We further show that the molecular weight of the polymer strongly affects the partition behavior and separation results for DNA-SWCNTs in PEG/dextran (DX) ATP systems. This leads to the identification of the PEG1.5kDa/DX250kDa ATP system as an effective vehicle for the chirality separation of DNA-SWCNTs. Additionally, this ATP system exhibits greatly reduced interfacial trapping, enabling for the first time continuous multistep sorting of four species of SWCNTs from a single dispersion. Enhanced stability of DNA-SWCNTs in the PEG1.5kDa/DX250kDa ATP system also allows us to investigate pH dependent sorting of SWCNTs wrapped by C-rich sequences. Our observations suggest that hydrogen bonding may form between the DNA bases at lower pH, enabling a more ordered wrapping structure on the SWCNTs and improvement in sorting (11,0). Together, these findings reveal that the new ATP system is suitable for searching DNA sequences leading toward more complete resolution of DNA-SWCNTs. A new concept of "resolving sequences", evolved from the old notion of "recognition sequences", is proposed to describe a broader range of behaviors of DNA/SWCNT interactions and sorting.

DNA-SWCNT Biosensors Allow Real-Time Monitoring of Therapeutic Responses in Pancreatic Ductal Adenocarcinoma.

Pancreatic ductal adenocarcinoma (PDAC) is a highly desmoplastic cancer with limited treatment options. There is an urgent need for tools that monitor therapeutic responses in real time. Drugs such as gemcitabine and irinotecan elicit their therapeutic effect in cancer cells by producing hydrogen peroxide (H2O2). In this study, specific DNA-wrapped single-walled carbon nanotubes (SWCNT), which precisely monitor H2O2, were used to determine the therapeutic response of PDAC cells in vitro and tumors in vivo. Drug therapeutic efficacy was evaluated in vitro by monitoring H2O2 differences in situ using reversible alteration of Raman G-bands from the nanotubes. Implantation of the DNA-SWCNT probe inside the PDAC tumor resulted in approximately 50% reduction of Raman G-band intensity when treated with gemcitabine versus the pretreated tumor; the Raman G-band intensity reversed to its pretreatment level upon treatment withdrawal. In summary, using highly specific and sensitive DNA-SWCNT nanosensors, which can determine dynamic alteration of hydrogen peroxide in tumor, can evaluate the effectiveness of chemotherapeutics. SIGNIFICANCE: A novel biosensor is used to detect intratumoral hydrogen peroxide, allowing real-time monitoring of responses to chemotherapeutic drugs.

Vibration analysis of single-stranded DNA-wrapped single-walled carbon nanotubes using finite element method

We analyzed the vibration characteristics of single-walled carbon nanotubes (SWCNTs)1 wrapped with single-stranded DNA (ssDNA) using the finite element method. The SWCNT model was calculated from the 1st-bending mode of 0.98 GHz to the radial breathing mode of 10.2 THz under free boundary conditions. The natural frequency of the SWCNTs was consistent with the well-known Bernoulli-Euler beam theory, and with the experimental relationship between the wave number and diameter of the SWCNTs. Additionally, the vibration modes and conditions for coupling with the 1st-bending mode of the ssDNA-SWCNTs were obtained under vacuum and water conditions.

Directed Evolution of the Optoelectronic Properties of Synthetic Nanomaterials

Directed evolution is a powerful approach for tailoring protein properties toward new or enhanced functions. This technique allows one to alter a protein in a directed manner even in the absence of a known relationship between protein structure and function. Several nanocomplexes, such as optical sensors based on DNA-wrapped single-walled carbon nanotubes (DNA-SWCNTs), similarly lack a known structure-function relationship. For example, DNA-SWCNT complexes exhibit variations in their fluorescence that depend on the sequence of the DNA wrapping. However, little is known about the relationship between the DNA sequence and its effects on the fluorescence properties of SWCNTs. In this study, we use directed evolution as a guided approach to tuning the optoelectronic properties of DNA-SWCNT complexes through DNA mutation. Applying this technique over two rounds of DNA mutagenesis and screening, we evolved a DNA-SWCNT sensor with a 57% enhancement in fluorescence intensity. Furthermore, this sensor shows retained selectivity and sensitivity towards the analyte of interest. Though we demonstrate this approach to improve sensor brightness, directed evolution offers far-reaching possibilities in the field that can also be applied to improve additional sensor properties such as sensitivity and selectivity.