Structural Characteristics of Oligomeric DNA Strands Adsorbed onto Single-Walled Carbon Nanotubes

Understanding DNA-encoded carbon nanotube sorting and sensing via sub-nm-resolution structural determination

DNA has demonstrated the abilities to differentiate single-wall carbon nanotubes (SWCNTs) with various chiralities and manipulate their analyte sensing properties. However, the fundamental mechanisms underlying these remarkable abilities remain unclear due to the lack of high-resolution determination of DNA structures on SWCNTs. Here, we combine atomic force microscopy and single-particle cryo-electron microscopy to determine DNA structures on five different types of single-chirality SWCNTs, achieving unprecedented subnanometer resolution. This resolution enables the direct observation of left-handed helical DNA structures with pitches ranging from 1.59 to 2.20 nm, depending on the DNA sequence and nanotube chirality. These findings provide structural insights into the mechanisms by which DNA differentiates the chirality of SWCNTs, and governs the sensitivity, dynamic response range, and analyte differentiability of SWCNT sensors. We propose a non-Watson-Crick hydrogen-bonding network model, which not only accounts for the observed ordered DNA structures but also facilitates the design of DNA sequences for targeted SWCNT purification and desired SWCNT sensor performance.

Accurate DNA Sequence Prediction for Sorting Target-Chirality Carbon Nanotubes and Manipulating Their Functionalities

Synthetic single-wall carbon nanotubes (SWCNTs) contain various chiralities, which can be sorted by DNA. However, finding DNA sequences for this purpose mainly relies on trial-and-error methods. Predicting the right DNA sequences to sort SWCNTs remains a substantial challenge. Moreover, it is even more daunting to predict sequences for sorting SWCNTs with target chirality. Here, we present a deep-learning (DL) enhanced strategy for the accurate prediction of DNA sequences capable of sorting target-chirality nanotubes. We first experimentally screened 216 DNA sequences using aqueous two-phase (ATP) separation, resulting in 116 resolving sequences that can purify 17 distinct single-chirality SWCNTs. These experimental results created a comprehensive training data set. We utilized the recently released 3D molecular representation learning framework, Uni-Mol, to construct a DL workflow that maps atomistic-level structural information on DNA sequences into the feature space. This information captures the structural features of DNA molecules that are crucial for their interactions with SWCNTs. This may account for the superior performance of our DL models. The models successfully predicted resolving sequences for (6,5), (6,6), and (7,4) SWCNTs with accuracy rates of 87.5, 90, and 70%, respectively. Importantly, the discovery of numerous resolving sequences for (6,5) SWCNTs allows us to systematically manipulate the sequence-dependent absorption spectral shift, photoluminescence intensity, and surfactant sensitivity of DNA-(6,5) hybrids and elucidate the underlying mechanisms.

High-Throughput Approaches to Engineer Fluorescent Nanosensors

Optical sensors are powerful tools to identify and image (biological) molecules. Because of their optoelectronic properties, nanomaterials are often used as building blocks. To transduce the chemical interaction with the analyte into an optical signal, the interplay between surface chemistry and nanomaterial photophysics has to be optimized. Understanding these aspects promises major opportunities for tailored sensors with optimal performance. However, this requires methods to create and explore the many chemical permutations. Indeed, many current approaches are limited in throughput. This affects the chemical design space that can be studied, the application of machine learning approaches as well as fundamental mechanistic understanding. Here, an overview of selection-limited and synthesis-limited approaches is provided to create and identify molecular nanosensors. Bottlenecks are discussed and opportunities of non-classical recognition strategies are highlighted such as corona phase molecular recognition as well as the requirements for high throughput and scalability. Fluorescent carbon nanotubes are powerful building blocks for sensors and their huge chemical design space makes them an ideal platform for high throughput approaches. Therefore, they are the focus of this article, but the insights are transferable to any nanosensor system. Overall, this perspective aims to provide a fresh perspective to overcome current challenges in the nanosensor field.

Porous organic cages as inhibitors of Aβ42 peptide aggregation: a simulation study

The aggregation of Aβ monomers into oligomers with β-sheet structures is an important cause of Alzheimer's disease (AD), while the Aβ42 peptide is more toxic and prone to aggregate. It is of great significance to study the inhibition mechanism of Aβ42 monomer aggregation and find excellent inhibitors for the treatment of AD. Research in recent years has focused on small molecule compounds and nanoparticles, but they all have certain limitations. As a new type of porous material, a porous organic cage (POC) has potential application feasibility in the biomedical field due to its unique physicochemical properties. In this work, molecular dynamics simulations were used for the first time to explore the interaction and conformational transformation of the Aβ42 peptide in CC3 crystals with different morphologies (planar and spherical). The results show that the adsorption of the Aβ42 peptide on different CC3 crystals is mainly achieved through strong van der Waals forces. During the simulations, the Aβ42 peptide undergoes various degrees of structural changes. Compared to that in water, this binding induces more irregular structures, such as turns and 3-helices, and inhibits the production of β-sheets, while enhancing the overall backbone rigidity of the Aβ42 peptide. The transformation analysis of peptide conformation is further complemented by free energy landscape and cluster analysis. These findings provide a strong basis for CC3 crystals as novel inhibitors to inhibit the toxicity and aggregation of the Aβ42 peptide.

Systematic Selection of High-Affinity ssDNA Sequences to Carbon Nanotubes

Single-walled carbon nanotubes (SWCNTs) have gained significant interest for their potential in biomedicine and nanoelectronics. The functionalization of SWCNTs with single-stranded DNA (ssDNA) enables the precise control of SWCNT alignment and the development of optical and electronic biosensors. This study addresses the current gaps in the field by employing high-throughput systematic selection, enriching high-affinity ssDNA sequences from a vast random library. Specific base compositions and patterns are identified that govern the binding affinity between ssDNA and SWCNTs. Molecular dynamics simulations validate the stability of ssDNA conformations on SWCNTs and reveal the pivotal role of hydrogen bonds in this interaction. Additionally, it is demonstrated that machine learning could accurately distinguish high-affinity ssDNA sequences, providing an accessible model on a dedicated webpage (http://service.k-medai.com/ssdna4cnt). These findings open new avenues for high-affinity ssDNA-SWCNT constructs for stable and sensitive molecular detection across diverse scientific disciplines.

Sequence-Dependent Surface Coverage of ssDNA Coatings on Single-Wall Carbon Nanotubes

A combination of experimental measurements and molecular dynamics (MD) simulations was used to investigate how the surfaces of single-wall carbon nanotubes (SWCNTs) are covered by adsorbed ssDNA oligos with different base compositions and lengths. By analyzing the UV absorption spectra of ssDNA-coated SWCNTs before and after coating displacement by a transparent surfactant, the mass ratios of adsorbed ssDNA to SWCNTs were determined for poly-T, poly-C, GT-containing, and AT-containing ssDNA oligos. Based on the measured mass ratios, it is estimated that an average of 20, 22, 26, or 32 carbon atoms are covered by one adsorbed thymine, cytosine, adenine, or guanine nucleotide, respectively. In addition, the UV spectra revealed electronic interactions of varying strengths between the nucleobase aromatic rings and the nanotube π-systems. Short poly-T DNA oligos show stronger π-π stacking interactions with SWCNT surfaces than do short poly-C DNA oligos, whereas both long poly-C and poly-T DNA oligos show strong interactions. These experiments were complemented by MD computations on simulated systems that were constrained to match the measured ssDNA/SWCNT mass ratios. The surface coverages computed from the MD results varied with oligo composition in a pattern that correlates higher measured yields of nanotube fluorescence with greater surface coverage.

Programming sp3 Quantum Defects along Carbon Nanotubes with Halogenated DNA

Atomic defect color centers in solid-state systems hold immense potential to advance various quantum technologies. However, the fabrication of high-quality, densely packed defects presents a significant challenge. Herein we introduce a DNA-programmable photochemical approach for creating organic color-center quantum defects on semiconducting single-walled carbon nanotubes (SWCNTs). Key to this precision defect chemistry is the strategic substitution of thymine with halogenated uracil in DNA strands that are orderly wrapped around the nanotube. Photochemical activation of the reactive uracil initiates the formation of sp3 defects along the nanotube as deep exciton traps, with a pronounced photoluminescence shift from the nanotube band gap emission (by 191 meV for (6,5)-SWCNTs). Furthermore, by altering the DNA spacers, we achieve systematic control over the defect placements along the nanotube. This method, bridging advanced molecular chemistry with quantum materials science, marks a crucial step in crafting quantum defects for critical applications in quantum information science, imaging, and sensing.

DNA-guided lattice remodeling of carbon nanotubes

Covalent modification of carbon nanotubes is a promising strategy for engineering their electronic structures. However, keeping modification sites in registration with a nanotube lattice is challenging. We report a solution using DNA-directed, guanine (G)-specific cross-linking chemistry. Through DNA screening we identify a sequence, C₃GC₇GC₃, whose reaction with an (8,3) enantiomer yields minimum disorder-induced Raman mode intensities and photoluminescence Stokes shift, suggesting ordered defect array formation. Single-particle cryo-electron microscopy shows that the C₃GC₇GC₃ functionalized (8,3) has an ordered helical structure with a 6.5 angstroms periodicity. Reaction mechanism analysis suggests that the helical periodicity arises from an array of G-modified carbon-carbon bonds separated by a fixed distance along an armchair helical line. Our findings may be used to remodel nanotube lattices for novel electronic properties.

Molecular dynamics simulations reveal single-stranded DNA (ssDNA) forms ordered structures upon adsorbing onto single-walled carbon nanotubes (SWCNT)

Replica exchange molecular dynamics were used to observe the adsorption of single-stranded DNA (ssDNA) onto the surface of single-walled carbon nanotubes (SWCNTs). The assembly of these systems has garnered interest as a method by which SWCNTs can be separated based on chirality. While the exact mechanism of separation is yet unknown, it is hypothesized that the structure of the ssDNA layer pays an important role. Characterization of such an adsorbed layer has been a matter of recent work with the focus being on atomic level detail or such as base-stacking and hydrogen bonding. In this manuscript, we detail a new observation of ssDNA organization and demonstrate how it can be used to infer additional information about the way in which such biopolymers wrap around the cylindrical SWCNT.

Detection of ovarian cancer via the spectral fingerprinting of quantum-defect-modified carbon nanotubes in serum by machine learning

Serum biomarkers are often insufficiently sensitive or specific to facilitate cancer screening or diagnostic testing. In ovarian cancer, the few established serum biomarkers are highly specific, yet insufficiently sensitive to detect early-stage disease and to impact the mortality rates of patients with this cancer. Here we show that a 'disease fingerprint' acquired via machine learning from the spectra of near-infrared fluorescence emissions of an array of carbon nanotubes functionalized with quantum defects detects high-grade serous ovarian carcinoma in serum samples from symptomatic individuals with 87% sensitivity at 98% specificity (compared with 84% sensitivity at 98% specificity for the current best clinical screening test, which uses measurements of cancer antigen 125 and transvaginal ultrasonography). We used 269 serum samples to train and validate several machine-learning classifiers for the discrimination of patients with ovarian cancer from those with other diseases and from healthy individuals. The predictive values of the best classifier could not be attained via known protein biomarkers, suggesting that the array of nanotube sensors responds to unidentified serum biomarkers.

The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations

Field-effect biosensors (bioFETs) offer a novel way to measure the kinetics of biomolecular events such as protein function and DNA hybridization at the single-molecule level on a wide range of time scales. These devices generate an electrical current whose fluctuations are correlated to the kinetics of the biomolecule under study. BioFETs are indeed highly sensitive to changes in the electrostatic potential (ESP) generated by the biomolecule. Here, using all-atom solvent explicit molecular dynamics simulations, we further investigate the molecular origin of the variation of this ESP for two prototypical cases of proteins or nucleic acids attached to a carbon nanotube bioFET: the function of the lysozyme protein and the hybridization of a 10-nt DNA sequence, as previously done experimentally. Our results show that the ESP changes significantly on the surface of the carbon nanotube as the state of these two biomolecules changes. More precisely, the ESP distributions calculated for these molecular states explain well the magnitude of the conductance fluctuations measured experimentally. The dependence of the ESP with salt concentration is found to agree with the reduced conductance fluctuations observed experimentally for the lysozyme, but to differ for the case of DNA, suggesting that other mechanisms might be at play in this case. Furthermore, we show that the carbon nanotube does not impact significantly the structural stability of the lysozyme, corroborating that the kinetic rates measured using bioFETs are similar to those measured by other techniques. For DNA, we find that the structural ensemble of the single-stranded DNA is significantly impacted by the presence of the nanotube, which, combined with the ESP analysis, suggests a stronger DNA-device interplay. Overall, our simulations strengthen the comprehension of the inner working of field-effect biosensors used for single-molecule kinetics measurements on proteins and nucleic acids.

Cytosine-Rich DNA Fragments Covalently Bound to Carbon Nanotube as Factors Triggering Doxorubicin Release at Acidic pH. A Molecular Dynamics Study

This works deals with analysis of properties of a carbon nanotube, the tips of which were functionalized by short cytosine-rich fragments of ssDNA. That object is aimed to work as a platform for storage and controlled release of doxorubicin in response to pH changes. We found that at neutral pH, doxorubicin molecules can be intercalated between the ssDNA fragments, and formation of such knots can effectively block other doxorubicin molecules, encapsulated in the nanotube interior, against release to the bulk. Because at the neutral pH, the ssDNA fragments are in form of random coils, the intercalation of doxorubicin is strong. At acidic pH, the ssDNA fragments undergo folding into i-motifs, and this leads to significant reduction of the interaction strength between doxorubicin and other components of the system. Thus, the drug molecules can be released to the bulk at acidic pH. The above conclusions concerning the storage/release mechanism of doxorubicin were drawn from the observation of molecular dynamics trajectories of the systems as well as from analysis of various components of pair interaction energies.

Dye Quenching of Carbon Nanotube Fluorescence Reveals Structure-Selective Coating Coverage

Many properties and applications of single-wall carbon nanotubes (SWCNTs) depend strongly on the coatings that allow their suspension in aqueous media. We report that SWCNT fluorescence is quenched by reversible physisorption of dye molecules such as methylene blue, and that measurements of that quenching can be used to infer structure-specific exposures of the nanotube surface to the surrounding solution. SWCNTs suspended in single-stranded DNA oligomers show quenching dependent on the combination of nanotube structure and ssDNA base sequence. Several sequences are found to give notably high or low surface coverages for specific SWCNT species. These effects seem correlated with the selective recognitions used for DNA-based structural sorting of nanotubes. One notable example is that dye quenching of fluorescence from SWCNTs coated with the (ATT)₄ base sequence is far stronger for one (7,5) enantiomer than for the other, showing that coating coverage is associated with the coating affinity difference reported previously for this system. Equilibrium modeling of quenching data has been used to extract parameters for comparative complexation constants and accessible surface areas. Further insights are obtained from molecular dynamics simulations, which give estimated contact areas between ssDNA and SWCNTs that correlate with experimentally inferred surface exposures and account for the enantiomeric discrimination of (ATT)₄.

Molecular Dynamics Study of the Interaction of Carbon Nanotubes With Telomeric DNA Fragment Containing Noncanonical G-quadruplex and i-Motif Forms

This work deals with molecular dynamics simulations of systems composed of telomeric dsDNA fragments, iG, and functionalized carbon nanotubes, fCNT. The iG contains 90 nucleotides in total and in its middle part the noncanonical i-motif and G-quadruplex are formed. Two chiralities of the fCNT were used, i.e., (10,0) and (20,0) and these nanotubes were either on-tip functionalized by guanine containing functional groups or left without functionalization. We proposed a dedicated computational procedure, based on the replica exchange concept, for finding a thermodynamically optimal conformation of iG and fCNT without destroying the very fragile noncanonical parts of the iG. We found that iG forms a V-shape spatial structure with the noncanonical fragments located at the edge and the remaining dsDNA strands forming the arms of V letter. The optimal configuration of iG in reference to fCNT strongly depends on the on-tip functionalization of the fCNT. The carbon nanotube without functionalization moves freely between the dsDNA arms, while the presence of guanine residues leads to immobilization of the fCNT and preferential location of the nanotube tip near the junction between the dsDNA duplex and i-motif and G-quadruplex. We also studied how the presence of fCNT affects the stability of the i-motif at the neutral pH when the cytosine pairs are nonprotonated. We concluded that carbon nanotubes do not improve the stability of the spatial structure of i-motif also when it is a part of a bigger structure like the iG. Such an effect was described in literature in reference to carboxylated nanotubes. Our current results suggest that the stabilization of i-motif is most probably related to easy formation of semiprotonated cytosine pairs at neutral pH due to interaction with carboxylated carbon nanotubes.

Multifunctional Heterogeneous Carbon Nanotube Nanocomposites Assembled by DNA-Binding Peptide Anchors

Although carbon nanotubes (CNTs) are remarkable materials with many exceptional characteristics, their poor chemical functionality limits their potential applications. Herein, a strategy is proposed for functionalizing CNTs, which can be achieved with any functional group (FG) without degrading their intrinsic structure by using a deoxyribonucleic acid (DNA)-binding peptide (DBP) anchor. By employing a DBP tagged with a certain FG, such as thiol, biotin, and carboxyl acid, it is possible to introduce any FG with a controlled density on DNA-wrapped CNTs. Additionally, different types of FGs can be introduced on CNTs simultaneously, using DBPs tagged with different FGs. This method can be used to prepare CNT nanocomposites containing different types of nanoparticles (NPs), such as Au NPs, magnetic NPs, and quantum dots. The CNT nanocomposites decorated with these NPs can be used as reusable catalase-like nanocomposites with exceptional catalytic activities, owing to the synergistic effects of all the components. Additionally, the unique DBP-DNA interaction allows the on-demand detachment of the NPs attached to the CNT surface; further, it facilitates a CNT chirality-specific NP attachment and separation using the sequence-specific programmable characteristics of oligonucleotides. The proposed method provides a novel chemistry platform for constructing new functional CNTs suitable for diverse applications.

Solvation Free Energy of Self-Assembled Complexes: Using Molecular Dynamics to Understand the Separation of ssDNA-Wrapped Single-Walled Carbon Nanotubes

Molecular dynamics simulations were used to characterize the self-assembly of single-stranded DNA (ssDNA) on a (6,5) single-walled carbon nanotube (SWCNT) in aqueous solution for the purpose of gaining an improved theoretical understanding of separation strategies for SWCNTs using ssDNA as a dispersant. Four separate ssDNA sequences, ((TAT)4, TTA(TAT)2ATT, C12, (GTC)2GT), at various levels of loading, were chosen for study based on published experimental work showing selective extraction of particular SWCNT species based on the ssDNA dispersant sequence. We develop a unique workflow based on free energy perturbation (FEP) and use this to determine the relative solubility of these complexes due to the adsorption of the ssDNA on the SWCNT surface, and hence, rank the favorability of separations observed during experiments. Results qualitatively agree with experiments and indicate that the nucleobase sequence of the adsorbed ssDNA greatly affects the free energy of complex solvation which ultimately drives SWCNT separation. Further, to elucidate the underlying physics governing the ssDNA-SWCNT solubility rankings, we also present calculations for four structural characteristics of ssDNA adsorption. We demonstrate that a unique type of intra-strand hydrogen bonding is the most important factor contributing to the stability of the ssDNA-SWCNT complexes and show how these adsorption characteristics are coupled with the FEP results.

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.

Interaction of Human Telomeric i-Motif DNA with Single-Walled Carbon Nanotubes: Insights from Molecular Dynamics Simulations

This work deals with molecular dynamics simulations of human telomeric i-motif DNA interacting with functionalized single-walled carbon nanotubes. We study two kinds of i-motifs differing by the protonation state of cytosines, i.e., unprotonated ones representative to neutral pH and with half of the cytosines protonated and representative to acidic conditions. These i-motifs interact with two kinds of carbon nanotubes differing mainly in chirality (diameter), i.e., (10, 0) and (20, 0). Additionally, these nanotubes were on-tip functionalized by amino groups or by guanine- containing residues. We found that protonated i-motif adsorbs strongly, although not specifically, on the nanotube surfaces with its 3' and 5' ends directed toward the surface and that adsorption does not affect the i-motif shape and hydrogen bonds existing between C:C⁺ pairs. The functional groups on the nanotube tips have minimal effect either on position of i-motif or on its binding strength. Unprotonated i-motif, in turn, deteriorates significantly during interaction with the nanotubes and its binding strength is rather high as well. We found that (10, 0) nanotubes destroy the i-motif shape faster than (20, 0). Moreover the i-motif either tries to wrap the nanotube or migrates to its tip and becomes immobilized due to interaction with guanine residue localized on the nanotube tip and attempts to incorporate its 3' end into the nanotube interior. No hydrogen bonds exist within the unprotonated i-motif prior to and after adsorption on the nanotube. Thus, carbon nanotubes do not improve the stability of unprotonated i-motif due to simple adsorption or just physical interactions. We hypothesize that the stabilizing effect of carbon nanotubes reported in the literature is due to proton transfer from the functional group in the nanotube to cytosines and subsequent formation of C:C⁺ pairs.

Anomalous Slowdown of Polymer Detachment Dynamics on Carbon Nanotubes

The "wrapping" of polymer chains on the surface of carbon nanotubes allows one to obtain multifunctional hybrid materials with unique properties for a wide range of applications in biomedicine, electronics, nanocomposites, biosensors, and solar cell technologies. We study by means of molecular dynamics simulations the force-assisted desorption kinetics of a polymer from the surface of a carbon nanotube. We find that, due to the geometric coupling between the adsorbing surface and the conformation of the macromolecule, the process of desorption slows down dramatically upon increasing the windings around the nanotube. This behavior can be rationalized in terms of an overdamped dynamics with a frictional force that increases exponentially with the number of windings of the macromolecule, resembling the Euler-Eytelwein mechanism that describes the interplay between applied tension and frictional forces on a rope wrapped around a curved surface. The results highlight the fundamental role played by the geometry to control the dynamics and mechanical stability of hybrid materials in order to tailor properties and maximize performance.

Quantification of DNA/SWCNT Solvation Differences by Aqueous Two-Phase Separation

Single-walled carbon nanotubes (SWCNTs) coated with single-stranded DNA can be effectively separated into various chiralities using an aqueous two-phase (ATP) system. Partitioning is driven by small differences in the dissolution characteristics of the hybrid between the two phases. Thus, in addition to being a separation technique, the ATP system potentially also offers a way to quantify and rank the dissolution properties of the solute (here the DNA/SWCNT hybrids), such as the solvation free energy and solubility. In this study, we propose two different approaches to quantitatively analyze the ATP partitioning of DNA/SWCNT hybrids. First, we present a model that extracts the relative solvation free energy of various DNA/SWCNT hybrids by using an expansion relative to a standard state. Second, we extract a solubility parameter by analyzing the partitioning of hybrids in the ATP system. The two approaches are found to be consistent, providing some confidence in each as a method of quantifying differences in the solubility of various DNA/SWCNT hybrids.

Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity

Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials.

Ionic Strength-Mediated Phase Transitions of Surface-Adsorbed DNA on Single-Walled Carbon Nanotubes

Single-stranded DNA oligonucleotides have unique, and in some cases sequence-specific molecular interactions with the surface of carbon nanotubes that remain the subject of fundamental study. In this work, we observe and analyze a generic, ionic strength-mediated phase transition exhibited by over 25 distinct oligonucleotides adsorbed to single-walled carbon nanotubes (SWCNTs) in colloidal suspension. The phase transition occurs as monovalent salts are used to modify the ionic strength from 500 mM to 1 mM, causing a reversible reduction in the fluorescence quantum yield by as much as 90%. The phase transition is only observable by fluorescence quenching within a window of pH and in the presence of dissolved O₂, but occurs independently of this optical quenching. The negatively charged phosphate backbone increases (decreases) the DNA surface coverage on an areal basis at high (low) ionic strength, and is well described by a two-state equilibrium model. The resulting quantitative model is able to describe and link, for the first time, the observed changes in optical properties of DNA-wrapped SWCNTs with ionic strength, pH, adsorbed O₂, and ascorbic acid. Cytosine nucleobases are shown to alter the adhesion of the DNA to SWCNTs through direct protonation from solution, decreasing the driving force for this phase transition. We show that the phase transition also changes the observed SWCNT corona phase, modulating the recognition of riboflavin. These results provide insight into the unique molecular interactions between DNA and the SWCNT surface, and have implications for molecular sensing, assembly, and nanoparticle separations.

Molecular dynamics simulation strategies for designing carbon-nanotube-based targeted drug delivery

The carbon nanotube (CNT)-based target-specific delivery of drugs, or other molecular cargo, has emerged as one of the most promising biomedical applications of nanotechnology. To achieve efficient CNT-based drug delivery, the interactions between the drug, CNT and biomolecular target need to be properly optimized. Recent advances in the computer-aided molecular design tools, in particular molecular dynamics (MD) simulation studies, offer an appropriate low-cost approach for such optimization. This review highlights the various potential MD approaches for the simulation of CNT interactions with cell membranes while emphasizing various methods of cellular internalization and toxicities of CNTs to build new strategies for designing rational CNT-based targeted drug delivery to circumvent the limitations associated with the various clinically available nonspecific therapeutic agents.

Single-walled carbon nanotubes as optical probes for bio-sensing and imaging

A review on the applications of single-walled carbon nanotube photoluminescence in biomolecular sensing and biomedical imaging.

Electrostatics of DNA nucleotide-carbon nanotube hybrids evaluated from QM:MM simulations

Biomolecule-functionalized carbon nanotubes (CNTs) have been studied vastly in recent years due to their potential applications for instance in cancer detection, purification and separation of CNTs, and nanoelectronics. Studying the electrostatic potential generated by a biomolecule-CNT hybrid is important in predicting its interactions with the surrounding environment such as charged particles and surfaces. In this paper, we performed atomistic simulations using a QM:MM approach to evaluate the electrostatic potential and charge transfer for a hybrid structure formed by a DNA nucleotide and a CNT in solution. Four types of DNA nucleotides and two CNTs with chiralities of (4,4) and (7,0) were considered. The types of nucleotides and CNTs were both found to play important roles in the electrostatic potential and charge transfer of the hybrid. At the same distance from the CNT axis, the electrostatic potential for the nucleotide-(4,4) CNT hybrids was found to be stronger compared with that for the nucleotide-(7,0) CNT hybrids. Higher electric charge was also shown to be transferred from the DNA nucleotides to the (7,0) CNT compared with the (4,4) CNT. These results correlate with the previous finding that the nucleotides bound more tightly to the (7,0) CNT compared with the (4,4) CNT.

Polypeptide A9K at nanoscale carbon: a simulation study

The amphiphilic nature of surfactant-like peptides is responsible for their propensity to aggregate at the nanoscale.

Water transport control in carbon nanotube arrays

Based on a recent scaling law of the water mobility under nanoconfined conditions, we envision novel strategies for precise modulation of water diffusion within membranes made of carbon nanotube arrays (CNAs). In a first approach, the water diffusion coefficient D may be tuned by finely controlling the size distribution of the pore size. In the second approach, D can be varied at will by means of externally induced electrostatic fields. Starting from the latter strategy, switchable molecular sieves are proposed, where membranes are properly designed with sieving and permeation features that can be dynamically activated/deactivated. Areas where a precise control of water transport properties is beneficial range from energy and environmental engineering up to nanomedicine.

DNA molecules site-specific immobilization and their applications

In addition to its role as a carrier of genetic information, DNA has been recognized as a construction material for the assembly of different objects and structural arrangements with nanoscale features. As a result of DNA’s self-recognition properties (based on the specific base-pairing of G-C and T-A), monolayer films of nucleic acids on solid supports have attracted an escalating attentions. Recently, numerous novel materials based on two-dimensional (2D) and three-dimensional (3D) DNA structures have been reported, which extends their utility to a large number of appliations. This review paper intends to be a new and comprehensive overview of recent strategies to site-specifically immobilized DNA on various materials, including carbonaceous substances, gold, and silica substrate, emphasizing the applications of site-specific DNA nanostructure-based devices for diagnostic, bioanalytical, food safety and environmental monitoring. Additionally, an up-to-date perspective is proposed at the end of this review.

Interaction of single-stranded DNA with curved carbon nanotube is much stronger than with flat graphite

We used single molecule force spectroscopy to measure the force required to remove single-stranded DNA (ssDNA) homopolymers from single-walled carbon nanotubes (SWCNTs) deposited on methyl-terminated self-assembled monolayers (SAMs). The peeling forces obtained from these experiments are bimodal in distribution. The cluster of low forces corresponds to peeling from the SAM surface, while the cluster of high forces corresponds to peeling from the SWCNTs. Using a simple equilibrium model of the single molecule peeling process, we calculated the free energy of binding per nucleotide. We found that the free energy of ssDNA binding to hydrophobic SAMs decreases as poly(A) > poly(G) ≈ poly(T) > poly(C) (16.9 ± 0.1; 9.7 ± 0.1; 9.5 ± 0.1; 8.7 ± 0.1 kBT, per nucleotide). The free energy of ssDNA binding to SWCNT adsorbed on this SAM also decreases in the same order poly(A) > poly(G) > poly(T) > poly(C), but its magnitude is significantly greater than that of DNA-SAM binding energy (38.1 ± 0.2; 33.9 ± 0.1; 23.3 ± 0.1; 17.1 ± 0.1 kBT, per nucleotide). An unexpected finding is that binding strength of ssDNA to the curved SWCNTs is much greater than to flat graphite, which also has a different ranking (poly(T) > poly(A) > poly(G) ≥ poly(C); 11.3 ± 0.8, 9.9 ± 0.5, 8.3 ± 0.2, and 7.5 ± 0.8 kBT, respectively, per nucleotide). Replica-exchange molecular dynamics simulations show that ssDNA binds preferentially to the curved SWCNT surface, leading us to conclude that the differences in ssDNA binding between graphite and nanotubes arise from the spontaneous curvature of ssDNA.

DNA-controlled partition of carbon nanotubes in polymer aqueous two-phase systems

Sorting single-wall carbon nanotubes (SWCNTs) of different chiralities is both scientifically interesting and technologically important. Recent studies have shown that polymer aqueous two-phase extraction is a very effective way to achieve nanotube sorting. However, works published to date have demonstrated only separation of surfactant-dispersed SWCNTs, and the mechanism of chirality-dependent SWCNT partition is not well understood. Here we report a systematic study of spontaneous partition of DNA-wrapped SWCNTs in several polymer aqueous two-phase systems. We show that partition of DNA-SWCNT hybrids in a given polymer two-phase system is strongly sequence-dependent and can be further modulated by salt and polymer additives. With the proper combination of DNA sequence, polymer two-phase system, and partition modulators, as many as 15 single-chirality nanotube species have been effectively purified from a synthetic mixture. As an attempt to provide a unified partition mechanism of SWCNTs dispersed by surfactants and by DNA, we present a qualitative analysis of solvation energy for SWCNT colloids in a polymer-modified aqueous phase. Our observation and analysis highlight the sensitive dependence of the hydration energy on the spatial distribution of hydrophilic functionalities.

Photodynamic effect of functionalized single-walled carbon nanotubes: a potential sensitizer for photodynamic therapy

Single-walled carbon nanotubes (SWNTs) possess unique physical and chemical properties, which make them very attractive for a wide range of applications. In particular, SWNTs and their composites have shown a great potential for photodynamic therapy (PDT). SWNTs have usually been used for photothermal therapy; herein, the photodynamic effect of two functionalized SWNTs are detected under visible light illumination in vitro and in vivo. The results indicated that the photodynamic effect is not entirely dependent on illumination time, but also on the modification method of the SWNTs. The ability of SWNTs complexes to combine with photodynamic therapy significantly improved the therapeutic efficacy of cancer treatment, and the combined treatment demonstrated a synergistic effect. These findings suggest that the SWNTs composite has great potential as sensitizer for PDT.

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.

Sequence-dependent electrical response of ssDNA-decorated carbon nanotube, field-effect transistors to dopamine

Single-walled carbon nanotube (SWCNT)-based field-effect transistors (FETs) have been explored for use as biological/chemical sensors. Dopamine (DA) is a biomolecule with great clinical significance for disease diagnosis, however, SWCNT FETs lack responsivity and selectivity for its detection due to the presence of interfering compounds such as uric acid (UA). Surface modification of CNTs using single-stranded deoxyribonucleic acid (ssDNA) renders the surface responsive to DA and screens the interferent. Due to the presence of different bases in ssDNA, it is necessary to investigate the effect of sequence on the FET-based molecular recognition of DA. SWCNT FETs were decorated with homo- and repeated-base ssDNA sequences, and the electrical response induced by DA in the presence and absence of UA was gauged in terms of the variation in transistor electrical parameters including conductance, transconductance, threshold voltage and hysteresis gap. Our results showed that the response of ssDNA-decorated devices to DA, irrespective of the presence or absence of UA, was DNA sequence dependent and exhibited the trend: G > A > C and GA > GT > AC > CT, for homo- and repeated-base sequences, respectively. The different response of various SWCNT-ssDNA systems to DA underlines the sequence selectivity, whereas the detection of DA in the presence of UA highlights the molecular selectivity of the ssDNA-decorated devices.