Simulation of adsorption of DNA on carbon nanotubes

How a mixture of microRNA-29a (miR-29a) and microRNA-144 (miR-144) cancer biomarkers interacts with a graphene quantum dot

MicroRNAs (miRNAs) which are small non-coding RNAs have been reported to be potential cancer biomarker. However, it is difficult to extract such short RNA from a sample matrix. New effective strategies are required. Recently, graphene quantum dots (GQDs) have been used to detect nucleotides in many biosensor platforms, but their applications for miRNA extraction remain limited. GQD was reported to be able to collect short miRNA, but its performance to collect miRNAs with different structure remains unknown. Thus, in this work, the capability of GQD to interact with two different miRNAs is investigated. A mixture of hairpin-like miR-29a and circular miR-144 molecules are used as a representative of two miRNA morphologies. Two systems (a miRNA mixture, comprising 4 of miR-29a and 4 of miR-144, with (miR_GQD) and without GQD (miR)) were studied in comparison. MiRNAs in a mixture (miR) can aggregate, but no permanent miRNA assembly is captured. In contrast, the presence of GQD can rapidly and spontaneously activate the permanent miRNA/GQD clustering. This finding highlights the ability of GQD to be a miRNA collector. Interestingly, all GQD-bound miRNAs do not unfold. This allows the easy accessibility for probes. Also, nano-sized GQD seems to prefer hairpin miR-29a. The free 5' terminus of miR-29a acts as the sticky end to adhere on GQD. This work highlights the importance of RNA secondary structure on GQD/miRNA aggregation capability. An insight obtained here will be useful for further design of miRNA isolation strategies.

Stability and conformation of DNA-hairpin in cylindrical confinement

We conducted atomistic Molecular Dynamics (MD) simulations of DNA-Hairpin molecules encapsulated within Single-Walled Carbon Nanotubes (SWCNTs) at a temperature of 300 K. Our investigation revealed that the structural integrity of the DNA-Hairpin can be maintained within SWCNTs, provided that the diameter of the SWCNT exceeds a critical threshold value. Conversely, when the SWCNT diameter falls below this critical threshold, the DNA-Hairpin undergoes denaturation, even at a temperature of 300 K. The DNA-Hairpin model we employed consisted of a 12-base pair stem and a 3-base loop, and we studied various SWCNTs with different diameters. Our analyses identified a critical SWCNT diameter of 3.39 nm at 300 K. Examination of key structural features, such as hydrogen bonds (H-bonds), van der Waals (vdW) interactions, and other inter-base interactions, demonstrated a significant reduction in the number of H-bonds, vdW energy, and electrostatic energies among the DNA hairpin's constituent bases when confined within narrower SWCNTs (with diameters of 2.84 nm and 3.25 nm). However, it was observed that the increased interaction energy between the DNA-Hairpin and the inner surface of narrower SWCNTs promoted the denaturation of the DNA-Hairpin. In-depth analysis of electrostatic mapping and hydration status further revealed that the DNA-Hairpin experienced inadequate hydration and non-uniform distribution of counter ions within SWCNTs having diameters below the critical value of 3.39 nm. Our inference is that the inappropriate hydration of counter ions, along with their non-uniform spatial distribution around the DNA hairpin, contributes to the denaturation of the molecule within SWCNTs of smaller diameters. For DNA-Hairpin molecules that remained undenatured within SWCNTs, we investigated their mechanical properties, particularly the elastic properties. Our findings demonstrated an increase in the persistence length of the DNA-Hairpin with increasing SWCNT diameter. Additionally, the stretch modulus and torsional stiffness of the DNA-Hairpin were observed to increase as a function of SWCNT diameter, indicating that confinement within SWCNTs enhances the mechanical flexibility of the DNA-Hairpin.

Molecular dynamics simulations reveal concentration-dependent blockage of graphene quantum dots to water channel protein openings

Graphene quantum dots (GQDs) have attracted significant attention across various scientific research areas due to their exceptional properties. However, studies on the potential toxicity of GQDs have yielded conflicting results. Therefore, a comprehensive evaluation of the toxicity profile of GQDs is essential for a thorough understanding of their biosafety. In this work, employing a molecular dynamics (MD) simulation approach, we investigate the interactions between GQDs and graphene oxide quantum dots (GOQDs) with the AQP1 water channel protein, aiming to explore the potential biological influence of GQDs/GOQDs. Our MD simulation results reveal that GQDs can adsorb to the loop region around the openings of AQP1 water channels, resulting in the blockage of these channels and potential toxicity. Interestingly, this blockage is concentration-dependent, with higher GQD concentrations leading to a greater likelihood of blockage. Additionally, GOQDs show a lower probability of blocking the openings of AQP1 water channels compared to GQDs, due to the hydrophobicity of the loop regions around the openings, which ultimately leads to lower interaction energy. Therefore, these findings provide new insights into the potential adverse impact of GQDs on AQP1 water channels through the blockage of their openings, offering valuable molecular insights into the toxicity profile of GQD nanomaterials.

Carbon-nanotube field-effect transistors for resolving single-molecule aptamer-ligand binding kinetics

Small molecules such as neurotransmitters are critical for biochemical functions in living systems. While conventional ultraviolet-visible spectroscopy and mass spectrometry lack portability and are unsuitable for time-resolved measurements in situ, techniques such as amperometry and traditional field-effect detection require a large ensemble of molecules to reach detectable signal levels. Here we demonstrate the potential of carbon-nanotube-based single-molecule field-effect transistors (smFETs), which can detect the charge on a single molecule, as a new platform for recognizing and assaying small molecules. smFETs are formed by the covalent attachment of a probe molecule, in our case a DNA aptamer, to a carbon nanotube. Conformation changes on binding are manifest as discrete changes in the nanotube electrical conductance. By monitoring the kinetics of conformational changes in a binding aptamer, we show that smFETs can detect and quantify serotonin at the single-molecule level, providing unique insights into the dynamics of the aptamer-ligand system. In particular, we show the involvement of G-quadruplex formation and the disruption of the native hairpin structure in the conformational changes of the serotonin-aptamer complex. The smFET is a label-free approach to analysing molecular interactions at the single-molecule level with high temporal resolution, providing additional insights into complex biological processes.

Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook

Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.

Metallic nanostructure-based aptasensors for robust detection of proteins

There is a significant need for fast, cost-effective, and highly sensitive protein target detection, particularly in the fields of food, environmental monitoring, and healthcare. The integration of high-affinity aptamers with metal-based nanomaterials has played a crucial role in advancing the development of innovative aptasensors tailored for the precise detection of specific proteins. Aptamers offer several advantages over commonly used molecular recognition methods, such as antibodies. Recently, a variety of metal-based aptasensors have been established. These metallic nanomaterials encompass noble metal nanoparticles, metal oxides, metal-carbon nanotubes, carbon quantum dots, graphene-conjugated metallic nanostructures, as well as their nanocomposites, metal-organic frameworks (MOFs), and MXenes. In general, these materials provide enhanced sensitivity through signal amplification and transduction mechanisms. This review primarily focuses on the advancement of aptasensors based on metallic materials for the highly sensitive detection of protein targets, including enzymes and growth factors. Additionally, it sheds light on the challenges encountered in this field and outlines future prospects. We firmly believe that this review will offer a comprehensive overview and fresh insights into metallic nanomaterials-based aptasensors and their capabilities, paving the way for the development of innovative point-of-care (POC) diagnostic devices.

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.

Evaluation of adsorption of DNA/PEI polyplexes to tubing materials

Nucleic acid drugs hold great promise for potential treatment of a variety of diseases. But efficient delivery is still the major challenge impeding translation. Nanoformulations based on polymers and lipids require preparation processes such as microfluidic mixing, spray drying or final filling, where pumping is a crucial step. Here, we studied the effect of pumping on the component and overall loss of a binary polyplex formulation made of DNA and polyethyleneimine (PEI). We varied tubing length and material with a focus on subsequent spray drying. Interestingly, product loss increased with the length of silicon tubing. Losses of DNA were prevented by using Pumpsil. The following spray drying process did not affect DNA content but caused PEI loss. Characterization of the different tubing materials revealed similar hydrophobicity of all tubing materials and showed neutral Pumpsil® surface charge, negative Santoprene™ surface charge, and a positive Silicon surface charge. Hence, adsorption of DNA onto tubing material was concluded to be the root cause for DNA loss after pumping and is based upon an interplay of ionic and hydrophobic interactions between polyplexes and tubing material. Overall, selecting the appropriate tubing material for processing nucleic acid nanoparticles is key to achieving satisfactory product quality.

Diameter Dependent Melting and Softening of dsDNA Under Cylindrical Confinement

Carbon nanotubes (CNTs) are considered promising candidates for biomolecular confinement, including DNA encapsulation for gene delivery. Threshold values of diameters have been reported for double-stranded DNA (dsDNA) encapsulation inside CNTs. We have performed all-atom molecular dynamics (MD) simulations of dsDNAs confined inside single-walled CNTs (SWCNTs) at the physiologically relevant temperature of 300 K. We found that the dsDNA can be confined without being denatured only when the diameter of the SWCNT exceeds a threshold value. Below this threshold diameter, the dsDNA gets denatured and melts even at the temperature of 300 K. Our simulations using SWCNTs with chirality indices (20,20) to (30,30) at 300 K found the critical diameter to be 3.25 nm (corresponding to (24,24) chirality). Analyses of the hydrogen bonds (H-bonds), Van der Walls (VdW) energy, and other inter-base interactions show drastic reduction in the number of H-bonds, VdW energy, and electrostatic energies between the bases of dsDNA when it is confined in narrower SWCNTs (up to diameter of 3.12 nm). On the other hand, the higher interaction energy between the dsDNA and the SWCNT surface in narrower SWCNTs assists in the melting of the dsDNA. Electrostatic mapping and hydration status analyses show that the dsDNA is not adequately hydrated and the counter ion distribution is not uniform below the critical diameter of the SWCNT. As properly hydrated counter ions provide stability to the dsDNA, we infer that the inappropriate hydration of counter ions and their non-uniform distribution around the dsDNA cause the melting of the dsDNA inside SWCNTs of diameter below the critical value of 3.25 nm. For confined dsDNAs that do not get denatured, we computed their elastic properties. The persistence length of dsDNA was found to increase by a factor of about two and the torsional stiffness by a factor of 1.5 for confinement inside SWCNTs of diameters up to 3.79 nm, the stretch modulus also following nearly the same trend. Interestingly, for higher diameters of SWCNT, 3.79 nm and above, the dsDNA becomes more flexible, demonstrating that the mechanical properties of the dsDNA under cylindrical confinement depend non-monotonically on the confinement diameter.

DNA-Mediated Assembly of Carbon Nanomaterials

Carbon nanomaterials (CNMs) have attracted extensive attentions on account of their superior electrical, mechanical, optical, and biological properties. However, the dimensional limit and irregular arrangement have hampered their further application. It is necessary to find an easy, efficient and controllable way to assemble CNMs into well-ordered array. DNA nanotechnology, owning to the advantages of precise programmability, highly structural predictability and spatial addressability, has been widely applied in the assembly of CNMs. Summarizing the progress and achievements in this field will be of great value to related studies. Herein, based on the different dimensions of CNMs containing 0-dimensional (0D) carbon dots (CDs), fullerenes, 1-dimensional (1D) carbon nanotubes (CNTs) and 2-dimensional (2D) graphene, we introduced the conjugation strategies between DNA and CNMs, their different assembly methods and their applications. In addition, we also discuss the existing challenges and future opportunities in the field.

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.

Probing the adsorption behavior and free energy landscape of single-stranded DNA oligonucleotides on single-layer MoS2with molecular dynamics

Interfacing single-stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self-assembled hybrids is still not well understood. Here, atomistic molecular dynamics simulation is employed to study the distinct adsorption behavior of ssDNA on a single-layer MoS₂in aqueous environment. The ssDNA sequences [T₁₀, G₁₀, A₁₀, C₁₀, U₁₀, (GT)₅, and (AC)₅] are chosen on the basis that short ssDNA segments can undergo a spontaneous conformational change upon adsorption and allow efficient sampling of the conformational landscape. Differences in hybridization is attributed to the inherent molecular recognition ability of the bases. While the binding appears to be primarily driven by energetically favorable van der Waalsπ-stacking interactions, equilibrium structures are modulated by the ssDNA conformational changes. The poly-purines demonstrate two concurrently competingπ-stacking interactions: nucleobase-nucleobase (intramolecular) and nucleobase-MoS₂(intermolecular). The poly-pyrimidines, on the other hand, reveal enhancedπ-stacking interactions, thereby maximizing the number of contacts. The results provide new molecular-level understanding of ssDNA adsorption on the MoS₂surface and facilitate future studies in design of functional DNA/MoS₂structure-based platforms for DNA sequencing, biosensing (optical, electrochemical, and electronic), and drug delivery.

Physical Surface Modification of Carbon-Nanotube/Polydimethylsiloxane Composite Electrodes for High-Sensitivity DNA Detection

The chemical modification of electrode surfaces has attracted significant attention for lowering the limit of detection or for improving the recognition of biomolecules; however, the chemical processes are complex, dangerous, and difficult to control. Therefore, instead of the chemical process, we physically modified the surface of carbon-nanotube/polydimethylsiloxane composite electrodes by dip coating them with functionalized multi-walled carbon nanotubes (F-MWCNTs). These electrodes are used as working electrodes in electrochemistry, where they act as a recognition layer for sequence-specific DNA sensing through π-π interactions. The F-MWCNT-modified electrodes showed a limit of detection of 19.9 fM, which was 1250 times lower than that of pristine carbon/polydimethylsiloxane electrodes in a previous study, with a broad linear range of 1-1000 pM. The physically modified electrode was very stable during the electrode regeneration process after DNA detection. Our method paves the way for utilizing physical modification to significantly lower the limit of detection of a biosensor system as an alternative to chemical processes.

Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies

Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers.

Modeling the Adsorption of the miR-29a Cancer Biomarker on a Graphene Quantum Dot

MicroRNAs (miRNAs) are small noncoding RNA molecules associated with the regulation of gene expression in organisms. MiRNAs are focused on as potential cancer biomarkers due to their involvement in cancer development. New potential techniques for miRNA detection are rapidly developed, while there is a lack of effective extraction approaches, especially for miRNAs. Recently, graphene quantum dots (GQDs) have been involved in many disease biosensor platforms including miRNA detection, but no application in miRNA extraction is studied. To extract miRNAs, miRNA adsorption and desorption on GQDs are the key. Thus, in this work, the adsorption mechanism of miRNA on GQDs in solution is revealed using molecular dynamics simulations. The aim is to explore the possibility of using GQDs for miRNA extraction. The folded miR-29a molecule, one of the key cancer biomarkers, is used as a miRNA model. Two systems with one (1miR) and four (4miR) chains of miR-29a were set. MiR-29a molecules in all systems are simultaneously adsorbed on the GQD surface. Our finding highlights the ability of the GQD in collecting miRNAs in solution. In 1miR, the whole miR-29a chain sits on the GQD face, whereas all miR-29a molecules in 4miR show the "clamping" conformation. No "lying flat" orientation of miR-29a is observed due to the existence of the preserved hairpin region. Interestingly, the 5' end shows tighter binding than the 3' terminus. A design of complementary DNA with the recognition segment involving the sequences close to the 3' end can promote effective miR-29a desorption.

Tracking the interaction between single-wall carbon nanotube and SARS-Cov-2 spike glycoprotein: A molecular dynamics simulations study

COVID-19, a newly discovered type of coronavirus, is the cause of the pandemic infection that was first reported in Wuhan, China, in December 2019. One of the most critical problems in this regard is to identify innovative drugs that may reduce or manage this global health concern. Nanoparticles have shown a pivotal role in drug delivery systems in recent decades. The surface of nanoparticles could be covered by a layer composed of different biomolecules (e.g., proteins and macromolecules) following the incubation with a biological fluid. This protein-rich layer is called “Protein Corona.” In this study, an all-atom molecular dynamics simulation was used for investigating the monomeric B domain of the spike glycoprotein due to its role in the accessibility of the spike glycoprotein to single-wall carbon nanotubes (SWCNTs). The interaction energy values between the carbon nanotube and B domain of the viral spike glycoprotein were evaluated. The obtained results, based on Lennard-Jones potentials, demonstrated that SWCNTs had an affinity to the B domain of the S1 subunit in the spike glycoprotein. The adsorption of SWCNTs on the B domain surface led to a significant change in solvent-accessible surface, internal hydrogen bonds, and finally in the tertiary structure, which could provide a reasonable method to impede the interaction between the angiotensin-converting enzyme II and SARS-CoV-2 spike glycoprotein. A decrease in the mean square displacement of the B domain was shown after the adsorption of SWCNTs as a result of increasing the hydrophobic-hydrophilic properties of the B domain. The arrangement of SWCNTs on the B domain surface and their interaction using the 2-acetamido-2-deoxy-β-d-glucopyranose group (988, 991, and 992) demonstrated that a change in the affinity of the S1 subunit could be used as a barrier to viral replication. The analysis of the SWCNT-B domain complex indicated that the presence of SWCNTs is able to cause alterations in the S1 subunit of the spike protein, and these nanotubes could be employed for further in-vitro and in-vivo antiviral studies. Also, SWCNTs are able to be utilized in drug delivery systems.

Binding Force and Site-Determined Desorption and Fragmentation of Antibiotic Resistance Genes from Metallic Nanomaterials

Interfacial interactions between antibiotic resistance genes (ARGs) and metallic nanomaterials (NMs) lead to adsorption and fragmentation of ARGs, which can provide new avenues for selecting NMs to control ARGs. This study compared the adsorptive interactions of ARGs (tetM-carrying plasmids) with two metallic NMs (ca. 20 nm), i.e., titanium dioxide (nTiO₂) and zero-valent iron (nZVI). nZVI had a higher adsorption rate (0.06 min^-1) and capacity (4.29 mg/g) for ARGs than nTiO₂ (0.05 min^-1 and 2.15 mg/g, respectively). No desorption of ARGs from either NMs was observed in the adsorptive background solution, isopropanol or urea solutions, but nZVI- and nTiO₂-adsorbed ARGs were effectively desorbed in NaOH and NaH₂PO₄ solutions, respectively. Molecular dynamics simulation revealed that nTiO₂ mainly bound with ARGs through electrostatic attraction, while nZVI bound with PO₄^3- of the ARG phosphate backbones through Fe-O-P coordination. The ARGs desorbed from nTiO₂ remained intact, while the desorbed ARGs from nZVI were splintered into small fragments irrelevant to DNA base composition or sequence location. The ARG removal by nZVI remained effective in the presence of PO₄^3-, natural organic matter, or protein at environmentally relevant concentrations and in surface water samples. These findings indicate that nZVI can be a promising nanomaterial to treat ARG pollution.

Nanotechnology as a viable alternative for the removal of antimicrobial resistance determinants from discharged municipal effluents and associated watersheds: A review

Effective and efficient utilization of antimicrobial drugs has been one of the important cornerstone of modern medicine. However, since antibiotics were first discovered by Alexander Fleming about a century ago, the time clock of antimicrobial resistance (AMR) started ticking somewhat leading to a global fear of a possible "post-antimicrobial era". Antibiotic resistance (AR) remains a serious challenge causing global outcry in both the clinical setting and the environment. The huge influence of municipal wastewater effluent discharges on the aquatic environment has made the niche a hotspot of research interest in the study of emergence and spread of AMR microbes and their resistance determinants/genes. The current review adopted a holistic approach in studying the proliferation of antibiotic resistance determinants (ARDs) as well as their impacts and fate in municipal wastewater effluents and the receiving aquatic environments. The various strategies deployed hitherto for the removal of resistance determinants in municipal effluents were carefully reviewed, while the potential for the use of nanotechnology as a viable alternative is explicitly explored. Also, highlighted in this review are the knowledge gaps to be filled in order to curtail the spread of AMR in aquatic environment and lastly, suggestions on the applicability of nanotechnology in eliminating AMR determinants in municipal wastewater treatment facilities are proffered.

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.

Effect of Octadecylamine Surfactant on DNA Interactions with Graphene Surfaces

Understanding of how to integrate DNA molecules with graphene materials is important for the development of biosensors and biomolecular logic circuits. For some of these applications, controlling DNA structural conformation on the graphene substrate is critically important and can be achieved through the use of self-assembled monolayers. Here, we performed all-atom molecular dynamics simulations to understand how various 1-octadecylamine (ODA) coatings of the graphene surface affect the conformation of double-stranded DNA (dsDNA) on the surface. The simulation results demonstrated that dsDNA structures become more stable as ODA concentration increases due to the formation of DNA-ODA hydrogen bonds and reduction of DNA-surface interactions, which aid in retaining internal DNA interactions. Specifically, the interaction of ODA molecules with DNA prevents nucleobases from forming π-π stacking interactions with the surface. Some dsDNA conformations, such as sharp kinks or unwinding, can occur more frequently in DNA with A-T sequences due to weaker pairing interactions than with G-C sequences. Furthermore, our results conclude that both DNA sequence and ODA concentration play an essential role in experimentally observed conformational changes of DNA on the graphene surface.

Reverse Translocation of Nucleotides through a Carbon Nanotube

We report molecular dynamics (MD) simulations of the reverse translocation of single nucleotides through a narrow carbon nanotube (CNT), with a diameter of 1.36 nm, immersed in a 1 M KCl electrolyte solution under an applied electric field along the tube axis. We observe ion selectivity by the narrow CNT, which leads to a high flow of K⁺ ions, in contrast to a negligible and opposing current of Cl^- ions. The K⁺ ions, driven by the electric field, force a negatively charged single nucleotide into the narrow CNT where it is trapped by the incoming K⁺ ions and water molecules, and the nucleotide is driven in the same direction as the K⁺ ions. This illustrates a novel mechanism of nucleotide reverse translocation that is controlled by ion selectivity. An increase in the CNT diameter to 2.71 nm or an increase in nucleotide chain length both lead to translocation in the normal direction of the applied field. The reverse translocation rate of single nucleotides is correlated to the ionic current of K⁺ ions in the narrow tube, unlike translocation in the normal direction in the wider tube.

A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification

We report a bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput (20 min) extraction of nucleic acids from physiological samples. The design uses a membrane ionic transistor to sustain low-ionic strength in a localized region at a junction, such that the resulting high field can selectively isolate high-charge density nucleic acids from the main flow channel and insert them into a standardized buffer in a side channel that bifurcates from the junction. The high local electric field and the bifurcated field-flow design facilitate concentration reduction of both divalent cation (Ca2+) and molecular PCR inhibitors by more than two orders of magnitude, even with high-throughput continuous loading. The unique design with a large (>20 mM mm-1) on-chip ionic-strength gradient allows miniaturization into a high-throughput field-flow fractionation chip that can be integrated with upstream lysing and downstream PCR/sensor modules for various nucleic acid detection/quantification applications. A concentration-independent 85% yield for extraction and an overall post-PCR yield exceeding 60% are demonstrated for a 111 bp dsDNA in 10 μL of human plasma, compared to no amplification with the raw sample. A net yield four times larger than a commercial extraction kit is demonstrated for miR-39 in human plasma.

Analysis of circulating non-coding RNAs in a non-invasive and cost-effective manner

Non-coding RNAs (ncRNAs) participate in regulation of gene expression, and are highly relevant to pathological development. They are found to be stably present in diverse body fluids, including those in the circulatory system, which can be sampled non-invasively for clinical tests. Thus, circulating ncRNAs have great potential to be disease biomarkers. However, tremendous efforts are desired to discover and utilize ncRNAs as biomarkers in clinical diagnosis, calling for technological advancement in analysis of circulating ncRNAs in biospecimens. Hence, this review summarizes the recent developments in this area, highlighting the works devoted to cancer diagnosis and prognosis. Three main directions are focused: 1) Extraction and purification of ncRNAs from body fluids; 2) Quantification of the purified circulating ncRNAs; and 3) Microfluidic platforms for integration of both steps to enable point-of-care diagnostics. These technologies have laid a solid foundation to move forward the applications of circulating ncRNAs in disease diagnosis and cure.

Non-Covalent Functionalization of Carbon Nanotubes for Electrochemical Biosensor Development

Carbon nanotubes (CNTs) have been widely studied and used for the construction of electrochemical biosensors owing to their small size, cylindrical shape, large surface-to-volume ratio, high conductivity and good biocompatibility. In electrochemical biosensors, CNTs serve a dual purpose: they act as immobilization support for biomolecules as well as provide the necessary electrical conductivity for electrochemical transduction. The ability of a recognition molecule to detect the analyte is highly dependent on the type of immobilization used for the attachment of the biomolecule to the CNT surface, a process also known as biofunctionalization. A variety of biofunctionalization methods have been studied and reported including physical adsorption, covalent cross-linking, polymer encapsulation etc. Each method carries its own advantages and limitations. In this review we provide a comprehensive review of non-covalent functionalization of carbon nanotubes with a variety of biomolecules for the development of electrochemical biosensors. This method of immobilization is increasingly being used in bioelectrode development using enzymes for biosensor and biofuel cell applications.

Direct Measurement of π Coupling at the Single-Molecule Level using a Carbon Nanotube Force Sensor

We report a carbon nanotube (CNT) force sensor that combines a suspended CNT transistor with dual-trap optical tweezers to explore the interactions between two individual molecules in the near-equilibrium regime with sub-piconewton resolution. The directly measured equilibrium force (1.2 ± 0.5 pN) is likely related to the binding force between a CNT and a single DNA base, where two aromatic rings spontaneously attract to each other due to the noncovalent forces between them. On the basis of our force measurements, the binding free energy per base is calculated (∼0.34 eV), which is in good agreement with theoretical simulations. Moreover, three-dimensional scanning photocurrent microscopy enables us to simultaneously monitor the morphology changes of the CNT, leading to a comprehensive reconstruction of the CNT-DNA binding dynamics. These experimental results shed light on the fundamental understanding of the mechanical coupling between CNTs and DNA molecules and, more importantly, provide a new platform for direct observation of intermolecular interfaces at the single-molecule level.

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.

Graphene Oxide-Facilitated Comprehensive Analysis of Cellular Nucleic Acid Binding Proteins for Lung Cancer

Nucleic acid binding proteins (NABPs) mediate a broad range of essential cellular functions. However, it is very challenging to comprehensively extract whole cellular NABPs due to the lack of approaches with high efficiency. To this end, carbon nanomaterials, including graphene oxide (GO), carboxylated graphene (cG), and carboxylated carbon nanotube (cCNT), were utilized to extract cellular NABPs in this study through a new strategy. Our data demonstrated that GO, cG, and cCNT could extract nearly 100% cellular DNA in vitro. Conversely, their RNA extraction efficiencies were 60, 50, and 29%, respectively, partially explaining why GO has the highest NABPs yield compared to cG and cCNT. We further found that ionic bond mediated by cations between RNA and functional groups of nanomaterials facilitated RNA absorption on nanomaterials. About 2400 proteins were successfully identified from GO-enriched NABPs sample, and 88% of annotated NABPs were enriched at least 2 times compared to cell lysate, indicating the high selectivity of our strategy. The developed method was further applied to compare the NABPs in two lung cancer cell lines with different tumor progression abilities. According to label-free quantification results, 118 differentially expressed NABPs were discovered and 6 candidate NABPs, including ACAA2, GTF2I, VIM, SAMHD1, LYAR, and IGF2BP1, were successfully validated by immunoassay. The level of SAMHD1 in the serum of lung cancer patients was measured, which significantly increased upon cancer progression. Our results collectively demonstrated that GO is an ideal nanomaterial for NABPs selective extraction, which could be broadly used in varied physiological and pathophysiological settings.

Transition Metal Dichalcogenide Nanosheets for Visual Monitoring PCR Rivaling a Real-Time PCR Instrument

Monitoring the progress of polymerase chain reactions (PCRs) is of critical importance in bioanalytical chemistry and molecular biology. Although real-time PCR thermocyclers are ideal for this purpose, their high cost has limited their applications in resource-poor areas. Direct visual detection would be a more attractive alternative. To monitor the PCR amplification, DNA-staining dyes, such as SYBR Green I (SG), are often used. Although these dyes give higher fluorescence when binding to double-stranded DNA products, they also yield strong background fluorescence in the presence of a high concentration of single-stranded (ss) DNA primers. In this work, we screened various nanomaterials and found that graphene oxide (GO), reduced GO, molybdenum disulfide (MoS₂), and tungsten disulfide (WS₂) can quench the fluorescence of nonamplified negative samples while still retaining strong fluorescence of positive ones. The signal ratio of positive-over-negative samples was enhanced by around 50-fold in the presence of these materials. In particular, MoS₂ and WS₂ nearly fully retained the fluorescence of the positive samples. The mechanism for MoS₂ and WS₂ to enhance PCR signaling is attributed to the adsorption of both the ssDNA PCR primers and SG with an appropriate strength. MoS₂ can also suppress nonspecific amplification caused by excess polymerase. Finally, this method was used to detect extracted transgenic soya GTS 40-3-2 DNA after PCR amplification. Compared with the samples without nanomaterials, the addition of MoS₂ could better distinguish the concentration difference of the template DNA, and the sensitivity of visual detection rivaled that from a real-time PCR instrument.

Controlling Polyelectrolyte Adsorption onto Carbon Nanotubes by Tuning Ion-Image Interactions

Understanding and controlling polyelectrolyte adsorption onto carbon nanotubes is a fundamental challenge in nanotechnology. Polyelectrolytes have been shown to stabilize nanotube suspensions through adsorbing onto the nanotube surface, and polyelectrolyte-coated nanotubes are emerging as building blocks for complex and addressable self-assembly. Conventional wisdom suggests that polyelectrolyte adsorption onto nanotubes is driven by specific chemical or van der Waals interactions. We develop a simple mean-field model and show that ion-image attraction significantly effects adsorption onto conducting nanotubes at low salt concentrations. Our theory suggests a simple strategy to selectively and reversibly functionalize carbon nanotubes on the basis of their electronic structures, which in turn modify the ion-image attraction.

Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design

We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base-graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene-aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine-graphene interactions.

Extraction of microRNAs from biological matrices with titanium dioxide nanofibers

MicroRNAs (miRNAs) are small RNAs that bind to mRNA targets and regulate their translation. A functional study of miRNAs and exploration of their utility as disease markers require miRNA extraction from biological samples, which contain large amounts of interfering compounds for downstream RNA identification and quantification. The most common extraction methods employ silica columns or the TRIzol reagent but give out low recovery for small RNAs probably due to their short strand lengths. Herein, we fabricated the titanium dioxide nanofibers using electrospinning to facilitate miRNA extraction and developed the optimal buffer conditions to improve miRNA recovery from biological matrices of cell lysate and serum. We found that our TiO₂ fibers could obtain a recovery of 18.0 ± 3.6% for miRNA fibers while carrying out the extraction in the more complex medium of cell lysate, much higher than the 0.02 ± 0.0001% recovery from the commercial kit. The much improved extraction of miRNAs from our fibers could be originated from the strong coordination between TiO₂ and RNA's phosphate backbone. In addition, the binding, washing, and elution buffers judiciously developed in the present study can achieve selective extraction of small RNA shorter than 500 nucleotides in length. Our results demonstrate that TiO₂ nanofibers can work as a valuable tool for extraction of miRNAs from biological samples with high recovery. Graphical abstract Schematic for extraction of small RNAs using TiO₂ nanofibers.

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.

Studying the adsorption of DNA nanostructures on graphene in the aqueous phase using molecular dynamic simulations

DNA nanostructures can undergo large structural fluctuations and deviate from their intended configurations. In this work, two model DNA nanostructures (i.e., Nan and Kai) were designed based on the shape of the two Chinese characters of the name of Nankai University, and additional single-stranded DNA fragments were added to interact with graphene. During four 50-ns molecular dynamic simulations in aqueous solution, the DNA nanostructures adsorbed onto graphene demonstrated more stable conformations with lower root mean square deviations and smaller coordinate changes in the z-axis direction than the DNA nanostructures that were not adsorbed onto graphene. The interaction analyses and energetic calculations show that π-π interactions between single-stranded DNA and graphene are necessary for adsorption of the DNA nanostructures. Overall, this work examined the interactions between DNA and graphene at a large spatial scale with the hope that it provides a new strategy to stabilize DNA nanostructures.

Nanoparticle exposure reactivates latent herpesvirus and restores a signature of acute infection

Background

Inhalation of environmental (nano) particles (NP) as well as persistent herpesvirus-infection are potentially associated with chronic lung disease and as both are omnipresent in human society a coincidence of these two factors is highly likely. We hypothesized that NP-exposure of persistently herpesvirus-infected cells as a second hit might disrupt immune control of viral latency, provoke reactivation of latent virus and eventually lead to an inflammatory response and tissue damage.

Results

To test this hypothesis, we applied different NP to cells or mice latently infected with murine gammaherpesvirus 68 (MHV-68) which provides a small animal model for the study of gammaherpesvirus-pathogenesis in vitro and in vivo. In vitro, NP-exposure induced expression of the typically lytic viral gene ORF50 and production of lytic virus. In vivo, lytic viral proteins in the lung increased after intratracheal instillation with NP and elevated expression of the viral gene ORF50 could be detected in cells from bronchoalveolar lavage. Gene expression and metabolome analysis of whole lung tissue revealed patterns with striking similarities to acute infection. Likewise, NP-exposure of human cells latently infected with Epstein-Barr-Virus also induced virus production.

Conclusions

Our results indicate that NP-exposure of persistently herpesvirus-infected cells – murine or human – restores molecular signatures found in acute virus infection, boosts production of lytic viral proteins, and induces an inflammatory response in the lung – a combination which might finally result in tissue damage and pathological alterations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12989-016-0181-1) contains supplementary material, which is available to authorized users.

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.