Understanding nature's design for a nanosyringe

Effect of Audible Sounds on the Forces Acting between Charged Surfaces in Water

We aimed to determine if audible sounds could change the forces acting between charged surfaces in water and their electric double layers (EDLs). This was achieved by using an atomic force microscope to measure force-distance curves between a microsized silica particle attached to a cantilever (probe) and a silicon wafer in water in the absence and presence of sound. Sound decreased the repulsive forces acting between the probe and silicon wafer, where the range and magnitude of the forces decreased with an increase in the sound frequency from 300 to 15000 Hz. The decrease in the force range was explained by a decrease in the EDL thickness. This result was explained by (1) the shrinkage of the EDL by a high-pressure region of the sound wave, where an increased sound frequency caused the number of high-pressure regions that passed between the probe and the substrate to increase and (2) the inability of the EDL to fully re-expand to its original thickness during the time that a low-pressure region of the sound wave was applied. The decrease in the force magnitude with a sound frequency increase was explained by the increased screening of charged surfaces that accompanies a decrease in the EDL thickness. An increase in the force measurement speed caused the sound waves to reduce the repulsive forces less. A faster speed decreased the time to measure a force curve, which reduced the number of high-pressure regions of the sound wave to pass through the water between the probe and the substrate. This reduced the number of times that the EDL was compressed by the sound wave.

Polystyrene-modified carbon nanotubes: Promising carriers in targeted drug delivery

To design drug-delivery agents for therapeutic and diagnostic applications, understanding the mechanisms by which covalently functionalized carbon nanotubes penetrate and interact with cell membranes is of great importance. Here, we report all-atom molecular dynamics results from polystyrene and carboxyl-terminated polystyrene-modified carbon nanotubes and show their translocation behavior across a model lipid bilayer together with their potential to deliver a molecule of the drug ibuprofen into the cell. Our results indicate that functionalized carbon nanotubes are internalized by the membrane in hundreds of nanoseconds and that drug loading increases the internalization speed further. Both loaded and unloaded tubes cross the closest leaflet of the bilayer by nonendocytic pathways, and for the times studied, the drug molecule remains trapped inside the pristine tube while remaining attached at the end of polystyrene-modified tube. On the other hand, carboxyl-terminated polystyrene functionalization allows the drug to be completely released into the lower leaflet of the bilayer without imposing damage to the membrane. This study shows that polystyrene functionalization is a promising alternative and facilitates drug delivery as a benchmark case.

Nano dimensions/adjuvants in COVID-19 vaccines

A favorable outcome of the COVID-19 crisis might be achieved with massive vaccination. The proposed vaccines contain several different vaccine active principles (VAP), such as inactivated virus, antigen, mRNA, and DNA, which are associated with either standard adjuvants or nanomaterials (NM) such as liposomes in Moderna's and BioNTech/Pfizer's vaccines. COVID-19 vaccine adjuvants may be chosen among liposomes or other types of NM composed for example of graphene oxide, carbon nanotubes, micelles, exosomes, membrane vesicles, polymers, or metallic NM, taking inspiration from cancer nano-vaccines, whose adjuvants may share some of their properties with those of viral vaccines. The mechanisms of action of nano-adjuvants are based on the facilitation by NM of targeting certain regions of immune interest such as the mucus, lymph nodes, and zones of infection or blood irrigation, the possible modulation of the type of attachment of the VAP to NM, in particular VAP positioning on the NM external surface to favor VAP presentation to antigen presenting cells (APC) or VAP encapsulation within NM to prevent VAP degradation, and the possibility to adjust the nature of the immune response by tuning the physico-chemical properties of NM such as their size, surface charge, or composition. The use of NM as adjuvants or the presence of nano-dimensions in COVID-19 vaccines does not only have the potential to improve the vaccine benefit/risk ratio, but also to reduce the dose of vaccine necessary to reach full efficacy. It could therefore ease the overall spread of COVID-19 vaccines within a sufficiently large portion of the world population to exit the current crisis.

Environmental Applications of Sorbents, High-Flux Membranes of Carbon-Based Nanomaterials

Carbon-based nanomaterials have unique and controllable properties, making it possible to find and treat environmental challenges. There are several environmental applications for carbon-based nanoparticles: sorbents, membranes, antimicrobial agents, and sensors. According to this review, carbon-based nanomaterials have a variety of environmental benefits. This article also looks at prospective uses of nanomaterials in environmental systems, utilizing carbonaceous nanoparticles as a guide for their physical, chemical, and electrical properties.

Current Understanding of Water Properties inside Carbon Nanotubes

Confined water inside carbon nanotubes (CNTs) has attracted a lot of attention in recent years, amassing as a result a very large number of dedicated studies, both theoretical and experimental. This exceptional scientific interest can be understood in terms of the exotic properties of nanoconfined water, as well as the vast array of possible applications of CNTs in a wide range of fields stretching from geology to medicine and biology. This review presents an overreaching narrative of the properties of water in CNTs, based mostly on results from systematic nuclear magnetic resonance (NMR) and molecular dynamics (MD) studies, which together allow the untangling and explanation of many seemingly contradictory results present in the literature. Further, we identify still-debatable issues and open problems, as well as avenues for future studies, both theoretical and experimental.

Membrane Nanopores Induced by Nanotoroids via an Insertion and Pore-Forming Pathway

The formation of membrane nanopores is one of the crucial activities of cells and has attracted considerable attention. However, the understanding of their types and mechanisms is still limited. Herein, we report a novel nanopore formation phenomenon achieved through the insertion of polymeric nanotoroids into the cellular membrane. As revealed by theoretical simulations, the nanotoroid can embed in the membrane, leaving a nanopore on the cell. The through-the-cavity wrapping of lipids is critical for the retention of the nanotoroid in the membrane, which is attributed to both a relatively large inner cavity of the nanotoroid and a moderate attraction between the nanotoroid and membrane lipids. Under the guidance of the simulation predictions, experiments using polypeptide toroids as pore-forming agents were performed, confirming the unique biophysical phenomenon. This work demonstrates a distinctive pore-forming pathway, deepens the understanding of the membrane nanopore phenomenon, and assists in the design of advanced pore-forming materials.

New Multi-Walled carbon nanotube of industrial interest induce cell death in murine fibroblast cells

The search for new nanomaterials has brought to the multifactorial industry several opportunities for use and applications for existing materials. Carbon nanotubes (CNT), for example, present excellent properties which allow us to assume a series of applications, however there is concern in the industrial scope about possible adverse health effects related to constant exposure for inhalation or direct skin contact. Thus, using cell models is the fastest and safest way to assess the effects of a new material. The aim of this study was to investigate the cytotoxic profile in LA9 murine fibroblast lineage, of a new multi-walled carbon nanotube (MWCNT) that was functionalized with tetraethylenepentamine (TEPA) to obtain better physical-chemical characteristics for industrial use. The modifications presented in the CNT cause concern, as they can change its initial characteristics, making this nanomaterial harmful. HR-TEM, FE-SEM and zeta potential were used for the characterization. Cytotoxicity and cell proliferation tests, oxidative and nitrosative stress analyzes and inflammatory cytokine assay (TNF-α) were performed. The main findings demonstrated a reduction in cell viability, increased release of intracellular ROS, accompanied by an increase in TNF-α, indicating an important inflammatory profile. Confirmation of the data was performed by flow cytometry and ImageXpress with apoptosis/necrosis markers. These data provide initial evidence that OCNT-TEPA has a cytotoxic profile dependent on the concentration of LA9 fibroblasts, since there was an increase in free radicals, inflammation induction and cell death, suggesting that continuous exposure to this nanoparticle can cause damage to different tissues in the organism.

Drug Delivery With Carbon-Based Nanomaterials as Versatile Nanocarriers: Progress and Prospects

With growing interest, a large number of researches have been conducted on carbon-based nanomaterials (CBNs). However, their uses are limited due to comprehensive potential environmental and human health effects. It is often confusing for researchers to make an informed choice regarding the versatile carbon-based nanocarrier system and its potential applications. This review has highlighted emerging applications and cutting-edge progress of CBNs in drug delivery. Some critical factors like enzymatic degradation, surface modification, biological interactions, and bio-corona have been discussed here. These factors will help to fabricate CBNs for effective drug delivery. This review also addresses recent advancements in carbon-based target specific and release controlled drug delivery to improve disease treatment. The scientific community has turned their research efforts into the development of novel production methods of CBNs to make their production more attractive to the industrial sector. Due to the nanosize and diversified physical properties, these CBNs have demonstrated distinct biological interaction. Thus long-term preclinical toxicity study is recommended before finally translating to clinical application.

Carbon nanotube transmembrane channel formation and single-stranded DNA spontaneous internalization: a dissipative particle dynamics study

Single-walled carbon nanotube (SWCNT) transmembrane channel formation in a pure 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) bilayer, and the spontaneous internalization of single-stranded DNA (ssDNA) into the formed pore were simulated. A combination of computational techniques, Dissipative Particle Dynamics-Monte Carlo hybrid simulations and quantum mechanical calculations at the hybrid-DFT level, was used as a new proposal to perform DPD simulations granting specific chemical identity to the model particles. The simulated transmembrane channels showed that, in the case of pristine SWCNTs and upon increasing the nanotube length, a higher tilt angle with respect to the bilayer normal is observed and more time is needed for the nanotube to stabilize. On the other hand, for SWCNTs with polar rims an almost perpendicular orientation is preferred with less than 15° of tilt with respect to the bilayer normal once the nanotubes have pierced both monolayers. These findings are supported by experimental observations where CNTs of average inner diameters of 1.51 ± 0.21 nm and lengths in the 5-15 nm range were inserted in DOPC membranes [J. Geng, et al., Nature, 2014, 514(7524), 612-615]. Moreover, the narrower the SWCNTs, the slower the spontaneous internalization of ssDNA becomes, and ssDNA ends hydrophobically trapped inside the artificial pore. A dependence on the nucleotide content is found indicating that the higher the presence of adenine and thymine in the ssDNA chains the slower the internalization becomes, in agreement with the experimental [A. M. Ababneh, et al., Biophys. J., 2003, 85(2), 1111-1127] and predicted solvation tendency in water for nucleic acid bases.

Nanomedicine & Nanotoxicology Future Could Be Reshaped Post-COVID-19 Pandemic

Since its first emergence in December 2019, the coronavirus-2 infection has quickly spread around the world and the severity of the pandemic has already re-shaped our lives. This review highlights the role of nanotechnology in the fight against this pandemic with a focus on the design of effective nano-based prevention and treatment options that overcome the limitations associated with conventional vaccines and other therapies. How nanotechnology could be utilized to understand the pathology of the ongoing pandemic is also discussed as well as how our knowledge about SARS-CoV-2 cellular uptake and toxicity could influence future nanotoxicological considerations and nanomedicine design of safe yet effective nanomaterials.

Preparation, characterisation and biological evaluation of biopolymer-coated multi-walled carbon nanotubes for sustained-delivery of silibinin

This research work represents the first major step towards constructing an effective therapeutic silibinin (SB) in cancer treatment using oxidised multi-walled carbon nanotubes (MWCNT-COOH) functionalised with biocompatible polymers as the potential drug carrier. In an attempt to increase the solubility and dispersibility of SB-loaded nanotubes (MWSB), four water-soluble polymers were adopted in the preparation process, namely polysorbate 20 (T20), polysorbate 80 (T80), polyethylene glycol (PEG) and chitosan (CHI). From the geometry point of view, the hydrophobic regions of the nanotubes were loaded with water-insoluble SB while the hydrophilic polymers functionalised on the outer surfaces of the nanotubes serve as a protective shell to the external environment. The chemical interaction between MWSB nanocomposites and polymer molecules was confirmed by Fourier transform infrared spectroscopy (FTIR) and Raman spectroscopy. Besides, high-resolution transmission electron microscopy (HR-TEM), field emission scanning electron microscopy (FESEM), thermogravimetric analysis (TGA) and UV–visible spectrophotometry were also employed to characterise the synthesised nanocomposites. The morphological study indicated that the polymers were deposited on the external surfaces of MWSB and the nanocomposites were seen to preserve their tubular structures even after the coating process was applied. The TGA results revealed that the incorporation of biopolymers practically improved the overall thermal stability of the coated MWSB nanocomposites. Evaluation of the in vitro effect on drug release rate by the nanocomposites was found to follow a biphasic release manner, showing a fast release at an initial stage and then a sustained-release over 2500 min. Besides, the drug release mechanisms of the nanocomposites demonstrated that the amount of SB released in the simulated environment was governed by pseudo-second order in which, the rate-limiting step mainly depends on diffusion of drug through chemisorption reaction. Finally, MTT assay showed that the coated MWSB nanocomposites on 3T3 cells were very much biocompatible at a concentration up to 100 g/mL, which is an evidence of MWSB reduced cytotoxicity.

Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors

Rosette nanotubes (RNTs) are a class of materials formed by molecular self-assembly of a fused guanine-cytosine base (G∧C base). An important feature of these self-assembled nanotubes is their precise atomic structure, intriguing for rational design and optimization as synthetic transmembrane porins. Here, we present experimental observations of ion transport across 1.1 nm inner diameter RNT porins (RNTPs) of various lengths in the range 5-200 nm. In a typical experiment, custom lipophilic RNTPs were first inserted into lipid vesicles; the vesicles then spontaneously fused with a planar lipid bilayer, which produced stepwise increases of ion current across the bilayer. Our measurements in 1 M KCl solution indicate ion transport rates of ∼50 ions s^-1 V^-1 m, which for short channels amounts to conductance values of ∼1 nS, commensurate with naturally occurring toxin channels such as α-hemolysin. Measurements of interaction times of α-cyclodextrin with RNTPs reveal two distinct unbinding time scales, which suggest that interactions of either face of α-cyclodextrin with the RNTP face are differentiable, backed with all-atom molecular dynamics simulations. Our results highlight the potential of RNTPs as self-assembled nonproteinaceous single-molecule sensors and selective nanofilters with tunable functionality through chemistry.

Structure and dynamics of liposomes designed for drug delivery: coarse-grained molecular dynamics simulations to reveal the role of lipopolymer incorporation

In this work, coarse-grained molecular dynamics simulations are carried out in NPTH and NVTE statistical ensembles in order to study the structure and dynamics properties of liposomes coated with polyethylene glycol (PEG).

Cytotoxicity effects and ionic diffusion of single-wall carbon nanotubes in cell membrane

While carbon nanotubes have been put into massive practical industrial, environmental and biomedicine applications, the cytotoxicity effects or the effect to the ionic channels they bring into the living cells need to be thoroughly investigated. In this work, molecular dynamic simulations have been carried out to investigate the ionic diffusion through the single wall armchair carbon nanotube embedded right inside the cell membrane. By modeling a two-membrane system, we build a virtual cytoplasm environment including a cell chamber and an extracellular space, in which a certain amount of solute is dissolved. The system is first brought to its equilibrium by deployment of minimization and then simulated. The results suggested that carbon nanotubes (CNTs) with size less than (12, 12) shall be less cytotoxic since it does not bring any ionic diffusion through the CNT channel, so as to maintain active cytoplasm environment. Another phenomenon we observed is a notable shifting angle of the carbon nanotube which was normal to the surface of cell membrane initially. In general, the inclination angle of the carbon nanotube increases with its radius.

Molecular Dynamics of Water Embedded Carbon Nanocones: Surface Waves Observation

We employed molecular dynamics simulations on the water solvation of conically shaped carbon nanoparticles. We explored the hydrophobic behaviour of the nanoparticles and investigated microscopically the cavitation of water in a conical confinement with different angles. We performed additional molecular dynamics simulations in which the carbon structures do not interact with water as if they were in vacuum. We detected a waving on the surface of the cones that resembles the shape agitations of artificial water channels and biological porins. The surface waves were induced by the pentagonal carbon rings (in an otherwise hexagonal network of carbon rings) concentrated near the apex of the cones. The waves were affected by the curvature gradients on the surface. They were almost undetected for the case of an armchair nanotube. Understanding such nanoscale phenomena is the key to better designed molecular models for membrane systems and nanodevices for energy applications and separation.

Self-Assembly-Directed Cancer Cell Membrane Insertion of Synthetic Analogues for Permeability Alteration

Inspired by the metamorphosis of pore-forming toxins from soluble inactive monomers to cytolytic transmembrane assemblies, we developed self-assembly-directed membrane insertion of synthetic analogues for permeability alteration. An expanded π-conjugation-based molecular precursor with an extremely high rigidity and a long hydrophobic length that is comparable to the hydrophobic width of plasma membrane was synthesized for membrane-inserted self-assembly. Guided by the cancer biomarker expression in vitro, the soluble precursors transform into hydrophobic monomers  forming assemblies inserted into the fluid phase of the membrane exclusively. Membrane insertion of rigid synthetic analogues destroys the selective permeability of the plasma membrane gradually. It eventually leads to cancer cell death, including drug resistant cancer cells.

Phage shock protein and gene responses of Escherichia coli exposed to carbon nanotubes

Two-dimensional electrophoretic, western blotting, and quantitative polymerase chain reaction analyses of Escherichia coli cells exposed to pristine single walled carbon nanotubes (SWCNTs), and hydroxyl and carboxylic functionalized SWCNTs (SWCNT-OHs and SWCNT-COOHs) were conducted. SWCNT concentration and length were experimental variables. Exposing E. coli cells to SWCNTs led to changes in protein and gene expressions. Several proteins altered their regulations at a low SWCNT concentration (10 μg/ml) and were shut down at a high SWCNT concentration (100 μg/ml). The expressions of the phage shock protein (psp) operon including pspA, pspB, and pspC genes responded to the membrane stressors, SWCNTs, were also examined. While pspA and pspC expressions were influenced by the length, concentration, and functional groups of SWCNTs, pspB expression was not induced by SWCNTs. The alterations in phage shock protein and gene expressions indicated that SWCNTs caused cell membrane perturbation.

Effect of a liquid flow on the forces between charged solid surfaces and the non-equilibrium electric double layer

The physical properties of fluids can change as they flow through confined charged solid areas, such as a charged pore or channel, allowing the transport of fluid through the channels to be controlled. The liquid flow is influenced by the electrical double layer (EDL) that is next to the charged surface. The overlap of the EDL of two nearby charged solid surfaces results in the formation of an electrostatic force. A flow will change the EDL from an equilibrium state to a non-equilibrium state, causing the forces to also change from an equilibrium (static) state to a non-equilibrium (dynamic) state. There are numerous studies that have been performed by molecular dynamics (MD) simulations and surface force experiments which concern the equilibrium EDL and the equilibrium surface forces. However, there are significantly less studies concerning the non-equilibrium EDL and non-equilibrium surface forces, including the effect of a liquid flow on the EDL and the surface forces. This review will focus on how a liquid flow changes the EDL and the surface forces of charged hydrophilic solid surfaces in aqueous electrolyte solutions. Results obtained by MD simulations and surface force experiments are discussed in this review. A flow was seen to be able to distort the EDL, causing the surface forces to change. The EDL and surface forces were affected by the surface charge, the structuring ability of the liquid molecules and ions near the surfaces, the ion type and their specificity towards the surface, the ionic concentration, and the rate of flow of the liquid. The physical properties of the system were shown to change with a flow, e.g. the increase in the fluid viscosity next to a charged solid surface that accompanies a flow. The number of counterions adsorbed to a charged solid surface was also seen to affect the direction of flow in an EDL. The surface forces were shown to change with a flow due to changes in hydrodynamic and electrostatic forces. Information on the effect of the liquid flow on the EDL and surface forces will help improve applications that require fluid to be transported in a defined way through a charged solid vessel.

Application of carbon nanotubes in cancer vaccines: Achievements, challenges and chances

Tumour-specific, immuno-based therapeutic interventions can be considered as safe and effective approaches for cancer therapy. Exploitation of nano-vaccinology to intensify the cancer vaccine potency may overcome the need for administration of high vaccine doses or additional adjuvants and therefore could be a more efficient approach. Carbon nanotube (CNT) can be described as carbon sheet(s) rolled up into a cylinder that is nanometers wide and nanometers to micrometers long. Stemming from the observed capacities of CNTs to enter various types of cells via diversified mechanisms utilising energy-dependent and/or passive routes of cell uptake, the use of CNTs for the delivery of therapeutic agents has drawn increasing interests over the last decade. Here we review the previous studies that demonstrated the possible benefits of these cylindrical nano-vectors as cancer vaccine delivery systems as well as the obstacles their clinical application is facing.

Morphological and mechanical determinants of cellular uptake of deformable nanoparticles

Understanding the interactions of nanoparticles (NPs) with cell membranes and regulating their cellular uptake processes are of fundamental importance to the design of drug delivery systems with minimum toxicity, high efficiency and long circulation time. Employing the procedure of coarse-graining, we built an elastically deformable NP model with tunable morphological and mechanical properties. We found that the cellular uptake of deformable NPs depends on their shape: an increase in the particle elasticity significantly slows the uptake rate of spherical NPs, slightly retards that of prolate NPs, and promotes the uptake of oblate NPs. The intrinsic mechanisms have been carefully investigated through analysis of the endocytic mechanisms and free energy calculations. These findings provide unique insights into how deformable NPs penetrate across cell membranes and offer novel possibilities for designing effective NP-based carriers for drug delivery.

Biocompatible properties of nano-drug carriers using TiO2-Au embedded on multiwall carbon nanotubes for targeted drug delivery

Nanomaterial-based drug carriers have become a hot spot of research at the interface of nanotechnology and biomedicine because they allow efficient loading, targeted delivery, controlled release of drugs, and therefore are promising for biomedical applications. The current study made an attempt to decorate the multiwalled carbon nanotubes (MWCNT) with titanium dioxide‑gold nanoparticles in order to enhance the biocompatibility for doxorubicin (DOX) delivery. The successful synthesis of nano drug carrier (NDC) was confirmed by XRD, XPS and UV-Visible spectroscopy. FESEM and TEM revealed that the morphology of NDC can be controlled by manipulating the reaction duration, MWCNT concentration and TiO₂-Au source concentration. Results showed that TiO₂ and Au nanoparticles were well coated on MWCNT. NDC had finely tuned biocompatible properties, as elucidated by hemolytic and antimicrobial assays. NDC also showed a high antioxidant potential, 80.7% expressed as ascorbic acid equivalents. Commercial DOX drug was utilized to treat A549 and MCF7 cancer cell lines showing improved efficiency by formulating it with NDC, which selectively delivered at the pH 5.5 with drug loading capacity of 0.45 mg/mL. The drug releasing capacity achieved by NDC was 90.66% for 10 h, a performance that far encompasses a wide number of current literature reports.

High-speed atomic force microscopy and its future prospects

Various techniques have been developed and used to investigate how proteins produce complex biological architectures and phenomena. Among these techniques, high-speed atomic force microscopy (HS-AFM) holds a unique position. It is only HS-AFM that allows the simultaneous assessment of structure and dynamics of single protein molecules in action. This new microscopy tool has been successfully applied to a variety of proteins, from motor proteins to membrane proteins, antibodies, enzymes, and even to intrinsically disordered proteins. And yet there still remain many biomolecular phenomena that cannot be addressed by HS-AFM in its current form. Here, I present a brief history of HS-AFM development, describe the current state of HS-AFM, and then discuss which new biological scanning probe microscopy techniques will be coming up next.

Understanding carbon nanotube channel formation in the lipid membrane

Carbon nanotubes (CNTs) have been considered a prominent nano-channel in cell membranes because of their prominent ion-conductance and ion-selectivity, offering agents for a biomimetic channel platform. Using a coarse-grained molecular dynamics simulation, we clarify a construction mechanism of vertical CNT nano-channels in a lipid membrane for a long period, which has been difficult to observe in previous CNT-lipid interaction simulations. The result shows that both the lipid coating density and length of CNT affect the suitable fabrication condition for a vertical and stable CNT channel. Also, simulation elucidated that a lipid coating on the surface of the CNT prevents the CNT from burrowing into the lipid membrane and the vertical channel is stabilized by the repulsion force between the lipids in the coating and membrane. Our study provides an essential understanding of how CNTs can form stable and vertical channels in the membrane, which is important for designing new types of artificial channels as biosensors for bio-fluidic studies.

Translocation of Bioactive Molecules through Carbon Nanotubes Embedded in the Lipid Membrane

One of the major challenges of nanomedicine and gene therapy is the effective translocation of drugs and genes across cell membranes. In this study, we describe a systematic procedure that could be useful for efficient drug and gene delivery into the cell. Using fully atomistic molecular dynamics (MD) simulations, we show that molecules of various shapes, sizes, and chemistries can be spontaneously encapsulated in a single-walled carbon nanotube (SWCNT) embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer, as we have exemplified with dendrimers, asiRNA, ssDNA, and ubiquitin protein. We compute the free energy gain by the molecules upon their entry inside the SWCNT channel to quantify the stability of these molecules inside the channel as well as to understand the spontaneity of the process. The free energy profiles suggest that all molecules can enter the channel without facing any energy barrier but experience a strong energy barrier (≫k_BT) to translocate across the channel. We propose a theoretical model for the estimation of encapsulation and translocation times of the molecules. Whereas the model predicts the encapsulation time to be of the order of few nanoseconds, which match reasonably well with those obtained from the simulations, it predicts the translocation time to be astronomically large for each molecule considered in this study. This eliminates the possibility of passive diffusion of the molecules through the CNT-nanopore spanning across the membrane. To counter this, we put forward a mechanical method of ejecting the encapsulated molecules by pushing them with other free-floating SWCNTs of diameter smaller than the pore diameter. The feasibility of the proposed method is also demonstrated by performing MD simulations. The generic strategy described here should work for other molecules as well and hence could be potentially useful for drug- and gene-delivery applications.

Molecular dynamics simulations of carbon nanotube porins in lipid bilayers

Carbon nanotube porins embedded in lipid membranes are studied by molecular dynamics simulations.

High-speed atomic force microscopy and its future prospects

Various techniques have been developed and used to investigate how proteins produce complex biological architectures and phenomena. Among these techniques, high-speed atomic force microscopy (HS-AFM) holds a unique position. It is only HS-AFM that allows the simultaneous assessment of structure and dynamics of single protein molecules in action. This new microscopy tool has been successfully applied to a variety of proteins, from motor proteins to membrane proteins, antibodies, enzymes, and even to intrinsically disordered proteins. And yet there still remain many biomolecular phenomena that cannot be addressed by HS-AFM in its current form. Here, I present a brief history of HS-AFM development, describe the current state of HS-AFM, and then discuss which new biological scanning probe microscopy techniques will be coming up next.

Pro-inflammatory cytokines reduce human TAFI expression via tristetraprolin-mediated mRNA destabilisation and decreased binding of HuR

Thrombin activatable fibrinolysis inhibitor (TAFI) is the zymogen form of a basic carboxypeptidase (TAFIa) with both anti-fibrinolytic and anti-inflammatory properties. The role of TAFI in inflammatory disease is multifaceted and involves modulation both of specific inflammatory mediators as well as of the behaviour of inflammatory cells. Moreover, as suggested by in vitro studies, inflammatory mediators are capable of regulating the expression of CPB2, the gene encoding TAFI. In this study we addressed the hypothesis that decreased TAFI levels observed in inflammation are due to post-transcriptional mechanisms. Treatment of human HepG2 cells with pro-inflammatory cytokines TNFα, IL-6 in combination with IL-1β, or with bacterial lipopolysaccharide (LPS) decreased TAFI protein levels by approximately two-fold over 24 to 48 hours of treatment. Conversely, treatment of HepG2 cells with the anti-inflammatory cytokine IL-10 increased TAFI protein levels by two-fold at both time points. We found that the mechanistic basis for this modulation of TAFI levels involves binding of tristetraprolin (TTP) to the CPB2 3′-UTR, which mediates CPB2 mRNA destabilisation. In this report we also identified that HuR, another ARE-binding protein but one that stabilises transcripts, is capable of binding the CBP2 3’UTR. We found that pro-inflammatory mediators reduce the occupancy of HuR on the CPB2 3’-UTR and that the mutation of the TTP binding site in this context abolishes this effect, although TTP and HuR appear to contact discrete binding sites. Interestingly, all of the mediators tested appear to increase TAFI protein expression in THP-1 macrophages, likewise through effects on CPB2 mRNA stability.

Dipeptides Embedded in a Lipid Bilayer Membrane as Synthetic Water Channels

Water channels are essential to life sciences and many biological processes. We report a molecular simulation study on dipeptides embedded in a lipid (dipalmitoylphosphatidylcholine) membrane as synthetic water channels. Five dipeptides are examined including FF, FL, LF, and LL (with hydrophilic channels) and AV (with hydrophobic channel). It is found that AV is unstable in the lipid membrane due to incompatible interaction between the hydrophilic external surface of AV and the hydrophobic lipid tails; whereas FF, FL, LF, and LL with hydrophobic external surface exhibit good stability. In the four hydrophilic channels FF, FL, LF, and LL, water chains are formed; the number of chains ranges from multiple, two to one depending on channel diameter; moreover, water undergoes single-file diffusion and the mobility is enhanced with increasing channel diameter. The permeation rate of water in the FF channel is 9.20/ns, about three times that in aquaporin; however, the rate in FL, LF, and LL is much slower. Intriguingly, the rate can be tuned by a lateral stress/strain on the lipid membrane. The simulation study provides fundamental understanding on the stability of dipeptide channels embedded in a lipid membrane, quantitatively characterizing water structure, dynamics, and permeation in the channels. These microscopic insights are useful for the development of new water channels.

Insight of Transmembrane Processes of Self-Assembling Nanotubes Based on a Cyclic Peptide Using Coarse Grained Molecular Dynamics Simulation

Transmembrane self-assembling cyclic peptide (SCP) nanotubes are promising candidates for delivering specific molecules through cell membranes. The detailed mechanisms behind the transmembrane processes, as well as stabilization factors of transmembrane structures, are difficult to elucidate through experiments. In this study, the effects of peptide sequence and oligomeric state on the transmembrane capabilities of SCP nanotubes and the perturbation of embedded SCP nanotubes acting on the membrane were investigated based on coarse grained molecular dynamics simulation. The simulation results reveal that hydrophilic SCP oligomers result in the elevation of the energy barrier while the oligomerization of hydrophobic SCPs causes the reduction of the energy barrier, further leading to membrane insertion. Once SCP nanotubes are embedded, membrane properties such as density, thickness, ordering state and lateral mobility are adjusted along the radial direction. This study provides insight into the transmembrane strategy of SCP nanotubes and sheds light on designing novel transport systems.

Stability and dynamics of membrane-spanning DNA nanopores

Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.

Although DNA nanopores are widely explored as synthetic membrane proteins, it is still unclear how the anionic DNA assemblies stably reside within the hydrophobic core of a lipid bilayer. Here, the authors use molecular dynamics simulations to reveal the key dynamic interactions and energetics stabilizing the nanopore-membrane interaction.

Carbon nanotubes as gene carriers: Focus on internalization pathways related to functionalization and properties

Carbon nanotubes represent promising transporters for delivery of DNA and other biomolecules into living cells. Various methods of CNTs surface functionalization have been developed. These are essential to improve CNTs dispersibility and permit their interactions with biological structures that broaden their use in advanced biomedical applications. The present review discusses the different single walled carbon nanotubes and multiwalled carbon nanotubes functionalization methods, leading to the formation of optimized and functionalized-CNT complexes with DNA. F-CNTs are recognized as efficient and promising gene carriers. Emphasis is then placed on the processes used by f-CNTs/DNA complexes to cross cell membranes. Energy independent pathways and uptake mechanisms dependent on energy, such as endocytosis or phagocytosis, are reported by many studies, and if these mechanisms seem contradictory at first sight, a detailed review of the literature illustrates that they are rather complementary. Preferential use of one or the other depends on the DNA and CNTs chemical nature and physical parameters, experimental procedures and cell types.

STATEMENT OF SIGNIFICANCE

Efficient non-viral gene delivery is desirable, yet challenging. CNTs appear as a promising solution to penetrate into cells and successfully deliver DNA. Moreover, the field of use of CNTs as gene carrier is large and is currently growing. This critical review summarizes the development and evaluation of CNTs as intracellular gene delivery system and provides an overview of functionalized CNTs/DNA cellular uptake mechanisms, depending on several parameters of CNTs/DNA complexes.

Surface patterning of single-walled carbon nanotubes enhances their perturbation on a pulmonary surfactant monolayer: frustrated translocation and bilayer vesiculation

In contrast to SWCNTs with unique surface properties, the surface patterning of SWCNTs is found to enhance their perturbation on the pulmonary surfactantsviafrustrated translocation and destructive bilayer vesiculation.

Structure of Carbon Nanotube Porins in Lipid Bilayers: An in Situ Small-Angle X-ray Scattering (SAXS) Study

Carbon nanotube porins (CNTPs), small segments of carbon nanotubes capable of forming defined pores in lipid membranes, are important future components for bionanoelectronic devices as they could provide a robust analog of biological membrane channels. In order to control the incorporation of these CNT channels into lipid bilayers, it is important to understand the structure of the CNTPs before and after insertion into the lipid bilayer as well as the impact of such insertion on the bilayer structure. Here we employed a noninvasive in situ probe, small-angle X-ray scattering, to study the integration of CNT porins into dioleoylphosphatidylcholine bilayers. Our results show that CNTPs in solution are stabilized by a monolayer of lipid molecules wrapped around their outer surface. We also demonstrate that insertion of CNTPs into the lipid bilayer results in decreased bilayer thickness with the magnitude of this effect increasing with the concentration of CNTPs.

Can Carbon Nanotubes Deliver on Their Promise in Biology? Harnessing Unique Properties for Unparalleled Applications

Carbon nanotubes (CNTs) are cylindrical sheets of hexagonally ordered carbon atoms, giving tubes with diameters on the order of a few nanometers and lengths typically in the micrometer range. They may be single- or multiwalled (SWCNTs and MWCNTs respectively). Since the seminal report of their synthesis in 1991, CNTs have fascinated scientists of all stripes. Physicists have been intrigued by their electrical, thermal, and vibrational potential. Materials scientists have worked on integrating them into ultrastrong composites and electronic devices, while chemists have been fascinated by the effects of curvature on reactivity and have developed new synthesis and purification techniques. However, to date no large-scale, real-life biotechnological CNT breakthrough has been industrially adopted and it is proving difficult to justify taking these materials forward into the clinic. We believe that these challenges are not the end of the story, but that a viable carbon nanotube biotechnology is one in which the unique properties of nanotubes bring about an effect that would be otherwise impossible. In this Outlook, we therefore seek to reframe the field by highlighting those biological applications in which the singular properties of CNTs provide some entirely new activity or biological effect as a pointer to "what could be".

Permeability across lipid membranes

Molecular permeation through lipid membranes is a fundamental biological process that is important for small neutral molecules and drug molecules. Precise characterization of free energy surface and diffusion coefficients along the permeation pathway is required in order to predict molecular permeability and elucidate the molecular mechanisms of permeation. Several recent technical developments, including improved molecular models and efficient sampling schemes, are illustrated in this review. For larger penetrants, explicit consideration of multiple collective variables, including orientational, conformational degrees of freedom, are required to be considered in addition to the distance from the membrane center along the membrane normal. Although computationally demanding, this method can provide significant insights into the molecular mechanisms of permeation for molecules of medical and pharmaceutical importance. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Regulation of angiogenesis through the efficient delivery of microRNAs into endothelial cells using polyamine-coated carbon nanotubes

MicroRNAs (miRNAs) directly regulate gene expression at a post-transcriptional level and represent an attractive therapeutic target for a wide range of diseases. Here, we report a novel strategy for delivering miRNAs to endothelial cells (ECs) to regulate angiogenesis, using polymer functionalized carbon nanotubes (CNTs). CNTs were coated with two different polymers, polyethyleneimine (PEI) or polyamidoamine dendrimer (PAMAM), followed by conjugation of miR-503 oligonucleotides as recognized regulators of angiogenesis. We demonstrated a reduced toxicity for both polymer-coated CNTs, compared with pristine CNTs or polymers alone. Moreover, polymer-coated CNT stabilized miR-503 oligonucleotides and allowed their efficient delivery to ECs. The functionality of PAMAM-CNT-miR-503 complexes was further demonstrated in ECs through regulation of target genes, cell proliferation and angiogenic sprouting and in a mouse model of angiogenesis. This comprehensive series of experiments demonstrates that the use of polyamine-functionalized CNTs to deliver miRNAs is a novel and effective means to regulate angiogenesis.

Fullerene mediates proliferation and cardiomyogenic differentiation of adipose-derived stem cells via modulation of MAPK pathway and cardiac protein expression

Zero-dimensional fullerenes can modulate the biological behavior of a variety of cell lines. However, the effects and molecular mechanisms of proliferation and cardiomyogenic differentiation in brown adipose-derived stem cells (BADSCs) are still unclear. In this study, we report the initial biological effects of fullerene-C₆₀ on BADSCs at different concentrations. Results suggest that fullerene-C₆₀ has no cytotoxic effects on BADSCs even at a concentration of 100 μg/mL. Fullerene-C₆₀ improves the MAPK expression level and stem cell survival, proliferation, and cardiomyogenesis. Further, we found that the fullerene-C₆₀ modulates cardiomyogenic differentiation. Fullerene-C₆₀ improves the expression of cardiomyocyte-specific proteins (cTnT and α-sarcomeric actinin). At elevated concentration, fullerene-C₆₀ reduces the incidence of diminished spontaneous cardiac differentiation of BADSCs with time. At the genetic level, fullerene-C₆₀ (5 μg/mL) also improves the expression of cTnT. In addition, fullerene-C₆₀ promotes the formation of gap junction among cells. These findings have important implications for clinical application of fullerenes in the treatment of myocardial infarction.

Evaluation of the efficacy of carbon nanotubes for delivering peptides into mitochondria

Future therapy for mitochondrial pathologies: CKKSFLSPRTALINFLVK peptide from mitochondrial-LeuRS has a mitochondrial targeting activity when conjugated with multi-walled carbon nanotubes.

Functionalized carbon nanotubes and their promising applications in therapeutics and diagnostics

Carbon nanotubes (CNTs) have attracted much attention from researchers worldwide in recent years due to their high aspect ratio, high surface area, and excellent material properties, such as electrical and thermal conductivities and mechanical strength. These rolled-up seamless cylinders of graphene sheets possess nanosized hollow-tube-shaped structures. The CNTs can be single-walled, double-walled or multi-walled, depending upon the number of graphene layers from which a single nanotube is composed. The CNTs, favoring encapsulation of drug molecules or by possible attachment of theranostic agents on the nanotube walls, have enabled their use in controlled drug delivery, and in targeting of drug molecules to specific sites such as the lymphatic system, brain, ocular system, and cancerous tissue. This chapter provides an overview of various types of CNTs, methods utilized for their commercial production, and the functionalization approaches employed in drug-delivery applications. In addition, the chapter also endeavors to provide a thoughtful insight into the toxicity and regulatory concerns that need to be addressed before the CNTs can be launched in the market.

Carbon nanotube biosensors

Nanomaterials possess unique features which make them particularly attractive for biosensing applications. In particular, carbon nanotubes (CNTs) can serve as scaffolds for immobilization of biomolecules at their surface, and combine several exceptional physical, chemical, electrical, and optical characteristics properties which make them one of the best suited materials for the transduction of signals associated with the recognition of analytes, metabolites, or disease biomarkers. Here we provide a comprehensive review on these carbon nanostructures, in which we describe their structural and physical properties, functionalization and cellular uptake, biocompatibility, and toxicity issues. We further review historical developments in the field of biosensors, and describe the different types of biosensors which have been developed over time, with specific focus on CNT-conjugates engineered for biosensing applications, and in particular detection of cancer biomarkers.

Potential of carbon nanotubes in algal biotechnology

A critical mass of knowledge is emerging on the interactions between plant cells and engineered nanomaterials, revealing the potential of plant nanobiotechnology to promote and support novel solutions for the development of a competitive bioeconomy. This knowledge can foster the adoption of new methodological strategies to empower the large-scale production of biomass from commercially important microalgae. The present review focuses on the potential of carbon nanotubes (CNTs) to enhance photosynthetic performance of microalgae by (i) widening the spectral region available for the energy conversion reactions and (ii) increasing the tolerance of microalgae towards unfavourable conditions occurring in mass production. To this end, current understanding on the mechanisms of uptake and localization of CNTs in plant cells is discussed. The available ecotoxicological data were used in an attempt to assess the feasibility of CNT-based applications in algal biotechnology, by critically correlating the experimental conditions with the observed adverse effects. Furthermore, main structural and physicochemical properties of single- and multi-walled CNTs and common approaches for the functionalization and characterization of CNTs in biological environment are presented. Here, we explore the potential that nanotechnology can offer to enhance functions of algae, paving the way for a more efficient use of photosynthetic algal systems in the sustainable production of energy, biomass and high-value compounds.

Properties of ultrathin cholesterol and phospholipid layers surrounding silicon-carbide nanotube: MD simulations

Computer simulation technique was used to study the dynamics of cholesterol and POPC phospholipid molecules forming a thin layer on the surface of the carbon and silicon-carbide nanotubes. Each nanotube was surrounded by an ultra-thin film formed by n lipid molecules, where n varies from 15 to 50. All studies were done for five temperatures, including physiological one (T=260, 285, 310, 335 and 360K). The influence of a nanotube on the dynamics of cholesterol or phospholipid molecules in a layer is presented and discussed. The water is ubiquitous in all biological milieus, where the cholesterol or lipids occur. Thus, simulations were performed in a water environment. Moreover, to show different behavior of lipids in systems with water the results were compared with the samples without it. The dynamical and structural observables, such as the mean square displacement, diffusion coefficient, radial distribution function, and activation energy were calculated to qualitatively investigate the behavior of cholesterol and phospholipid molecules in the layers. We observed remarkable differences between the cholesterol dynamics depending whether the ultrathin film surrounds carbon or silicon-carbide nanotube and whether the water environment appeared.