Evaluation of Different Single-Walled Carbon Nanotube Surface Coatings for Single-Particle Tracking Applications in Biological Environments

Single-walled carbon nanotubes as near-infrared fluorescent probes for bio-inspired supramolecular self-assembled hydrogels

Hydrogels derived from fluorenylmethoxycarbonyl (Fmoc)-conjugated amino acids and peptides demonstrate remarkable potential in biomedical applications, including drug delivery, tissue regeneration, and tissue engineering. These hydrogels can be injectable, offering a minimally invasive approach to hydrogel implantation. Given their potential for prolonged application, there is a need for non-destructive evaluation of their properties over extended periods. Thus, we introduce a hydrogel characterization platform employing single-walled carbon nanotubes (SWCNTs) as near-infrared (NIR) fluorescent probes. Our approach involves generating supramolecular self-assembling hydrogels from aromatic Fmoc-amino acids. Integrating SWCNTs into the hydrogels maintains their structural and mechanical properties, establishing SWCNTs as optical probes for hydrogels. We demonstrate that the SWCNT NIR-fluorescence changes during the gelation process correlate to rheological changes within the hydrogels. Additionally, single particle tracking of SWCNTs incorporated in the hydrogels provides insights into differences in hydrogel morphologies. Furthermore, the disassembly process of the hydrogels can be monitored through the SWCNT fluorescence modulation. The unique attribute of SWCNTs as non-photobleaching fluorescent sensors, emitting at the biologically transparent window, offers a non-destructive method for studying hydrogel dynamics over extended periods. This platform could be applied to a wide range of self-assembling hydrogels to advance our understanding and applications of supramolecular assembly technologies.

Expanding the Palette of SWIR Emitting Nanoparticles Based on Au Nanoclusters for Single-Particle Tracking Microscopy

Single-molecule localization microscopy has proved promising to unravel the dynamics and molecular architecture of thin biological samples down to nanoscales. For applications in complex, thick biological tissues shifting single-particle emission wavelengths to the shortwave infrared (SWIR also called NIR II) region between 900 to 2100 nm, where biological tissues are more transparent is key. To date, mainly single-walled carbon nanotubes (SWCNTs) enable such applications, but they are inherently 1D objects. Here, 0D ultra-small luminescent gold nanoclusters (AuNCs, <3 nm) and ≈25 nm AuNC-loaded-polymeric particles that can be detected at the single-particle level in the SWIR are presented. Thanks to high brightness and excellent photostability, it is shown that the dynamics of the spherical polymeric particles can be followed at the single-particle level in solution at video rates for minutes. We compared single particle tracking of AuNC-loaded-polymeric particles with that of SWCNT diffusing in agarose gels demonstrating the specificity and complementarity of diffusion properties of these SWIR-emitting nano-objects when exploring a complex environment. This extends the library of photostable SWIR emitting nanomaterials to 0D nano-objects of variable size for single-molecule localization microscopy in the second biological window, opening unprecedented possibilities for mapping the structure and dynamics of complex biological systems.

Identification of Early Stage Liver Fibrosis by Modifications in the Interstitial Space Diffusive Microenvironment Using Fluorescent Single-Walled Carbon Nanotubes

During liver fibrosis, recurrent hepatic injuries lead to the accumulation of collagen and other extracellular matrix components in the interstitial space, ultimately disrupting liver functions. Early stages of liver fibrosis may be reversible, but opportunities for diagnosis at these stages are currently limited. Here, we show that the alterations of the interstitial space associated with fibrosis can be probed by tracking individual fluorescent single-walled carbon nanotubes (SWCNTs) diffusing in that space. In a mouse model of early liver fibrosis, we find that nanotubes generally explore elongated areas, whose lengths decrease as the disease progresses, even in regions where histopathological examination does not reveal fibrosis yet. Furthermore, this decrease in nanotube mobility is a purely geometrical effect as the instantaneous nanotube diffusivity stays unmodified. This work establishes the promise of SWCNTs both for diagnosing liver fibrosis at an early stage and for more in-depth studies of the biophysical effects of the disease.

Near-Infrared Carbon Nanotube Tracking Reveals the Nanoscale Extracellular Space around Synapses

We provide evidence of a local synaptic nanoenvironment in the brain extracellular space (ECS) lying within 500 nm of postsynaptic densities. To reveal this brain compartment, we developed a correlative imaging approach dedicated to thick brain tissue based on single-particle tracking of individual fluorescent single wall carbon nanotubes (SWCNTs) in living samples and on speckle-based HiLo microscopy of synaptic labels. We show that the extracellular space around synapses bears specific properties in terms of morphology at the nanoscale and inner diffusivity. We finally show that the ECS juxta-synaptic region changes its diffusion parameters in response to neuronal activity, indicating that this nanoenvironment might play a role in the regulation of brain activity.

Supramolecular Self-Assembly of Dipalmitoylphosphatidylcholine and Carbon Nanotubes: A Dissipative Particle Dynamics Simulation Study

Dissipative particle dynamics simulations were performed to investigate the self-assembly of dipalmitoylphosphatidylcholine (DPPC) as a model lipid membrane on the surface of carbon nanotubes (CNTs). The influence of surface curvature of CNTs on self-assembly was investigated by performing simulations on solutions of DPPC in water in contact with CNTs of different diameters: CNT (10, 10), CNT (14, 14), CNT (20, 20), and CNT (34, 34). DPPC solutions with a wide range of concentrations were chosen to allow for formation of lipid structures of various surface densities, ranging from a submonolayer to a well-organized monolayer and a CNT covered with a lipid monolayer immersed in a planar lipid bilayer. Our results are indicative of a sequence of phase-ordering processes for DPPC on the surface of CNTs. At low surface coverages, the majority of hydrocarbon tail groups of DPPC are in contact with the CNT surface. Increasing the surface coverage leads to the formation of hemimicellar aggregates, and at high surface coverages close to the saturation limit, an organized lipid monolayer self-assembles. An examination of the mechanism of self-assembly reveals a two-step mechanism. The first step involves densification of DPPC on the CNT surface. Here, the lipid molecules do not adopt the order of the target phase (lipid monolayer on the CNT surface). In the second step, when the lipid density on the CNT surface is above a threshold value (close to saturation), the lipid molecules reorient themselves to form an organized monolayer around the tube. Here, the DPPC molecules adopt stretched conformations normal to the surface, the end hydrocarbon groups adsorb on the surface, and the head groups occupy the outermost part of the monolayer. The saturation density and the degree of lipid ordering on the CNT surface depend on the surface curvature. The saturation density increases with increased surface curvature, and better-ordered structures are formed on less curved surfaces.

When Super-Resolution Localization Microscopy Meets Carbon Nanotubes

We recently assisted in a revolution in the realm of fluorescence microscopy triggered by the advent of super-resolution techniques that surpass the classic diffraction limit barrier. By providing optical images with nanometer resolution in the far field, super-resolution microscopy (SRM) is currently accelerating our understanding of the molecular organization of bio-specimens, bridging the gap between cellular observations and molecular structural knowledge, which was previously only accessible using electron microscopy. SRM mainly finds its roots in progress made in the control and manipulation of the optical properties of (single) fluorescent molecules. The flourishing development of novel fluorescent nanostructures has recently opened the possibility of associating super-resolution imaging strategies with nanomaterials’ design and applications. In this review article, we discuss some of the recent developments in the field of super-resolution imaging explicitly based on the use of nanomaterials. As an archetypal class of fluorescent nanomaterial, we mainly focus on single-walled carbon nanotubes (SWCNTs), which are photoluminescent emitters at near-infrared (NIR) wavelengths bearing great interest for biological imaging and for information optical transmission. Whether for fundamental applications in nanomaterial science or in biology, we show how super-resolution techniques can be applied to create nanoscale images “in”, “of” and “with” SWCNTs.

Single-Chirality Near-Infrared Carbon Nanotube Sub-Cellular Imaging and FRET Probes

Applications of single-walled carbon nanotubes (SWCNTs) in bioimaging and biosensing have been limited by difficulties with isolating single-chirality nanotube preparations with desired functionalities. Unique optical properties, such as multiple narrow near-infrared bands and several modes of signal transduction, including solvatochromism and FRET, are ideal for live cell/organism imaging and sensing applications. However, internanotube FRET has not been investigated in biological contexts. We developed single-chirality subcellular SWCNT imaging probes and investigated their internanotube FRET capabilities in live cells. To functionalize SWCNTs, we replaced the surfactant coating of aqueous two-phase extraction-sorted single-chirality nanotubes with helical polycarbodiimide polymers containing different functionalities. We achieved single-chirality SWCNT targeting of different subcellular structures, including the nucleus, to enable multiplexed imaging. We also targeted purified (6,5) and (7,6) chiralities to the same structures and observed internanotube FRET within these organelles. This work portends the use of single-chirality carbon nanotube optical probes for applications in biomedical research.

Advances in engineering near-infrared luminescent materials

Near-infrared (NIR) luminescent materials have emerged as a growing field of interest, particularly for imaging and optics applications in biology, chemistry, and physics. However, the development of materials for this and other use cases has been hindered by a range of issues that prevents their widespread use beyond benchtop research. This review explores emerging trends in some of the most promising NIR materials and their applications. In particular, we focus on how a more comprehensive understanding of intrinsic NIR material properties might allow researchers to better leverage these traits for innovative and robust applications in biological and physical sciences.

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

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

An efficient method for the determination of enantiomeric purity of racemic amino acids using micellar chromatography, a green approach

A simple, sensitive and green micellar liquid chromatographic method (RP-HPLC) was developed for enantioseparation of four racemic amino acids, namely, (RS)-selenomethionine, (RS)-methionine, (RS)-cysteine and (RS)-penicillamine. An aqueous solution of sodium dodecyl sulfate and Brij-35 was prepared and used as mobile phase for HPLC analysis. Activated esters of (S)-ibuprofen, (S)-ketoprofen and (S)-levofloxacin were synthesized by reacting them with N-hydroxybenzotriazole. These esters were characterized by UV, IR, ¹ HNMR, HRMS and elemental analysis. These chiral reagents (activated esters) were used for the synthesis of diastereomeric derivatives of the chosen amino acids. The diastereomeric derivatives were separated on a C₁₈ column by micellar liquid chromatography. Chromatographic conditions were optimized by varying concentration of surfactant in aqueous solution, and by varying the concentration and pH of the buffer. The green assessment score was calculated for the developed method (78, an excellent green method score). In addition, density functional theory calculations were performed, using Gaussian 09 rev. A.02 and hybrid density functional B3LYP with a 6-31G* basis set program, in order to develop lowest energy optimized structures of diastereomeric derivatives. The method was validated according to International Conference on Harmonization guidelines and the retention factor (k), selectivity factor (α), resolution factor (R_S ) and limit of detection (0.295 ng ml^-1 ) and limit of quantification (0.896 ng ml^-1 ) were calculated.

Fluorescent sp3 Defect-Tailored Carbon Nanotubes Enable NIR-II Single Particle Imaging in Live Brain Slices at Ultra-Low Excitation Doses

Cellular and tissue imaging in the second near-infrared window (NIR-II, ~1000–1350 nm) is advantageous for in vivo studies because of low light extinction by biological constituents at these wavelengths. However, deep tissue imaging at the single molecule sensitivity has not been achieved in the NIR-II window due to lack of suitable bio-probes. Single-walled carbon nanotubes have emerged as promising near-infrared luminescent molecular bio-probes; yet, their inefficient photoluminescence (quantum yield ~1%) drives requirements for sizeable excitation doses (~1–10 kW/cm²) that are significantly blue-shifted from the NIR-II region (<850 nm) and may thus ultimately compromise live tissue. Here, we show that single nanotube imaging can be achieved in live brain tissue using ultralow excitation doses (~0.1 kW/cm²), an order of magnitude lower than those currently used. To accomplish this, we synthesized fluorescent sp³-defect tailored (6,5) carbon nanotubes which, when excited at their first order excitonic transition (~985 nm) fluoresce brightly at ~1160 nm. The biocompatibility of these functionalized nanotubes, which are wrapped by encapsulation agent (phospholipid-polyethylene glycol), is demonstrated using standard cytotoxicity assays. Single molecule photophysical studies of these biocompatible nanotubes allowed us to identify the optimal luminescence properties in the context of biological imaging.

Fluorescent Single-Walled Carbon Nanotubes for Protein Detection

Nanosensors have a central role in recent approaches to molecular recognition in applications like imaging, drug delivery systems, and phototherapy. Fluorescent nanoparticles are particularly attractive for such tasks owing to their emission signal that can serve as optical reporter for location or environmental properties. Single-walled carbon nanotubes (SWCNTs) fluoresce in the near-infrared part of the spectrum, where biological samples are relatively transparent, and they do not photobleach or blink. These unique optical properties and their biocompatibility make SWCNTs attractive for a variety of biomedical applications. Here, we review recent advancements in protein recognition using SWCNTs functionalized with either natural recognition moieties or synthetic heteropolymers. We emphasize the benefits of the versatile applicability of the SWCNT sensors in different systems ranging from single-molecule level to in-vivo sensing in whole animal models. Finally, we discuss challenges, opportunities, and future perspectives.

Photoswitchable single-walled carbon nanotubes for super-resolution microscopy in the near-infrared

The design of single-molecule photoswitchable emitters was the first milestone toward the advent of single-molecule localization microscopy, setting a new paradigm in the field of optical imaging. Several photoswitchable emitters have been developed, but they all fluoresce in the visible or far-red ranges, missing the desirable near-infrared window where biological tissues are most transparent. Moreover, photocontrol of individual emitters in the near-infrared would be highly desirable for elementary optical molecular switches or information storage elements since most communication data transfer protocols are established in this spectral range. Here, we introduce a type of hybrid nanomaterials consisting of single-wall carbon nanotubes covalently functionalized with photoswitching molecules that are used to control the intrinsic luminescence of the single nanotubes in the near-infrared (beyond 1 μm). Through the control of photoswitching, we demonstrate super-localization imaging of nanotubes unresolved by diffraction-limited microscopy.

Xeno Nucleic Acid Nanosensors for Enhanced Stability Against Ion-Induced Perturbations

The omnipresence of salts in biofluids creates a pervasive challenge in designing sensors suitable for in vivo applications. Fluctuations in ion concentrations have been shown to affect the sensitivity and selectivity of optical sensors based on single-walled carbon nanotubes wrapped with single-stranded DNA (ssDNA-SWCNTs). We herein observe fluorescence wavelength shifting for ssDNA-SWCNT-based optical sensors in the presence of divalent cations at concentrations above 3.5 mM. In contrast, no shifting was observed for concentrations up to 350 mM for sensors bioengineered with increased rigidity using xeno nucleic acids (XNAs). Transient fluorescence measurements reveal distinct optical transitions for ssDNA- and XNA-based wrappings during ion-induced conformation changes, with XNA-based sensors showing increased permanence in conformational and signal stability. This demonstration introduces synthetic biology as a complementary means for enhancing nanotube optoelectronic behavior, unlocking previously unexplored possibilities for developing nanobioengineered sensors with augmented capabilities.

Ultrashort Carbon Nanotubes That Fluoresce Brightly in the Near-Infrared

The intrinsic near-infrared photoluminescence observed in long single-walled carbon nanotubes is known to be quenched in ultrashort nanotubes due to their tiny size as compared to the exciton diffusion length in these materials (>100 nm). Here, we show that intense photoluminescence can be created in ultrashort nanotubes (∼40 nm length) upon incorporation of exciton-trapping sp³ defect sites. Using super-resolution photoluminescence imaging at <25 nm resolution, we directly show the preferential localization of excitons at the nanotube ends, which separate by less than 40 nm and behave as independent emitters. This unexpected observation opens the possibility to synthesize fluorescent ultrashort nanotubes-a goal that has been long thought impossible-for bioimaging applications, where bright near-infrared photoluminescence and small size are highly desirable, and for quantum information science, where high quality and well-controlled near-infrared single photon emitters are needed.