Morphological control of bundled actin networks subject to fixed-mass depletion.

Depletion interactions are thought to significantly contribute to the organization of intracellular structures in the crowded cytosol. The strength of depletion interactions depends on physical parameters such as the depletant number density and the depletant size ratio. Cells are known to dynamically regulate these two parameters by varying the copy number of proteins of a wide distribution of sizes. However, mammalian cells are also known to keep the total protein mass density remarkably constant, to within 0.5% throughout the cell cycle. We thus ask how the strength of depletion interactions varies when the total depletant mass is held fixed, a.k.a. fixed-mass depletion. We answer this question via scaling arguments, as well as by studying depletion effects on networks of reconstituted semiflexible actin in silico and in vitro. We examine the maximum strength of the depletion interaction potential U∗ as a function of q, the size ratio between the depletant and the matter being depleted. We uncover a scaling relation U∗ ∼ qζ for two cases: fixed volume fraction φ and fixed mass density ρ. For fixed volume fraction, we report ζ < 0. For the fixed mass density case, we report ζ > 0, which suggests that the depletion interaction strength increases as the depletant size ratio is increased. To test this prediction, we prepared our filament networks at fixed mass concentrations with varying sizes of the depletant molecule poly(ethylene glycol) (PEG). We characterize the depletion interaction strength in our simulations via the mesh size. In experiments, we observe two distinct actin network morphologies, which we call weakly bundled and strongly bundled. We identify a mass concentration where different PEG depletant sizes lead to weakly bundled or strongly bundled morphologies. For these conditions, we find that the mesh size and intra-bundle spacing between filaments across the different morphologies do not show significant differences, while the dynamic light scattering relaxation time and storage modulus between the two states do show significant differences. Our results demonstrate the ability to tune actin network morphology and mechanics by controlling depletant size and give insights into depletion interaction mechanisms under the fixed-depletant-mass constraint relevant to living cells.

Assembling Inorganic Nanocrystal Gels.

Inorganic nanocrystal gels retain distinct properties of individual nanocrystals while offering tunable, network-structure-dependent characteristics. We review different mechanisms for assembling gels from colloidal nanocrystals including (1) controlled destabilization, (2) direct bridging, (3) depletion, as well as linking mediated by (4) coordination bonding or (5) dynamic covalent bonding, and we highlight how each impacts gel properties. These approaches use nanocrystal surface chemistry or the addition of small molecules to mediate inter-nanocrystal attractions. Each method offers advantages in terms of gel stability, reversibility, or tunability and presents new opportunities for the design of reconfigurable materials and fueled assemblies.

Colloidal Nanocrystal Gels from Thermodynamic Principles.

Gels assembled from solvent-dispersed nanocrystals are of interest for functional materials because they promise the opportunity to retain distinctive properties of individual nanocrystals combined with tunable, structure-dependent collective behavior. By incorporating stimuli-responsive components, these materials could also be dynamically reconfigured between structurally distinct states. However, nanocrystal gels have so far been formed mostly through irreversible aggregation, which has limited the realization of these possibilities. Meanwhile, gelation strategies for larger colloidal microparticles have been developed using reversible physical or chemical interactions. These approaches have enabled the experimental navigation of theoretically predicted phase diagrams, helping to establish an understanding of how thermodynamic behavior can guide gel formation in these materials. However, the translation of these principles to the nanoscale poses both practical and fundamental challenges. The molecules guiding assembly can no longer be safely assumed to be vanishingly small compared to the particles nor large compared to the solvent.In this Account, we discuss recent progress toward the assembly of tunable nanocrystal gels using two strategies guided by equilibrium considerations: (1) reversible chemical bonding between functionalized nanocrystals and difunctional linker molecules and (2) nonspecific, polymer-induced depletion attractions. The effective nanocrystal attractions, mediated in both approaches by a secondary molecule, compete against stabilizing repulsions to promote reversible assembly. The structure and properties of the nanocrystal gels are controlled microscopically by the design of the secondary molecule and macroscopically by its concentration. This mode of control is compelling because it largely decouples nanocrystal synthesis and functionalization from the design of interactions that drive assembly. Statistical thermodynamic theory and computer simulation have been applied to simple models that describe the bonding motifs in these assembling systems, furnish predictions for conditions under which gelation is likely to occur, and suggest strategies for tuning and disassembling the gel networks. Insights from these models have guided experimental realizations of reversible gels with optical properties in the infrared range that are sensitive to the gel structure. This process avoids time-consuming and costly trial-and-error experimental investigations to accelerate the development of nanocrystal gel assemblies.These advances highlight the need to better understand interactions between nanocrystals, how interactions give rise to gel structure, and properties that emerge. Such an understanding could suggest new approaches for creating stimuli-responsive and dissipative assembled materials whose properties are tunable on demand through directed reconfiguration of the underlying gel microstructure. It may also make nanocrystal gels amenable to computationally guided design using inverse methods to rapidly optimize experimental parameters for targeted functionalities.

Universal Gelation of Metal Oxide Nanocrystals via Depletion Attractions.

Nanocrystal gelation provides a powerful framework to translate nanoscale properties into bulk materials and to engineer emergent properties through the assembled microstructure. However, many established gelation strategies rely on chemical reactions and specific interactions, e.g., stabilizing ligands or ions on the nanocrystals' surfaces, and are therefore not easily transferable. Here, we report a general gelation strategy via nonspecific and purely entropic depletion attractions applied to three types of metal oxide nanocrystals. The gelation thresholds of two compositionally distinct spherical nanocrystals agree quantitatively, demonstrating the adaptability of the approach for different chemistries. Consistent with theoretical phase behavior predictions, nanocrystal cubes form gels at a lower polymer concentration than nanocrystal spheres, allowing shape to serve as a handle to control gelation. These results suggest that the fundamental underpinnings of depletion-driven assembly, traditionally associated with larger colloidal particles, are also applicable at the nanoscale.

Surface-Enhanced Infrared Absorption Spectroscopy by Resonant Vibrational Coupling with Plasmonic Metal Oxide Nanocrystals.

Coupling between plasmonic resonances and molecular vibrations in nanocrystals (NCs) offers a promising approach for detecting molecules at low concentrations and discerning their chemical identities. Metallic NC superlattices can enhance vibrational signals under far-field detection by generating a myriad of intensified electric field hot spots between the NCs. Yet, their effectiveness is limited by the fixed electron concentration dictated by the metal composition and inefficient hot spot creation due to the large mode volume. Doped metal oxide NCs, such as tin-doped indium oxide (ITO), could overcome these limitations by enabling broad tunability of resonance frequencies in the mid-infrared range through independent variation of size and doping concentration. This study investigates the potential of close-packed ITO NC monolayers for surface-enhanced infrared absorption by quantifying trends in the coupling between their plasmon modes and various molecular vibrations. We show that maximum vibrational signal intensity occurs in monolayers composed of larger, more highly doped NCs, where the plasmon resonance peak lies at higher frequency than the molecular vibration. Using finite element and mutual polarization methods, we establish that near-field enhancement is stronger on the low-frequency side of the plasmon resonance and for more strongly coupled plasmonic NCs, thus rationalizing the design rules we experimentally uncovered. Our results can guide the development of optimal metal oxide NC-based superstructures for sensing target molecules or modifying their chemical properties through vibrational coupling.

Wavelength Tunable Infrared Perfect Absorption in Plasmonic Nanocrystal Monolayers.

The ability to efficiently absorb light in ultrathin (subwavelength) layers is essential for modern electro-optic devices, including detectors, sensors, and nonlinear modulators. Tailoring these ultrathin films' spectral, spatial, and polarimetric properties is highly desirable for many, if not all, of the above applications. Doing so, however, often requires costly lithographic techniques or exotic materials, limiting scalability. Here we propose, demonstrate, and analyze a mid-infrared absorber architecture leveraging monolayer films of nanoplasmonic colloidal tin-doped indium oxide nanocrystals (ITO NCs). We fabricate a series of ITO NC monolayer films using the liquid-air interface method; by synthetically varying the Sn dopant concentration in the NCs, we achieve spectrally selective perfect absorption tunable between wavelengths of two and five micrometers. We achieve monolayer thickness-controlled coupling strength tuning by varying NC size, allowing access to different coupling regimes. Furthermore, we synthesize a bilayer film that enables broadband absorption covering the entire midwave IR region (λ = 3-5 µm). We demonstrate a scalable platform, with perfect absorption in monolayer films only hundredths of a wavelength in thickness, enabling strong light-matter interaction, with potential applications for molecular detection and ultrafast nonlinear optical applications.

Binding of FANCI-FANCD2 Complex to RNA and R-Loops Stimulates Robust FANCD2 Monoubiquitination.

Fanconi anemia (FA) is characterized by developmental abnormalities, bone marrow failure, and cancer predisposition. FA cells are hypersensitive to DNA replicative stress and accumulate co-transcriptional R-loops. Here, we use the Damage At RNA Transcription assay to reveal colocalization of FANCD2 with R-loops in a highly transcribed genomic locus upon DNA damage. We further demonstrate that highly purified human FANCI-FANCD2 (ID2) complex binds synthetic single-stranded RNA (ssRNA) and R-loop substrates with high affinity, preferring guanine-rich sequences. Importantly, we elucidate that human ID2 binds an R-loop structure via recognition of the displaced ssDNA and ssRNA but not the RNA:DNA hybrids. Finally, a series of RNA and R-loop substrates are found to strongly stimulate ID2 monoubiquitination, with activity corresponding to their binding affinity. In summary, our results support a mechanism whereby the ID2 complex suppresses the formation of pathogenic R-loops by binding ssRNA and ssDNA species, thereby activating the FA pathway.

Nusinersen in later-onset spinal muscular atrophy: Long-term results from the phase 1/2 studies.

OBJECTIVE: To report results of intrathecal nusinersen in children with later-onset spinal muscular atrophy (SMA). METHODS: Analyses included children from a phase 1b/2a study (ISIS-396443-CS2; NCT01703988) who first received nusinersen during that study and were eligible to continue treatment in the extension study (ISIS-396443-CS12; NCT02052791). The phase 1b/2a study was a 253-day, ascending dose (3, 6, 9, 12 mg), multiple-dose, open-label, multicenter study that enrolled children with SMA aged 2-15 years. The extension study was a 715-day, single-dose level (12 mg) study. Time between studies varied by participant (196-413 days). Assessments included the Hammersmith Functional Motor Scale-Expanded (HFMSE), Upper Limb Module (ULM), 6-Minute Walk Test (6MWT), compound muscle action potential (CMAP), and quantitative multipoint incremental motor unit number estimation. Safety also was assessed. RESULTS: Twenty-eight children were included (SMA type II, n = 11; SMA type III, n = 17). Mean HFMSE scores, ULM scores, and 6MWT distances improved by the day 1,150 visit (HFMSE: SMA type II, +10.8 points; SMA type III, +1.8 points; ULM: SMA type II, +4.0 points; 6MWT: SMA type III, +92.0 meters). Mean CMAP values remained relatively stable. No children discontinued treatment due to adverse events. CONCLUSIONS: Nusinersen treatment over ∼3 years resulted in motor function improvements and disease activity stabilization not observed in natural history cohorts. These results document the long-term benefit of nusinersen in later-onset SMA, including SMA type III. CLINICALTRIALSGOV IDENTIFIER: NCT01703988 (ISIS-396443-CS2); NCT02052791 (ISIS-396443-CS12). CLASSIFICATION OF EVIDENCE: This study provides Class IV evidence that nusinersen improves motor function in children with later-onset SMA.

Fanconi anemia.

Fanconi anemia (FA) is an autosomal and X-linked recessive disorder characterized by bone marrow failure, acute myelogenous leukemia, solid tumors, and developmental abnormalities. Recent years have seen a dramatic improvement in FA patient treatment, resulting in a greater survival of children into adulthood. These improvements have been made despite the fact that a definitive cellular function for the proteins in the FA pathway has yet to be elucidated. Delineating the cellular functions of the FA pathway could help further improve the treatment options for FA patients and further reduce the probability of succumbing to the disease. This article reviews the current clinical aspects of FA including presentation, diagnosis, and treatment followed by a review of the molecular aspects of FA as they are currently understood.

Human T-cell leukemia virus I tax protein sensitizes p53-mutant cells to DNA damage.

Mutations in p53 are a common cause of resistance of cancers to standard chemotherapy and, thus, treatment failure. Reports have shown that Tax, a human T-cell leukemia virus type I encoded protein that has been associated with genomic instability and perturbation of transcription and cell cycle, sensitizes HeLa cells to UV treatment. The extent to which Tax can sensitize cells and the mechanism by which it exerts its effect are unknown. In this study, we show that Tax sensitizes p53-mutant cells to a broad range of DNA-damaging agents, including mitomycin C, a bifunctional alkylator, etoposide, a topoisomerase II drug, and UV light, but not ionizing radiation, a double-strand break agent, or vinblastine, a tubulin poison. Tax caused hypersensitivity in all p53-deleted cell lines and several, but not all, mutant-expressed p53-containing cell lines, while unexpectedly being protective in p53 wild-type (wt) cells. The effect observed in p53-deleted lines could be reversed for this by transfection of wt p53. We also show that Tax activates a p53-independent proapoptotic program through decreased expression of the retinoblastoma protein and subsequent increased E2F1 expression. The expression of several proapoptotic proteins was also induced by Tax, including Puma and Noxa, culminating in a substantial increase in Bax dimerization. Our results show that Tax can sensitize p53-mutant cells to DNA damage while protecting p53 wt cells, a side benefit that might result in reduced toxicity in normal cells. Such studies hold the promise of a novel adjunctive therapy that could make cancer chemotherapy more effective.