DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) facilitates multiplexing in superresolution microscopy but is practically limited by slow imaging speed. To address this issue, we propose the additions of ethylene carbonate (EC) to the imaging buffer, sequence repeats to the docking strand, and a spacer between the docking strand and the affinity agent. Collectively termed DNA-PAINT-ERS (E = EC, R = Repeating sequence, and S = Spacer), these strategies can be easily integrated into current DNA-PAINT workflows for both accelerated imaging speed and improved image quality through optimized DNA hybridization kinetics and efficiency. We demonstrate the general applicability of DNA-PAINT-ERS for fast, multiplexed superresolution imaging using previously validated oligonucleotide constructs with slight modifications.

Fluorophores are powerful tools for interrogating biological systems. Carbon nanotubes (CNTs) have long been attractive materials for biological imaging due to their nearinfrared excitation and bright, tunable optical properties. The difficulty in synthesizing and functionalizing these materials with precision, however, has hampered progress in this area. Carbon nanohoops, which are macrocyclic CNT substructures, are carbon nanostructures that possess ideal photophysical characteristics of nanomaterials, while maintaining the precise synthesis of small molecules. However, much work remains to advance the nanohoop class of fluorophores as biological imaging agents. Herein, we report an intracellular targeted nanohoop. This fluorescent nanostructure is noncytotoxic at concentrations up to 50 μM, and cellular uptake investigations indicate internalization through endocytic pathways. Additionally, we employ this nanohoop for two-photon fluorescence imaging, demonstrating a high two-photon absorption cross-section (65 GM) and photostability comparable to a commercial probe. This work further motivates continued investigations into carbon nanohoop photophysics and their biological imaging applications.

Superresolution microscopy (SRM) has become an enabling tool for biomedical research. A major limitation of SRM, however, is the small field-of-view (FOV), typically ~50μm x 50μm and up to ~200μm x 200μm in recent attempts, hampering its use in imaging large cell populations or clinical tissues. Here we report PRism-Illumination and Microfluidics-Enhanced DNA-PAINT (PRIME-PAINT) for efficient, multiplexed SRM across millimeter-scale FOVs. Unlike existing SRM, PRIME-PAINT uses prism-type illumination for robust DNA-PAINT with single FOVs up to ~0.5mm x 0.5mm. Through stitching, imaging >1 mm2 FOVs can be completed in as little as an hour per target. The on-stage microfluidics not only facilitates multiplexing but enhances image quality, particularly for tissue sections. We demonstrate the utility of PRIME-PAINT by analyzing ~106 caveolae structures in ~1,000 cells and imaging entire pancreatic cancer lesions from patient tissue biopsies. Thus, we expect PRIME-PAINT to be useful toward building multiscale, Google-Earth-like views of biological systems.

Myosin 10 (Myo10) is a vertebrate-specific motor protein well known for its role in filopodia formation. Although Myo10-driven filopodial dynamics have been characterized, there is no information about the numbers of Myo10 in filopodia. To better understand molecular stoichiometries and packing restraints in filopodia, we measured Myo10 abundance in these structures. Here we combined SDS-PAGE analysis with epifluorescence microscopy to quantitate HaloTag-labeled Myo10 in U2OS cells. About 6% of total intracellular Myo10 localizes to filopodia, where it tends to be enriched at opposite ends of the cell. Hundreds of Myo10 are found in a typical filopodium, and their distribution across filopodia is log-normal. Some filopodial tips even contain more Myo10 than accessible binding sites on the actin filament bundle. Our estimates of Myo10 molecules in filopodia provide insight into the physics of packing Myo10, its cargo, and other filopodia-associated proteins in narrow membrane deformations in addition to the numbers of Myo10 required for filopodia initiation. Our protocol provides a framework for future work analyzing Myo10 abundance and distribution upon perturbation.

Eukaryotic cells form biomolecular condensates to sense and adapt to their environment1,2. Poly(A)-binding protein (Pab1), a canonical stress granule marker3,4, condenses upon heat shock or starvation, promoting adaptation5. The molecular basis of condensation has remained elusive due to a dearth of techniques to probe structure directly in condensates. Here we apply hydrogen-deuterium exchange/mass spectrometry (HDX-MS) to investigate the molecular mechanism of Pab1's condensation. We find that Pab1's four RNA recognition motifs (RRMs) undergo different levels of partial unfolding upon condensation, and the changes are similar for thermal and pH stresses. Although structural heterogeneity is observed, the ability of MS to describe individual subpopulations allows us to identify which regions become partially unfolded and contribute to the condensate's interaction network. Our data yield a clear molecular picture of Pab1's stress-triggered condensation, which we term sequential activation, wherein each RRM becomes activated at a temperature where it partially unfolds and associates with other likewise activated RRMs to form the condensate. This model thus implies that sequential activation is dictated by the underlying free energy surface, an effect we refer to as thermodynamic specificity. Our study represents a methodological advance for elucidating the interactions that drive biomolecular condensation that we anticipate will be widely applicable. Furthermore, our findings demonstrate how condensation can use thermodynamic specificity to perform an acute response to multiple stresses, a potentially general mechanism for stress-responsive proteins.

DNA point accumulation for imaging in nanoscale topography (DNA-PAINT) facilitates multiplexing in superresolution microscopy but is practically limited by slow imaging speed. We have developed DNA-PAINT-ERS, where E=ethylene carbonate, R=repeating sequence, and S=spacer, for fast and multiplexed superresolution imaging with DNA-PAINT. Here we describe detailed procedures for DNA-PAINT-ERS including reagent preparation, sample labeling, as well as image acqusition and analysis.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Interpreting cancer genomes requires a broad understanding of the composition and organization of cellular processes under selective pressure for mutations. Here, we integrate systematic screens for protein interaction with tumor genetic analysis to elucidate a multiscale hierarchical map of 378 protein systems recurrently altered in one or more cancer types. Diverse gene mutations converge on commonly mutated systems, from small protein complexes in specific tumor types to large molecular assemblies and organelles disrupted in most cancers. Unexpected findings include collagen structural alterations with significant prognostic value; mutations impacting the desmosome in 65% melanomas; complexes related to splicing and DNA repair; and an expanded actomyosin cluster involving PIK3CA. The map implicates 556 cancer genes, many well supported by functional assays, including canonical genes implicated in new tissues (e.g., BRCA1/2 mutations in bladder cancer). This work explains mutational heterogeneity as a collection of convergence points across scales of cell biology. This abstract is also being presented as Poster B52. Citation Format: Fan Zheng, Keiichiro Ono, Erica Silva, Danielle Swaney, Minkyu Kim, Julia Shangguan, Dexter Pratt, Xiaolin Nan, Nevan Krogan, Trey Ideker. A multiscale map of recurrently mutated systems in cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR14.