Analysis of sparse molecular distributions in fibrous arrangements based on the distance to the first neighbor in single molecule localization microscopy

Szalai, Alan M.; Lopez, Lucía F.; Morales-Vásquez, Miguel Ángel; Stefani, Fernando D.; Aramendı́a, Pedro F.

doi:10.1039/c9nr10805j

Cited by 2 publications

(3 citation statements)

References 53 publications

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“…S18 ). Underlying architectures were identified for nanoprobe labeling densities of ~10 2 /µm 2 based on distribution of distances from every nanoprobe to its first neighbor following a distribution function 50 (Fig. S19 ), enabling continuous features to be defined from the discrete nanoprobe distributions in agreement with scanning electron microscopy (Fig.…”

Section: Resultsmentioning

confidence: 98%

“…In this work, we achieved PINE-resolved images with nanoprobe densities of ~10 2 /µm 2 , whereas higher nanoprobe densities are typically utilized in traditional fluorescence super-resolution. Since the distribution of distances from every nanoprobe to its first neighbor follows a distribution function 50 (Fig. S19 ), underlying protein architectures can be identified for nanoprobe labeling densities of ~10 2 /µm 2 , albeit lower than nanoprobe densities typically used in traditional fluorescence super-resolution.…”

Section: Discussionmentioning

confidence: 99%

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Phase intensity nanoscope (PINE) opens long-time investigation windows of living matter

Cui

Liu

et al. 2023

Nat Commun

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Fundamental to all living organisms and living soft matter are emergent processes in which the reorganization of individual constituents at the nanoscale drives group-level movements and shape changes at the macroscale over time. However, light-induced degradation of fluorophores, photobleaching, is a significant problem in extended bioimaging in life science. Here, we report opening a long-time investigation window by nonbleaching phase intensity nanoscope: PINE. We accomplish phase-intensity separation such that nanoprobe distributions are distinguished by an integrated phase-intensity multilayer thin film (polyvinyl alcohol/liquid crystal). We overcame a physical limit to resolve sub-10 nm cellular architectures, and achieve the first dynamic imaging of nanoscopic reorganization over 250 h using PINE. We discover nanoscopic rearrangements synchronized with the emergence of group-level movements and shape changes at the macroscale according to a set of interaction rules with importance in cellular and soft matter reorganization, self-organization, and pattern formation.

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Section: Resultsmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Phase intensity nanoscope (PINE) opens long-time investigation windows of living matter

Cui

Liu

et al. 2023

Nat Commun

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show abstract

“…4D. The complementary cumulative distribution function of the distance to the first neighbor, CCDF(r), should be linear with the square of the distance, [29,30] according to Furthermore, if we consider the complete set of singlemolecule localizations of Fig. 4A, a value for Q CA smaller than the one for a random distribution is obtained (see Table S1).…”

Section: Single Molecule Experimentsmentioning

confidence: 99%

Determination of association equilibrium constant from single molecule fluorescence localization microscopy

Cappellari

Marcano-García

Simoncelli

et al. 2022

Photochem Photobiol Sci

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Single molecule fluorescence localization microscopy provides molecular localization with a precision in the tens of nanometer range in the plane perpendicular to the light propagation. This opens the possibility to count molecules and correlate their locations, starting from a map of the actual positions in a single molecule super resolution image. Considering molecular pair correlation as an indication of interaction, and a way to discern them from free molecules, we describe a method to calculate thermodynamic equilibrium constants. In this work, we use as a test system two complementary homo-oligonucleotides, one strand marked with Cyanine 3.5 and the other with Alexa Fluor 647. Hybridization is controlled by the amount of each strand, temperature, and the ionic force, and measured in steady state emission. The same samples are examined in Stochastic Optical Reconstruction Microscopy (STORM) experiments with split-field simultaneous two-colour detection. The effect of multiblinking, labelling-detection efficiency, and determination of the critical distance for association are discussed. We consistently determine values in STORM coincident with those of the bulk experiment.

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Analysis of sparse molecular distributions in fibrous arrangements based on the distance to the first neighbor in single molecule localization microscopy

Abstract: We introduce a robust and sensitive metric to characterize the underlying structure responsible for the molecular distribution, even at a very low labeling density.

Cited by 2 publications

References 53 publications

Phase intensity nanoscope (PINE) opens long-time investigation windows of living matter

Phase intensity nanoscope (PINE) opens long-time investigation windows of living matter

Determination of association equilibrium constant from single molecule fluorescence localization microscopy

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