DNA Origami Nanopillars as Standards for Three-Dimensional Superresolution Microscopy

Nano Letters ◽  
2013 ◽  
Vol 13 (2) ◽  
pp. 781-785 ◽  
Author(s):  
Jürgen J. Schmied ◽  
Carsten Forthmann ◽  
Enrico Pibiri ◽  
Birka Lalkens ◽  
Philipp Nickels ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dna Origami ◽  
Superresolution Microscopy

scholarly journals Picosecond time-resolved photon antibunching measures nanoscale exciton motion and the true number of chromophores

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gordon J. Hedley ◽  
Tim Schröder ◽  
Florian Steiner ◽  
Theresa Eder ◽  
Felix J. Hofmann ◽  
...  
Keyword(s):  
Rational Design ◽  
Three Dimensional ◽  
Dna Origami ◽  
Fluorescent Nanoparticles ◽  
Time Resolved ◽  
Exciton Diffusion ◽  
Polymer Aggregates ◽  
True Number ◽  
Particle Level ◽  
Photon Antibunching

AbstractThe particle-like nature of light becomes evident in the photon statistics of fluorescence from single quantum systems as photon antibunching. In multichromophoric systems, exciton diffusion and subsequent annihilation occurs. These processes also yield photon antibunching but cannot be interpreted reliably. Here we develop picosecond time-resolved antibunching to identify and decode such processes. We use this method to measure the true number of chromophores on well-defined multichromophoric DNA-origami structures, and precisely determine the distance-dependent rates of annihilation between excitons. Further, this allows us to measure exciton diffusion in mesoscopic H- and J-type conjugated-polymer aggregates. We distinguish between one-dimensional intra-chain and three-dimensional inter-chain exciton diffusion at different times after excitation and determine the disorder-dependent diffusion lengths. Our method provides a powerful lens through which excitons can be studied at the single-particle level, enabling the rational design of improved excitonic probes such as ultra-bright fluorescent nanoparticles and materials for optoelectronic devices.

Modular Reconfigurable DNA Origami: From Two‐Dimensional to Three‐Dimensional Structures

2020 ◽  
Vol 59 (51) ◽  
pp. 23277-23282 ◽  
Author(s):  
Yan Liu ◽  
Jin Cheng ◽  
Sisi Fan ◽  
Huan Ge ◽  
Tao Luo ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dna Origami ◽  
Two Dimensional

scholarly journals Three-Dimensional DNA Origami as Programmable Anchoring Points for Bioreceptors in Fiber Optic Surface Plasmon Resonance Biosensing

2018 ◽  
Vol 10 (28) ◽  
pp. 23539-23547 ◽  
Author(s):  
Devin Daems ◽  
Wolfgang Pfeifer ◽  
Iene Rutten ◽  
Barbara Saccà ◽  
Dragana Spasic ◽  
...  
Keyword(s):  
Surface Plasmon Resonance ◽  
Surface Plasmon ◽  
Plasmon Resonance ◽  
Fiber Optic ◽  
Three Dimensional ◽  
Dna Origami

Direct Mechanical Measurements Reveal the Material Properties of Three-Dimensional DNA Origami

Nano Letters ◽  
2011 ◽  
Vol 11 (12) ◽  
pp. 5558-5563 ◽  
Author(s):  
Dominik J. Kauert ◽  
Thomas Kurth ◽  
Tim Liedl ◽  
Ralf Seidel
Keyword(s):  
Material Properties ◽  
Three Dimensional ◽  
Dna Origami ◽  
Mechanical Measurements

scholarly journals Superresolution microscopy reveals the three-dimensional organization of meiotic chromosome axes in intact Caenorhabditis elegans tissue

2017 ◽  
Vol 114 (24) ◽  
pp. E4734-E4743 ◽  
Author(s):  
Simone Köhler ◽  
Michal Wojcik ◽  
Ke Xu ◽  
Abby F. Dernburg
Keyword(s):  
Caenorhabditis Elegans ◽  
Fluorescent Protein ◽  
Germ Line ◽  
Meiotic Chromosome ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Molecular Organization ◽  
Superresolution Microscopy ◽  
Specific Proteins ◽  
Optical Reconstruction

When cells enter meiosis, their chromosomes reorganize as linear arrays of chromatin loops anchored to a central axis. Meiotic chromosome axes form a platform for the assembly of the synaptonemal complex (SC) and play central roles in other meiotic processes, including homologous pairing, recombination, and chromosome segregation. However, little is known about the 3D organization of components within the axes, which include cohesin complexes and additional meiosis-specific proteins. Here, we investigate the molecular organization of meiotic chromosome axes in Caenorhabditis elegans through STORM (stochastic optical reconstruction microscopy) and PALM (photo-activated localization microscopy) superresolution imaging of intact germ-line tissue. By tagging one axis protein (HIM-3) with a photoconvertible fluorescent protein, we established a spatial reference for other components, which were localized using antibodies against epitope tags inserted by CRISPR/Cas9 genome editing. Using 3D averaging, we determined the position of all known components within synapsed chromosome axes to high spatial precision in three dimensions. We find that meiosis-specific HORMA domain proteins span a gap between cohesin complexes and the central region of the SC, consistent with their essential roles in SC assembly. Our data further suggest that the two different meiotic cohesin complexes are distinctly arranged within the axes: Although cohesin complexes containing the kleisin REC-8 protrude above and below the plane defined by the SC, complexes containing COH-3 or -4 kleisins form a central core, which may physically separate sister chromatids. This organization may help to explain the role of the chromosome axes in promoting interhomolog repair of meiotic double-strand breaks by inhibiting intersister repair.

scholarly journals Obtaining 3D Super-resolution Information from 2D Super-resolution Images through a 2D-to-3D Transformation Algorithm

2017 ◽  
Author(s):  
Andrew Ruba ◽  
Wangxi Luo ◽  
Joseph Kelich ◽  
Weidong Yang
Keyword(s):  
Single Molecule ◽  
Rotational Symmetry ◽  
Three Dimensional ◽  
Super Resolution ◽  
Live Cells ◽  
Limited Information ◽  
Spatiotemporal Resolution ◽  
Superresolution Microscopy ◽  
Localization Analysis ◽  
Probability Information

AbstractCurrently, it is highly desirable but still challenging to obtain three-dimensional (3D) superresolution information of structures in fixed specimens as well as dynamic processes in live cells with a high spatiotemporal resolution. Here we introduce an approach, without using 3D superresolution microscopy or real-time 3D particle tracking, to achieve 3D sub-diffraction-limited information with a spatial resolution of ≤ 1 nm. This is a post-localization analysis that transforms 2D super-resolution images or 2D single-molecule localization distributions into their corresponding 3D spatial probability information. The method has been successfully applied to obtain structural and functional information for 25-300 nm sub-cellular organelles that have rotational symmetry. In this article, we will provide a comprehensive analysis of this method by using experimental data and computational simulations.

scholarly journals Particle localization using local gradients and its application to nanometer stabilization of a microscope

2021 ◽  
Author(s):  
Anatolii V. Kashchuk ◽  
Oleksandr Perederiy ◽  
Chiara Caldini ◽  
Lucia Gardini ◽  
Francesco Saverio Pavone ◽  
...  
Keyword(s):  
Single Molecule ◽  
Three Dimensional ◽  
Universal Method ◽  
Superresolution Microscopy ◽  
Accurate Localization ◽  
Micro Particles ◽  
Localization Algorithms ◽  
Gradient Calculation ◽  
Particle Localization ◽  
Local Gradient

Accurate localization of single particles plays an increasingly important role in a range of biological techniques, including single molecule tracking and localization-based superresolution microscopy. Such techniques require fast and accurate particle localization algorithms as well as nanometer-scale stability of the microscope. Here, we present a universal method for three-dimensional localization of single labeled and unlabeled particles based on local gradient calculation of microscopy images. The method outperforms current techniques in high noise conditions, and it is capable of nanometer accuracy localization of nano- and micro-particles with sub-ms calculation time. By localizing a fixed particle as fiducial mark and running a feedback loop, we demonstrate its applicability for active drift correction in sensitive nanomechanical measurements such as optical trapping and superresolution imaging. A multiplatform open software package comprising a set of tools for local gradient calculation in brightfield and fluorescence microscopy is shared to the scientific community.

scholarly journals Three dimensional particle averaging for structural imaging of macromolecular complexes by localization microscopy

2019 ◽  
Author(s):  
Hamidreza Heydarian ◽  
Adrian Przybylski ◽  
Florian Schueder ◽  
Ralf Jungmann ◽  
Ben van Werkhoven ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Dna Origami ◽  
Particle Analysis ◽  
Nuclear Pore ◽  
Single Particle Analysis ◽  
Macromolecular Complexes ◽  
Localization Microscopy ◽  
Structural Template ◽  
Microscopy Techniques

AbstractWe present an approach for 3D particle fusion in localization microscopy which dramatically increases signal-to-noise ratio and resolution in single particle analysis. Our method does not require a structural template, and properly handles anisotropic localization uncertainties. We demonstrate 3D particle reconstructions of the Nup107 subcomplex of the nuclear pore complex (NPC), cross-validated using multiple localization microscopy techniques, as well as two-color 3D reconstructions of the NPC, and reconstructions of DNA-origami tetrahedrons.

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