Three-dimensional super-resolution fluorescence imaging of DNA

Yardimci, Sevim; Burnham, Daniel R.; Terry, Samantha Y.A.; Yardimci, Hasan

doi:10.1038/s41598-020-68892-5

Cited by 12 publications

(14 citation statements)

References 26 publications

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“…3D imaging displayed chromatid breaks after radiation exposure and thinned chromosomal regions after sonication. Further STORM of telomeres with Alexa647labelled protein nucleic acid probe showed localization on the top (exterior) region of chromosomes while others bound to the interior regions and displayed extended shapes (Yardimci et al 2020) (Fig. 8f).…”

Section: Super-resolution Microscopy For Studying Chromosome Nanostrumentioning

confidence: 99%

“…This would require investigation into the structure/compaction of DNA together with specific protein labelling of histones (DNA-histone and histone-histone interactions), scaffold and structural proteins that will provide the nanoscale architecture of mitotic chromosomes. Considering FLIM can be Yardimci et al 2020) applied to live samples to study both DNA and proteins, the combination of SRM and FLIM offers an opportunity to investigate chromosome structure in live cell. This is currently not possible using electrons or X-rays.…”

Section: Future Prospectsmentioning

confidence: 99%

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Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure

et al. 2021

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The organization of chromatin into higher-order structures and its condensation process represent one of the key challenges in structural biology. This is important for elucidating several disease states. To address this long-standing problem, development of advanced imaging methods has played an essential role in providing understanding into mitotic chromosome structure and compaction. Amongst these are two fast evolving fluorescence imaging technologies, specifically fluorescence lifetime imaging (FLIM) and super-resolution microscopy (SRM). FLIM in particular has been lacking in the application of chromosome research while SRM has been successfully applied although not widely. Both these techniques are capable of providing fluorescence imaging with nanometer information. SRM or “nanoscopy” is capable of generating images of DNA with less than 50 nm resolution while FLIM when coupled with energy transfer may provide less than 20 nm information. Here, we discuss the advantages and limitations of both methods followed by their contribution to mitotic chromosome studies. Furthermore, we highlight the future prospects of how advancements in new technologies can contribute in the field of chromosome science.

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Section: Super-resolution Microscopy For Studying Chromosome Nanostrumentioning

confidence: 99%

Section: Future Prospectsmentioning

confidence: 99%

Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure

et al. 2021

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“…The potential inclusion of a live/dead stain to visualize cell clusters' viability and advances in light microscopy technologies, such as optical projection tomography (OPT) and digital holographic microscopy [93,94], may facilitate microscopic observations under these difficult conditions. Super-resolution fluorescence imaging technologies could also be applied to understand the process of tick cell aggregation in 3-D culture systems [95].…”

Section: Discussionmentioning

confidence: 99%

Three-Dimensional Culture of Rhipicephalus (Boophilus) microplus BmVIII-SCC Cells on Multiple Synthetic Scaffold Systems and in Rotating Bioreactors

Suderman

Temeyer

Schlechte

et al. 2021

Insects

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Tick cell culture facilitates research on the biology of ticks and their role as vectors of pathogens that affect humans, domestic animals, and wildlife. Because two-dimensional cell culture doesn’t promote the development of multicellular tissue-like composites, we hypothesized that culturing tick cells in a three-dimensional (3-D) configuration would form spheroids or tissue-like organoids. In this study, the cell line BmVIII-SCC obtained from the cattle fever tick, Rhipicephalus (Boophilus) microplus (Canestrini, 1888), was cultured in different synthetic scaffold systems. Growth of the tick cells on macrogelatinous beads in rotating continuous culture system bioreactors enabled cellular attachment, organization, and development into spheroid-like aggregates, with evidence of tight cellular junctions between adjacent cells and secretion of an extracellular matrix. At least three cell morphologies were identified within the aggregates: fibroblast-like cells, small endothelial-like cells, and larger cells exhibiting multiple cytoplasmic endosomes and granular vesicles. These observations suggest that BmVIII-SCC cells adapted to 3-D culture retain pluripotency. Additional studies involving genomic analyses are needed to determine if BmVIII-SCC cells in 3-D culture mimic tick organs. Applications of 3-D culture to cattle fever tick research are discussed.

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“…Conversely, YOYO-1 was observed in groove binding (Figure 6c) and the middle of the planar bases of DNA, suggesting the bis-intercalation (Figure 6d) mode [32]. Yardimci et al accomplished BALM with a combination of fluorescent double-stranded DNA intercalators and optical astigmatism to acquire 3D SR images of DNA, using microspheres to make DNA visible in the 3D SR images (Figure 7) [33]. DNA with a biotin-modified end is tethered to a streptavidin-coated glass coverslip (Figure 7a).…”

Section: Balmmentioning

confidence: 99%

“… ( a ) Three-dimensional BALM images of 10 kb linear dsDNA tethered to the surface of the glass at both ends, ( b ) tethered to the surface at one end and to a 1 μm diameter bead at the other end, and ( c ) tethered to a 1 μm diameter bead at one end and a 0.4 μm diameter bead at the other end. The image was reproduced with permission from Yardimci et al, published by Nature Publishing Group, 2020 [ 33 ]. …”

Section: Figurementioning

confidence: 99%

Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy

Lee

Batjikh

Kang

2020

Sensors

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The natural characteristics of deoxyribonucleic acid (DNA) enable its advanced applications in nanotechnology as a special tool that can be detected by high-resolution imaging with precise localization. Super-resolution (SR) microscopy enables the examination of nanoscale molecules beyond the diffraction limit. With the development of SR microscopy methods, DNA nanostructures can now be optically assessed. Using the specific binding of fluorophores with their target molecules, advanced single-molecule localization microscopy (SMLM) has been expanded into different fields, allowing wide-range detection at the single-molecule level. This review discusses the recent progress in the SR imaging of DNA nano-objects using SMLM techniques, such as direct stochastic optical reconstruction microscopy, binding-activated localization microscopy, and point accumulation for imaging nanoscale topography. Furthermore, we discuss their advantages and limitations, present applications, and future perspectives.

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Three-dimensional super-resolution fluorescence imaging of DNA

Cited by 12 publications

References 26 publications

Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure

Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure

Three-Dimensional Culture of Rhipicephalus (Boophilus) microplus BmVIII-SCC Cells on Multiple Synthetic Scaffold Systems and in Rotating Bioreactors

Toward Sub-Diffraction Imaging of Single-DNA Molecule Sensors Based on Stochastic Switching Localization Microscopy

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