Toward Visualizing Genomic DNA Using Electron Microscopy via DNA Metallization

Jin, Xuelin; Kannappan, Shrute; Hapsari, Natalia Diyah; Jin, Yu; Kim, Kyeong Kyu; Lee, Jung Heon; Jo, Kyubong

doi:10.1002/sstr.202200361

Cited by 6 publications

(2 citation statements)

References 198 publications

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“…However, implementing this method is challenging in carbon-film-based TEM imaging of DNA molecules. As a result, most TEM DNA images documented to date exhibit random arrangements, [21] similar to those observed in Figure 1a.…”

Section: Sem Imaging Of Dna With Novel Electro-stainsupporting

confidence: 61%

Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal‐Free Electro‐Stain Composed of DNA‐Binding Proteins and Synthetic Polymers

Noh,

Kang,

Heo

et al. 2024

Advanced Science

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This paper presents the first scanning electron microscopy (SEM)‐based DNA imaging in biological samples. This novel approach incorporates a metal‐free electro‐stain reagent, formulated by combining DNA‐binding proteins and synthetic polymers to enhance the visibility of 2‐nm‐thick DNA under SEM. Notably, DNA molecules stain with proteins and polymers appear as dark lines under SEM. The resulting DNA images exhibit a thickness of 15.0±4.0 nm. As SEM is the primary platform, it integrates seamlessly with various chemically functionalized large surfaces with the aid of microfluidic devices. The approach allows high‐resolution imaging of various DNA structures including linear, circular, single‐stranded DNA and RNA, originating from nuclear and mitochondrial genomes. Furthermore, quantum dots are successfully visualized as bright labels that are sequence‐specifically incorporated into DNA molecules, which highlights the potential for SEM‐based optical DNA mapping. In conclusion, DNA imaging using SEM with the novel electro‐stain offers electron microscopic resolution with the ease of optical microscopy.

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Section: Sem Imaging Of Dna With Novel Electro-stainsupporting

confidence: 61%

Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal‐Free Electro‐Stain Composed of DNA‐Binding Proteins and Synthetic Polymers

Noh,

Kang,

Heo

et al. 2024

Advanced Science

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“…243 It serves as a blueprint for life and provides instructions for the development and functioning of all living organisms. 244,245 The DNA molecule comprises two complementary strands that run in opposite directions and are held together by H bonds between nitrogenous bases. It consists of repeating units of four nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T), and a sugar-phosphate backbone.…”

Section: Deoxyribose Nucleic Acid (Dna)-inspired Moleculesmentioning

confidence: 99%

Multifunctional small biomolecules as key building blocks in the development of hydrogel-based strain sensors

Zaidi¹,

Saeed²,

Heo³

et al. 2023

J. Mater. Chem. A

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Artificial Intelligence‐Enhanced Analysis of Genomic DNA Visualized with Nanoparticle‐Tagged Peptides under Electron Microscopy

Sundharbaabu,

Chang,

Kim

et al. 2024

Small

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DNA visualization has advanced across multiple microscopy platforms, albeit with limited progress in the identification of novel staining agents for electron microscopy (EM), notwithstanding its ability to furnish a broad magnification range and high‐resolution details for observing DNA molecules. Herein, a non‐toxic, universal, and simple method is proposed that uses gold nanoparticle‐tagged peptides to stain all types of naturally occurring DNA molecules, enabling their visualization under EM. This method enhances the current DNA visualization capabilities, allowing for sequence‐specific, genomic‐scale, and multi‐conformational visualization. Importantly, an artificial intelligence (AI)‐enabled pipeline for identifying DNA molecules imaged under EM is presented, followed by classification based on their size, shape, or conformation, and finally, extraction of their significant dimensional features, which to the best of authors' knowledge, has not been reported yet. This pipeline strongly improved the accuracy of obtaining crucial information such as the number and mean length of DNA molecules in a given EM image for linear DNA (salmon sperm DNA) and the circumferential length and diameter for circular DNA (M13 phage DNA), owing to its image segmentation capability. Furthermore, it remained robust to several variations in the raw EM images arising from handling during the DNA staining stage.

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Toward Visualizing Genomic DNA Using Electron Microscopy via DNA Metallization

Cited by 6 publications

References 198 publications

Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal‐Free Electro‐Stain Composed of DNA‐Binding Proteins and Synthetic Polymers

Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal‐Free Electro‐Stain Composed of DNA‐Binding Proteins and Synthetic Polymers

Multifunctional small biomolecules as key building blocks in the development of hydrogel-based strain sensors

Artificial Intelligence‐Enhanced Analysis of Genomic DNA Visualized with Nanoparticle‐Tagged Peptides under Electron Microscopy

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