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

• Published in: Advanced science 2024-07, Vol.11 (28), p.e2309702-n/a
• Main Authors: Noh, Chanyoung, Kang, Yoonjung, Heo, Sujung, Kim, Taesoo, Kim, Hayeon, Chang, Junhyuck, Sundharbaabu, Priyannth Ramasami, Shim, Sanghee, Lim, Kwang‐il, Lee, Jung Heon, Jo, Kyubong
• Format: Article
• Language: English
• Subjects: DNA - chemistry; DNA - metabolism; DNA binding protein; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; DNA-Binding Proteins - ultrastructure; Methods; Microscopy, Electron, Scanning - methods; Mitochondrial DNA; Polymers; Polymers - chemistry; polyvinylpyrrolidone; Proteins; quantum dot labeling; Quantum dots; Quantum Dots - chemistry; Scanning electron microscopy; SEM DNA imaging; SEM optical DNA mapping; Silicon wafers; Stains & staining; Visualization
• ISSN: 2198-3844; 2198-3844
• DOI: 10.1002/advs.202309702

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. This work demonstrates SEM‐based DNA imaging using a metal‐free electro‐stain reagent. It enhances the visibility of 2‐nm‐thick DNA as a dark line. DNA images exhibit 15.0 ± 4.0 nm thickness, enabling high‐resolution imaging of various DNA structures. Quantum dots, serving as bright labels on DNA, are successfully visualized, suggesting potential for SEM‐based optical DNA mapping, combining electron microscopic resolution with optical microscopy ease.