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Small, Oct 09 2024, | https://doi.org/10.1002/smll.202405065 Artificial Intelligence-Enhanced Analysis of Genomic DNA Visualized with Nanoparticle-Tagged Peptides under Electron Microscopy

Priyannth Ramasami Sundharbaabu ¹, Junhyuck Chang ¹, Yunchul Kim¹, Youmin Shim ¹, Byoungsang Lee ¹, Chanyoung Noh ², Sujung Heo ², Seung Seo Lee ³, Sang-Hee Shim ⁴, Kwang-I Lim ⁵, Kyubong Jo ², Jung Heon Lee ^1,6

¹School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, South Korea.

²Department of Chemistry & Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea.

³School of Chemistry and Chemical Engineering, University of Southampton, Southampton, SO17 1BJ, UK.

⁴Department of Chemistry, Korea University, Seoul, 02841, South Korea.

⁵Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, 04312, South Korea.

⁶Department of MetaBioHealth, Sungkyunkwan University (SKKU), Suwon, 16419, South Korea.

P.R.S., J.C. and Y.K. contributed equally to this work.

Corresponding Authors: Byoungsang Lee, Kyubong Jo, Jung Heon Lee

Abstract

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.

논문정보

형식Research article
게재일2024년 10월 (BRIC 등록일 2024-10-10)
연구진국내(교신)+국외 연구진
분야 바이오·의료융합 > 바이오소재

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