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

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.

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

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.

Negative nanopore sequencing for mapping biochemical processes on DNA molecules.

Nanopore sequencing maps biochemical processes on DNA by detecting negative peaks in the sequence alignment profile. Protein-bound DNA and single-strand broken DNA cannot pass through nanopores, resulting in unaligned regions in the genome MAP. This novel approach provides a clear representation of genomic biochemical events.

Origin of minicircular mitochondrial genomes in red algae.

Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.

Counting DNA molecules on a microchannel surface for quantitative analysis.

Microscopic visualization of DNA molecules is a simple, intuitive, and powerful method. Nonetheless, DNA-molecule quantification methods that employ microscopic visualization have not been reported so far. In this study, a new quantitative approach is presented that enables the counting of individual DNA molecules that have been rendered visible by fluorescence microscopy.