Three-Way DNA Junction as an End Label for DNA in Atomic Force Microscopy Studies

• Published in: International journal of molecular sciences 2022-09, Vol.23 (19), p.11404
• Main Authors: Sun, Zhiqiang, Stormberg, Tommy, Filliaux, Shaun, Lyubchenko, Yuri L.
• Format: Article
• Language: English
• Subjects: Atomic force microscopy; Atomic Force Microscopy (AFM); Binding sites; Deoxyribonucleic acid; DNA; DNA label; Experiments; Flexibility; Labeling; Labels; Microscopy; Nucleosomes; Nucleotides; Proteins; three-way junction (3WJ); Visualization
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms231911404

Atomic Force Microscopy (AFM) is widely used for topographic imaging of DNA and protein-DNA complexes in ambient conditions with nanometer resolution. In AFM studies of protein-DNA complexes, identifying the protein’s location on the DNA substrate is one of the major goals. Such studies require distinguishing between the DNA ends, which can be accomplished by end-specific labeling of the DNA substrate. We selected as labels three-way DNA junctions (3WJ) assembled from synthetic DNA oligonucleotides with two arms of 39–40 bp each. The third arm has a three-nucleotide overhang, GCT, which is paired with the sticky end of the DNA substrate generated by the SapI enzyme. Ligation of the 3WJ results in the formation of a Y-type structure at the end of the linear DNA mole cule, which is routinely identified in the AFM images. The yield of labeling is 69%. The relative orientation of arms in the Y-end varies, such dynamics were directly visualized with time-lapse AFM studies using high-speed AFM (HS-AFM). This labeling approach was applied to the characterization of the nucleosome arrays assembled on different DNA templates. HS-AFM experiments revealed a high dynamic of nucleosomes resulting in a spontaneous unraveling followed by disassembly of nucleosomes.