Direct measurement of the mechanical properties of a chromatin analog and the epigenetic effects of para-sulphonato-calix[4]arene

• Published in: Scientific reports 2019-04, Vol.9 (1), p.5816, Article 5816
• Main Authors: Tauran, Yannick, Kumemura, Momoko, Tarhan, Mehmet C., Perret, Grégoire, Perret, Florent, Jalabert, Laurent, Collard, Dominique, Fujita, Hiroyuki, Coleman, Anthony W.
• Format: Article
• Language: English
• Subjects: 38/71; 631/154/309/555; 631/1647/350/59; 639/166/988; 9/10; 96/95; Acidity; Animals; Atomic force microscopy; Bacteriophage lambda - genetics; Calf thymus; Cattle; Chemical Sciences; Chromatin; Chromatin - chemistry; Chromatin - genetics; Chromosomes, Artificial; Deoxyribonucleic acid; DNA; DNA structure; DNA, Viral - chemistry; DNA, Viral - genetics; Epigenetics; Histones - chemistry; Humanities and Social Sciences; Life Sciences; Light microscopy; Lysine; Material chemistry; Mechanical properties; Microfluidics; Microscopy; Microscopy, Atomic Force; multidisciplinary; Nucleic Acid Conformation; Nucleosomes - chemistry; Nucleosomes - genetics; Optical Tweezers; Phages; Proof of Concept Study; Proteins; Science; Science (multidisciplinary)
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-019-42267-x

By means of Silicon Nano Tweezers (SNTs) the effects on the mechanical properties of λ-phage DNA during interaction with calf thymus nucleosome to form an artificial chromatin analog were measured. At a concentration of 100 nM, a nucleosome solution induced a strong stiffening effect on DNA (1.1 N m −1 ). This can be compared to the effects of the histone proteins, H1, H2A, H3 where no changes in the mechanical properties of DNA were observed and the complex of the H3/H4 proteins where a smaller increase in the stiffness is observed (0.2 N m −1 ). Para -sulphonato-calix[4]arene, SC4, known for epigenetic activity by interacting specifically with the lysine groups of histone proteins, was studied for its effect on an artificial chromatin. Using a microfluidic SNT device, SC4 was titrated against the artificial chromatin, at a concentration of 1 mM in SC4 a considerable increase in stiffness, 15 N m −1 , was observed. Simultaneously optical microscopy showed a physical change in the DNA structure between the tips of the SNT device. Electronic and Atomic Force microscopy confirmed this structural re-arrangement. Negative control experiments confirmed that these mechanical and physical effects were induced neither by the acidity of SC4 nor through nonspecific interactions of SC4 on DNA.