Azam Askari - Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
Parisa Mokaberi - Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
Maryam Dareini - Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
Morvarid Medalian - Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
Mahtab Pejhan - Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
Maryam Erfani - Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
Maryam Asadzadeh-Lotfabad - Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
Mohammad-Reza Saberi - Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
Jamshidkhan Chamani - Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran

Objective(s): This study aimed to evaluate the role of the linker histone (H۱) in the binding interaction between ambochlorin (Amb), and calf thymus DNA (ctDNA) as binary and ternary systems. Materials and Methods: The project was accomplished through the means of absorbance, fluorescence, stopped-flow circular dichroism spectroscopy, viscosity, thermal melting, and molecular modeling techniques.Results: Spectroscopic analysis revealed that although Amb was strongly bound to both ctDNA and ctDNA-H۱, it showed a greater tendency to ctDNA in the presence of the linker histone. The obtained thermodynamic parameters revealed that both Amb-ctDNA and Amb-ctDNA-H۱ interactions were spontaneous, endothermic, and entropy-favored, and hydrophobic interactions played the main role in the formation and stabilization of complexes. Analysis of the stopped-flow circular dichroism results revealed that the binding process of Amb-ctDNA and Amb-ctDNA-H۱ required a time of more than ۱۵۰ milliseconds to complete. Moreover, Amb-ctDNA complex formation was marginally decelerated in the presence of the linker histone. The docking results suggested that the presence of the  linker histone may alter the binding sites of Amb from ctDNA minor grooves to major grooves. Conclusion: All quenching processes were governed by a dynamic mechanism. Additionally, Amb did not stabilize or induce considerable conformational changes in ctDNA and ctDNA-H۱ complex upon binding. In silico molecular docking results confirmed that Amb was bound to the double-helical ctDNA and ctDNA-H۱ via ctDNA grooves. In summary, some binding properties of the interactions between Amb and ctDNA change in the presence of the linker histone.

Calf thymus DNA, Linker histone, Molecular modeling, Spectroscopy, Circular dichroism