Study on the Interaction between Chalcone and DNA with Spectroscopy and Molecular Docking Technique

Abstract

Chalcone (Cha) and its derivatives have been used in drug development, biomedicine, and other fields due to their wide range of pharmacological activities. However, there is still a lack of research on the activity of its parent nucleus structure. The interaction between Cha and calf thymus DNA (ctDNA) was analyzed by making use of a variety of spectroscopic methods combined with molecular docking techniques, including UV–vis absorption spectroscopy, fluorescence spectroscopy, and resonance scattering spectroscopy. Besides, the interaction mechanism was also explored. Spectral experiments confirmed that under the action of Cha, the melting point (T_m) of ctDNA increased by 6.5 °C, the absorbance at 260 nm increased, the EB-ctDNA system was quenched by mixed fluorescence, and a new resonance scattering peak appeared. These phenomena indicated that Cha could bind to ctDNA. Cha self-aggregates were formed at the ctDNA binding site, which had no significant effect on the structure and conformation of ctDNA. Molecular docking experiments drew conclusions that there was a π–π accumulating action between the B aromatic ring of Cha and the aromatic ring of ctDNA bases. They could be bound by the intercalation interaction and further combined by groove interaction. The above experimental results analyzed the interaction mechanism between Cha and ctDNA at the molecular level, which is helpful to further clarify the pharmacological mechanism of Cha.

Graphical Abstract

Keywords:

• Chalcone
• Calf thymus DNA
• intercalation interaction
• groove interaction
• spectroscopy
• molecular docking techniques

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

This work was supported by the Project of Jilin Provincial Department of science and technology [20191102011YY, 20210204194YY], Jilin Provincial Department of Education Science and Technology Research Project [JJKH20210848KJ, JJKH20210850KJ, JJKH20210852KJ], and Innovation and Entrepreneurship Training Program for College Students of Changchun University of Science and Technology [2021131].