[Comprehensive analytical chemistry experiment： analysis of non-covalent interactions between double-stranded deoxyribonucleic acid and a natural drug by electrospray ionization mass spectrometry]

Abstract

Analytical chemistry experiments are essential foundational courses for first- and second-year undergraduates in chemistry， chemical engineering， materials science， and pharmacy. These courses provide students with principles and operational skills of analytical instruments， alongside training in qualitative and quantitative analysis. However， current teaching practices face three main challenges： （1） insufficient focus on instrumental analysis； （2） outdated experimental content misaligned with modern scientific advancements； and （3） limited experimental hours due to curriculum constraints. To systematically address these issues， we proposed educational objectives， competency goals， and course objectives based on outcome-based education （OBE） philosophy. Building upon this backdrop， a comprehensive experiment utilizing electrospray ionization mass spectrometry （ESI-MS） was designed to investigate non-covalent interactions between double-stranded deoxyribonucleic acid （DNA） and naringin， a flavonoid natural drug. The experiment is offered to third-year undergraduate students as an elective. In the implementation process， a blended teaching model combining online and offline methods is adopted. The experimental teaching process is structured into three stages： pre-class preparation， in-class practice， and post-class review. Pre-class tasks include literature reviews， artificial intelligence （AI）-assisted summaries， pre-lab report writing and group discussions. This part is mainly conducted online without occupying class hours. During in-class practice， students synthesized double-stranded DNA by annealing single-stranded DNA （heated at 90 ℃ for 15 min， followed by slowly cooling to （25±1） ℃ overnight and stored at -20 ℃）. The resulting DNA was incubated with naringin at a 1∶4 concentration ratio in ammonium acetate for 15 min. The mixture was then analyzed by ESI-MS on a linear ion trap mass spectrometer. Both negative and positive ion modes were employed with optimized parameters encompassing spray voltage， capillary voltage， tube lens offset， heated capillary temperature， nitrogen sheath and auxiliary gas flows. Data acquisition involved 150 averaged scans using Xcalibur software. ESI-MS under negative ion mode was used to detect the non-covalent complexes. Secondary mass spectrometry （MS/MS） of 5-charged complex ions showed guanine base loss and minimal drug dissociation， indicating strong non-covalent interactions. In positive ion mode， MS yielded lower complex abundance， likely due to charge redistribution during ionization. The results reveal that naringin binds DNA predominantly via π-π stacking and hydrogen bonding， with a 1∶1 stoichiometry （relative abundance 60.91%） and a relative binding affinity of 39.20%. Post-class， students were required to process data， write formal lab reports， create presentations for defense， and design a feasible extension experiment. At the same time， a grading system was established for these three phases. The evaluation system emphasizes formative assessment， focusing on aspects such as compliance with experimental procedures， workflow efficiency， safety measures， teamwork， problem-solving skills， and experimental data handling. This multidimensional approach ensures equitable grading and pedagogical validity. This curriculum bridges research and education by introducing MS-based non-covalent interaction analysis into undergraduate curricula. The extended experimental design permits curricular expansion of the course. Some students designed structure-activity relationship （SAR） investigations of flavonoids （e.g.， naringenin vs. naringin）， revealing the role of glycosylation in DNA binding affinity. In addition， students designed a fluorescence quenching spectroscopy experiment， demonstrating interdisciplinary problem-solving skills. It closely aligns with the OBE philosophy， a student-centered framework that fosters innovation. Feedback indicates that 96% of undergraduates perceived significant improvements in their research capabilities and interdisciplinary integration skills. However， some challenges were noted， including students' initial hesitancy with advanced instrumentation and limited instruments and drugs. We plan to improve teaching in these areas in the future. In conclusion， this OBE-driven experiment successfully modernized analytical chemistry education in mass spectrometry applications by integrating theoretical knowledge with cutting-edge research skills. The project establishes a comprehensive teaching platform and constructs a holistic teaching system， featuring operational safety and accessibility while offering strong demonstrative value in fostering interest， extensibility and innovation. The experiment not only enriches the content of analytical chemistry courses， inspires students' research interests， and hones their critical thinking abilities， but also enhances their safety awareness and lays a solid foundation for future research endeavors， thus achieving the comprehensive educational goals of experimental teaching.

Keywords: analytical chemistry; chemistry education; experimental teaching; mass spectrometry analysis; non-covalent interaction.